Selected Publications


2015

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T et al. (Jun 2015) Social evolution. Genomic signatures of evolutionary transitions from solitary to group living Science 348 (6239): 1139-43. doi:10.1126/science.aaa4788. PMID:25977371.

Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG et al. (Apr 2015) The genomes of two key bumblebee species with primitive eusocial organization Genome biology 16: 76. doi:10.1186/s13059-015-0623-3. PMID:25908251.

Kim D, Langmead B, Salzberg SL (Apr 2015) HISAT: a fast spliced aligner with low memory requirements Nature methods 12 (4): 357-60. doi:10.1038/nmeth.3317. PMID:25751142.

Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS (Mar 2015) Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space PeerJ 3: e808. doi:10.7717/peerj.808. PMID:25780763.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT (Mar 2015) Ballgown bridges the gap between transcriptome assembly and expression analysis Nature biotechnology 33 (3): 243-6. doi:10.1038/nbt.3172. PMID:25748911.

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL (Mar 2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature biotechnology 33 (3): 290-5. doi:10.1038/nbt.3122. PMID:25690850.

Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK et al. (Feb 2015) Genomic variation. Impact of regulatory variation from RNA to protein Science 347 (6222): 664-7. doi:10.1126/science.1260793. PMID:25657249.

Deng K, Pertea M, Rongvaux A, Wang L, Durand CM, Ghiaur G et al. (Jan 2015) Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations Nature 517 (7534): 381-5. doi:10.1038/nature14053. PMID:25561180.

2014

Song L, Florea L, Langmead B (2014) Lighter: fast and memory-efficient sequencing error correction without counting Genome biology 15 (11): 509. doi:10.1186/PREACCEPT-9663167051308943. PMID:25398208.

Martinson VG, Magoc T, Koch H, Salzberg SL, Moran NA (Jul 2014) Genomic features of a bumble bee symbiont reflect its host environment Applied and environmental microbiology 80 (13): 3793-803. doi:10.1128/AEM.00322-14. PMID:24747890.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW et al. (Mar 2014) Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies Genome biology 15 (3): R59. doi:10.1186/gb-2014-15-3-r59. PMID:24647006.

Wood DE, Salzberg SL (Mar 2014) Kraken: ultrafast metagenomic sequence classification using exact alignments Genome biology 15 (3): R46. doi:10.1186/gb-2014-15-3-r46. PMID:24580807.

Salzberg SL, Pertea M, Fahrner JA, Sobreira N (Mar 2014) DIAMUND: direct comparison of genomes to detect mutations Human mutation 35 (3): 283-8. doi:10.1002/humu.22503. PMID:24375697.

2013

Florea L, Song L, Salzberg SL (Sep 2013) Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues F1000Research 2: 188. doi:10.12688/f1000research.2-188.v2. PMID:24555089.

Schatz MC, Langmead B (Jul 2013) The DNA Data Deluge: Fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze IEEE spectrum 50 (7): 26-33. doi:10.1109/MSPEC.2013.6545119. PMID:24920863.

Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D et al. (Jul 2013) GAGE-B: an evaluation of genome assemblers for bacterial organisms Bioinformatics 29 (14): 1718-25. doi:10.1093/bioinformatics/btt273. PMID:23665771.

Neale DB, Langley CH, Salzberg SL, Wegrzyn JL (Jun 2013) Open access to tree genomes: the path to a better forest Genome biology 14 (6): 120. doi:10.1186/gb-2013-14-6-120. PMID:23796049.

Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K et al. (May 2013) ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data Bioinformatics 29 (9): 1182-9. doi:10.1093/bioinformatics/btt108. PMID:23457041.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (Apr 2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Genome biology 14 (4): R36. doi:10.1186/gb-2013-14-4-r36. PMID:23618408.

Ji H, Li X, Wang QF, Ning Y (Apr 2013) Differential principal component analysis of ChIP-seq Proceedings of the National Academy of Sciences of the United States of America 110 (17): 6789-94. doi:10.1073/pnas.1204398110. PMID:23569280.

Leek JT, Salzberg SL (Mar 2013) Sequestration: inadvertently killing biomedical research to score political points Genome biology 14 (3): 109. doi:10.1186/gb-2013-14-3-109. PMID:23651812.

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G et al. (Mar 2013) Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies Briefings in bioinformatics 14 (2): 213-24. doi:10.1093/bib/bbr074. PMID:22199379.

Magoc T, Wood D, Salzberg SL (Mar 2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes Evolutionary bioinformatics online 9: 127-36. doi:10.4137/EBO.S11250. PMID:23531787.

Herbrich SM, Cole RN, West KP Jr, Schulze K, Yager JD, Groopman JD et al. (Feb 2013) Statistical inference from multiple iTRAQ experiments without using common reference standards Journal of proteome research 12 (2): 594-604. doi:10.1021/pr300624g. PMID:23270375.

Salzberg SL (Jan 2013) NIH funding: It does support innovators Nature 493 (7430): 26. doi:10.1038/493026b. PMID:23282352.

2012

Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP et al. (Oct 2012) Thousands of missed genes found in bacterial genomes and their analysis with COMBREX Biology direct 7: 37. doi:10.1186/1745-6150-7-37. PMID:23111013.

Salzberg S (Aug 2012) A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo BioTechniques 53 (2): 71. doi:10.2144/000113898. PMID:22873510.

Schwender H, Taub MA, Beaty TH, Marazita ML, Ruczinski I (Sep 2012) Rapid testing of SNPs and gene-environment interactions in case-parent trio data based on exact analytic parameter estimation Biometrics 68 (3): 766-73. doi:10.1111/j.1541-0420.2011.01713.x. PMID:22150644.

Zimin AV, Kelley DR, Roberts M, Marcais G, Salzberg SL, Yorke JA (Aug 2012) Mis-assembled "segmental duplications" in two versions of the Bos taurus genome PloS one 7 (8): e42680. doi:10.1371/journal.pone.0042680. PMID:22880081.

Kornegoor R, Moelans CB, Verschuur-Maes AH, Hogenes MC, de Bruin PC, Oudejans JJ et al. (Aug 2012) Oncogene amplification in male breast cancer: analysis by multiplex ligation-dependent probe amplification Breast cancer research and treatment 135 (1): 49-58. doi:10.1007/s10549-012-2051-3. PMID:22527098.

Huang Z, Hurley PJ, Simons BW, Marchionni L, Berman DM, Ross AE et al. (Jun 2012) Sox9 is required for prostate development and prostate cancer initiation Oncotarget 3 (6): 651-63. doi:10.18632/oncotarget.531. PMID:22761195.

Jiao X, Wood LD, Lindman M, Jones S, Buckhaults P, Polyak K et al. (May 2012) Somatic mutations in the Notch, NF-KB, PIK3CA, and Hedgehog pathways in human breast cancers Genes, chromosomes & cancer 51 (5): 480-9. doi:10.1002/gcc.21935. PMID:22302350.

Wheless L, Kistner-Griffin E, Jorgensen TJ, Ruczinski I, Berthier-Schaad Y, Kessing B et al. (May 2012) A community-based study of nucleotide excision repair polymorphisms in relation to the risk of non-melanoma skin cancer The Journal of investigative dermatology 132 (5): 1354-62. doi:10.1038/jid.2012.4. PMID:22336945.

Scholl PF, Cole RN, Ruczinski I, Gucek M, Diez R, Rennie A et al. (May 2012) Maternal serum proteome changes between the first and third trimester of pregnancy in rural southern Nepal Placenta 33 (5): 424-32. doi:10.1016/j.placenta.2012.02.009. PMID:22385826.

Huang TC, Sahasrabuddhe NA, Kim MS, Getnet D, Yang Y, Peterson JM et al. (Apr 2012) Regulation of lipid metabolism by Dicer revealed through SILAC mice Journal of proteome research 11 (4): 2193-205. doi:10.1021/pr2009884. PMID:22313051.

Shi M, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB et al. (Apr 2012) Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts American journal of medical genetics. Part A 158A (4): 784-94. doi:10.1002/ajmg.a.35257. PMID:22419666.

Hansen KD, Irizarry RA, Wu Z (Apr 2012) Removing technical variability in RNA-seq data using conditional quantile normalization Biostatistics (Oxford, England) 13 (2): 204-16. doi:10.1093/biostatistics/kxr054. PMID:22285995.

Mularoni L, Zhou Y, Bowen T, Gangadharan S, Wheelan SJ, Boeke JD (Apr 2012) Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots Genome research 22 (4): 693-703. doi:10.1101/gr.129460.111. PMID:22219510.

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD (Mar 2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments Bioinformatics (Oxford, England) 28 (6): 882-3. doi:10.1093/bioinformatics/bts034. PMID:22257669.

Saxena R, Elbers CC, Guo Y, Peter I, Gaunt TR, Mega JL et al. (Mar 2012) Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci American journal of human genetics 90 (3): 410-25. doi:10.1016/j.ajhg.2011.12.022. PMID:22325160.

Langmead B, Salzberg SL (Apr 2012) Fast gapped-read alignment with Bowtie 2 Nature methods 9 (4): 357-9. doi:10.1038/nmeth.1923. PMID:22388286.

Benassi B, Flavin R, Marchionni L, Zanata S, Pan Y, Chowdhury D et al. (Mar 2012) MYC is activated by USP2a-mediated modulation of microRNAs in prostate cancer Cancer discovery 2 (3): 236-47. doi:10.1158/2159-8290.CD-11-0219. PMID:22585994.

Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S et al. (Mar 2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms Genome research 22 (3): 557-67. doi:10.1101/gr.131383.111. PMID:22147368.

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR et al. (Mar 2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature protocols 7 (3): 562-78. doi:10.1038/nprot.2012.016. PMID:22383036.

Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z et al. (Feb 2012) Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK Nature 482 (7384): 251-5. doi:10.1038/nature10804. PMID:22318606.

Wu T, Fallin MD, Shi M, Ruczinski I, Liang KY, Hetmanski JB et al. (Feb 2012) Evidence of gene-environment interaction for the RUNX2 gene and environmental tobacco smoke in controlling the risk of cleft lip with/without cleft palate Birth defects research. Part A, Clinical and molecular teratology 94 (2): 76-83. doi:10.1002/bdra.22885. PMID:22241686.

Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP et al. (Feb 2012) Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies International journal of epidemiology 41 (1): 200-9. doi:10.1093/ije/dyr238. PMID:22422453.

Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C et al. (Feb 2012) DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth International journal of epidemiology 41 (1): 188-99. doi:10.1093/ije/dyr237. PMID:22422452.

Jaffe AE, Feinberg AP, Irizarry RA, Leek JT (Jan 2012) Significance analysis and statistical dissection of variably methylated regions Biostatistics (Oxford, England) 13 (1): 166-78. doi:10.1093/biostatistics/kxr013. PMID:21685414.

Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL (Jan 2012) Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering Nucleic acids research 40 (1): e9. doi:10.1093/nar/gkr1067. PMID:22102569.

Karchin R, Ochs MF, Stuart JM, Bader JS (2012) IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 17: 1-6. PMID:22174257.

Treangen TJ, Salzberg SL (Jan 2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions Nature reviews. Genetics 13 (1): 36-46. doi:10.1038/nrg3117. PMID:22124482.

2011

Wu J, Jiao Y, Dal Molin M, Maitra A, de Wilde RF, Wood LD et al. (Dec 2011) Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways Proceedings of the National Academy of Sciences of the United States of America 108 (52): 21188-93. doi:10.1073/pnas.1118046108. PMID:22158988.

Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G et al. (Dec 2011) Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies Briefings in bioinformatics . doi:10.1093/bib/bbr074. PMID:22199379.

Lee D, Karchin R, Beer MA (Dec 2011) Discriminative prediction of mammalian enhancers from DNA sequence Genome research 21 (12): 2167-80. doi:10.1101/gr.121905.111. PMID:21875935.

Zhang X, Reis M, Khoriaty R, Li Y, Ouillette P, Samayoa J et al. (Dec 2011) Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K 25 (12): 1908-10. doi:10.1038/leu.2011.163. PMID:21701494.

Frazee AC, Langmead B, Leek JT (Nov 2011) ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets BMC bioinformatics 12: 449. doi:10.1186/1471-2105-12-449. PMID:22087737.

Wang H, Zhang T, Wu T, Hetmanski JB, Ruczinski I, Schwender H et al. (Nov 2011) The FGF&FGFR Gene Family and Risk of Cleft Lip with/without Cleft Palate The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association . doi:10.1597/11-132. PMID:22074045.

Jamonnak N, Creamer TJ, Darby MM, Schaughency P, Wheelan SJ, Corden JL (Nov 2011) Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing RNA (New York, N.Y.) 17 (11): 2011-25. doi:10.1261/rna.2840711. PMID:21954178.

Colantuoni C, Lipska BK, Ye T, Hyde TM, Tao R, Leek JT et al. (Oct 2011) Temporal dynamics and genetic control of transcription in the human prefrontal cortex Nature 478 (7370): 519-23. doi:10.1038/nature10524. PMID:22031444.

Tyekucheva S, Marchionni L, Karchin R, Parmigiani G (Oct 2011) Integrating diverse genomic data using gene sets Genome biology 12 (10): R105. doi:10.1186/gb-2011-12-10-r105. PMID:22018358.

Tyekucheva S, Yolken RH, McCombie WR, Parla J, Kramer M, Wheelan SJ et al. (Oct 2011) Establishing the baseline level of repetitive element expression in the human cortex BMC genomics 12: 495. doi:10.1186/1471-2164-12-495. PMID:21985647.

Sobreira NL, Gnanakkan V, Walsh M, Marosy B, Wohler E, Thomas G et al. (Oct 2011) Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing Genome research 21 (10): 1720-7. doi:10.1101/gr.122986.111. PMID:21890680.

Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB et al. (Oct 2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp Journal of bacteriology 193 (19): 5450-64. doi:10.1128/JB.05262-11. PMID:21784931.

Hong S, Skaist AM, Wheelan SJ, Friedman AD (Oct 2011) AP-1 protein induction during monopoiesis favors C/EBP: AP-1 heterodimers over C/EBP homodimerization and stimulates FosB transcription Journal of leukocyte biology 90 (4): 643-51. doi:10.1189/jlb.0111043. PMID:21543584.

Liu Y, Woods NT, Kim D, Sweet M, Monteiro AN, Karchin R (Oct 2011) Yeast two-hybrid junk sequences contain selected linear motifs Nucleic acids research 39 (19): e128. doi:10.1093/nar/gkr600. PMID:21785140.

Creamer TJ, Darby MM, Jamonnak N, Schaughency P, Hao H, Wheelan SJ et al. (Oct 2011) Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1 PLoS genetics 7 (10): e1002329. doi:10.1371/journal.pgen.1002329. PMID:22028667.

Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R et al. (Sep 2011) Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis Genome biology 12 (9): R93. doi:10.1186/gb-2011-12-9-r93. PMID:21955804.

Faraday N, Yanek LR, Yang XP, Mathias R, Herrera-Galeano JE, Suktitipat B et al. (Sep 2011) Identification of a specific intronic PEAR1 gene variant associated with greater platelet aggregability and protein expression Blood 118 (12): 3367-75. doi:10.1182/blood-2010-11-320788. PMID:21791418.

McCall MN, Irizarry RA (Sep 2011) Thawing Frozen Robust Multi-array Analysis (fRMA) BMC bioinformatics 12: 369. doi:10.1186/1471-2105-12-369. PMID:21923903.

Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S et al. (Sep 2011) Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection American journal of human genetics 89 (3): 368-81. doi:10.1016/j.ajhg.2011.07.025. PMID:21907010.

Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB et al. (Sep 2011) Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate Genetic epidemiology 35 (6): 469-78. doi:10.1002/gepi.20595. PMID:21618603.

Allen JM, Simcha DM, Ericson NG, Alexander DL, Marquette JT, Van Biber BP et al. (Sep 2011) Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication Nucleic acids research 39 (16): 7020-33. doi:10.1093/nar/gkr157. PMID:21622658.

Guthrie VB, Allen J, Camps M, Karchin R (Sep 2011) Network models of TEM beta-lactamase mutations coevolving under antibiotic selection show modular structure and anticipate evolutionary trajectories PLoS computational biology 7 (9): e1002184. doi:10.1371/journal.pcbi.1002184. PMID:21966264.

Stevens EL, Heckenberg G, Roberson ED, Baugher JD, Downey TJ, Pevsner J (Sep 2011) Inference of relationships in population data using identity-by-descent and identity-by-state PLoS genetics 7 (9): e1002287. doi:10.1371/journal.pgen.1002287. PMID:21966277.

Desai KH, Tan CS, Leek JT, Maier RV, Tompkins RG, Storey JD (Sep 2011) Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study PLoS medicine 8 (9): e1001093. doi:10.1371/journal.pmed.1001093. PMID:21931541.

Kim D, Salzberg SL (Aug 2011) TopHat-Fusion: an algorithm for discovery of novel fusion transcripts Genome biology 12 (8): R72. doi:10.1186/gb-2011-12-8-r72. PMID:21835007.

Wong WC, Kim D, Carter H, Diekhans M, Ryan MC, Karchin R (Aug 2011) CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer Bioinformatics (Oxford, England) 27 (15): 2147-8. doi:10.1093/bioinformatics/btr357. PMID:21685053.

Ross AE, Emadi A, Marchionni L, Hurley PJ, Simons BW, Schaeffer EM et al. (Aug 2011) Dimeric naphthoquinones, a novel class of compounds with prostate cancer cytotoxicity BJU international 108 (3): 447-54. doi:10.1111/j.1464-410X.2010.09907.x. PMID:21176082.

Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE et al. (Sep 2011) Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations Nature genetics 43 (9): 887-92. doi:10.1038/ng.888. PMID:21804549.

Wegmann D, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR et al. (Sep 2011) Recombination rates in admixed individuals identified by ancestry-based inference Nature genetics 43 (9): 847-53. doi:10.1038/ng.894. PMID:21775992.

Hansen KD, Wu Z, Irizarry RA, Leek JT (Jul 2011) Sequencing technology does not eliminate biological variability Nature biotechnology 29 (7): 572-3. doi:10.1038/nbt.1910. PMID:21747377.

Pertea M, Pertea GM, Salzberg SL (Jul 2011) Detection of lineage-specific evolutionary changes among primate species BMC bioinformatics 12: 274. doi:10.1186/1471-2105-12-274. PMID:21726447.

McDonald OG, Wu H, Timp W, Doi A, Feinberg AP (Aug 2011) Genome-scale epigenetic reprogramming during epithelial-to-mesenchymal transition Nature structural & molecular biology 18 (8): 867-74. doi:10.1038/nsmb.2084. PMID:21725293.

Cesselli D, Beltrami AP, D'Aurizio F, Marcon P, Bergamin N, Toffoletto B et al. (Jul 2011) Effects of age and heart failure on human cardiac stem cell function The American journal of pathology 179 (1): 349-66. doi:10.1016/j.ajpath.2011.03.036. PMID:21703415.

Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-Lopez L, Macia-Colon G et al. (Jul 2011) NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva Cancer prevention research (Philadelphia, Pa.) 4 (7): 1061-72. doi:10.1158/1940-6207.CAPR-11-0006. PMID:21558411.

Masica DL, Karchin R (Jul 2011) Correlation of somatic mutation and expression identifies genes important in human glioblastoma progression and survival Cancer research 71 (13): 4550-61. doi:10.1158/0008-5472.CAN-11-0180. PMID:21555372.

Huang H, Chanda P, Alonso A, Bader JS, Arking DE (Jul 2011) Gene-based tests of association PLoS genetics 7 (7): e1002177. doi:10.1371/journal.pgen.1002177. PMID:21829371.

Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H (Jun 2011) Improving pan-genome annotation using whole genome multiple alignment BMC bioinformatics 12: 272. doi:10.1186/1471-2105-12-272. PMID:21718539.

(Jun 2011) Integrated genomic analyses of ovarian carcinoma Nature 474 (7353): 609-15. doi:10.1038/nature10166. PMID:21720365.

Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG et al. (Aug 2011) Increased methylation variation in epigenetic domains across cancer types Nature genetics 43 (8): 768-75. doi:10.1038/ng.865. PMID:21706001.

Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R et al. (Jun 2011) Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences BMC genomics 12: 313. doi:10.1186/1471-2164-12-313. PMID:21669002.

Leek JT (Jun 2011) Asymptotic conditional singular value decomposition for high-dimensional genomic data Biometrics 67 (2): 344-52. doi:10.1111/j.1541-0420.2010.01455.x. PMID:20560929.

Ling S, Chang X, Schultz L, Lee TK, Chaux A, Marchionni L et al. (Jun 2011) An EGFR-ERK-SOX9 signaling cascade links urothelial development and regeneration to cancer Cancer research 71 (11): 3812-21. doi:10.1158/0008-5472.CAN-10-3072. PMID:21512138.

Shan L, Yang HC, Rabi SA, Bravo HC, Shroff NS, Irizarry RA et al. (Jun 2011) Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model Journal of virology 85 (11): 5384-93. doi:10.1128/JVI.02536-10. PMID:21430059.

Mathias RA, Sergeant S, Ruczinski I, Torgerson DG, Hugenschmidt CE, Kubala M et al. (May 2011) The impact of FADS genetic variants on omega6 polyunsaturated fatty acid metabolism in African Americans BMC genetics 12: 50. doi:10.1186/1471-2156-12-50. PMID:21599946.

Liu H, Kim Y, Sharkis S, Marchionni L, Jang YY (May 2011) In vivo liver regeneration potential of human induced pluripotent stem cells from diverse origins Science translational medicine 3 (82): 82ra39. doi:10.1126/scitranslmed.3002376. PMID:21562231.

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA (May 2011) Assessing affymetrix GeneChip microarray quality BMC bioinformatics 12: 137. doi:10.1186/1471-2105-12-137. PMID:21548974.

Ross AE, Marchionni L, Phillips TM, Miller RM, Hurley PJ, Simons BW et al. (May 2011) Molecular effects of genistein on male urethral development The Journal of urology 185 (5): 1894-8. doi:10.1016/j.juro.2010.12.095. PMID:21421236.

Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B et al. (Apr 2011) Performance assessment of copy number microarray platforms using a spike-in experiment Bioinformatics (Oxford, England) 27 (8): 1052-60. doi:10.1093/bioinformatics/btr106. PMID:21478196.

Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S et al. (Apr 2011) Accurate genome-scale percentage DNA methylation estimates from microarray data Biostatistics (Oxford, England) 12 (2): 197-210. doi:10.1093/biostatistics/kxq055. PMID:20858772.

Pasaniuc B, Zaitlen N, Lettre G, Chen GK, Tandon A, Kao WH et al. (Apr 2011) Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium PLoS genetics 7 (4): e1001371. doi:10.1371/journal.pgen.1001371. PMID:21541012.

Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR et al. (Mar 2011) Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation Proceedings of the National Academy of Sciences of the United States of America 108 (12): 5027-32. doi:10.1073/pnas.1016657108. PMID:21383169.

Ritchie ME, Liu R, Carvalho BS, Irizarry RA (Mar 2011) Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips BMC bioinformatics 12: 68. doi:10.1186/1471-2105-12-68. PMID:21385424.

Ji H, Jiang H, Ma W, Wong WH (Mar 2011) Using CisGenome to analyze ChIP-chip and ChIP-seq data Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 2: Unit2.13. doi:10.1002/0471250953.bi0213s33. PMID:21400695.

Kral BG, Mathias RA, Suktitipat B, Ruczinski I, Vaidya D, Yanek LR et al. (Mar 2011) A common variant in the CDKN2B gene on chromosome 9p21 protects against coronary artery disease in Americans of African ancestry Journal of human genetics 56 (3): 224-9. doi:10.1038/jhg.2010.171. PMID:21270820.

Ross AE, Marchionni L, Vuica-Ross M, Cheadle C, Fan J, Berman DM et al. (Feb 2011) Gene expression pathways of high grade localized prostate cancer The Prostate . doi:10.1002/pros.21373. PMID:21360566.

Woo S, Leek JT, Storey JD (Feb 2011) A computationally efficient modular optimal discovery procedure Bioinformatics (Oxford, England) 27 (4): 509-15. doi:10.1093/bioinformatics/btq701. PMID:21186247.

Cline MS, Karchin R (Feb 2011) Using bioinformatics to predict the functional impact of SNVs Bioinformatics (Oxford, England) 27 (4): 441-8. doi:10.1093/bioinformatics/btq695. PMID:21159622.

Angiuoli SV, Salzberg SL (Feb 2011) Mugsy: fast multiple alignment of closely related whole genomes Bioinformatics (Oxford, England) 27 (3): 334-42. doi:10.1093/bioinformatics/btq665. PMID:21148543.

Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC et al. (Jan 2011) The genetic landscape of the childhood cancer medulloblastoma Science (New York, N.Y.) 331 (6016): 435-9. doi:10.1126/science.1198056. PMID:21163964.

Murthy S, Hayward GS, Wheelan S, Forman MS, Ahn JH, Pass RF et al. (Jan 2011) Detection of a single identical cytomegalovirus (CMV) strain in recently seroconverted young women PloS one 6 (1): e15949. doi:10.1371/journal.pone.0015949. PMID:21264339.

Schwender H, Bowers K, Fallin MD, Ruczinski I (Jan 2011) Importance measures for epistatic interactions in case-parent trios Annals of human genetics 75 (1): 122-32. doi:10.1111/j.1469-1809.2010.00623.x. PMID:21118192.

Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA (Jan 2011) A multilevel model to address batch effects in copy number estimation using SNP arrays Biostatistics (Oxford, England) 12 (1): 33-50. doi:10.1093/biostatistics/kxq043. PMID:20625178.

Schwender H, Ruczinski I, Ickstadt K (Jan 2011) Testing SNPs and sets of SNPs for importance in association studies Biostatistics (Oxford, England) 12 (1): 18-32. doi:10.1093/biostatistics/kxq042. PMID:20601626.

Sosnay PR, Castellani C, Corey M, Dorfman R, Zielenski J, Karchin R et al. (2011) Evaluation of the disease liability of CFTR variants Methods in molecular biology (Clifton, N.J.) 742: 355-72. doi:10.1007/978-1-61779-120-8_21. PMID:21547743.

McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA (Jan 2011) The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes Nucleic acids research 39 (Database issue): D1011-5. doi:10.1093/nar/gkq1259. PMID:21177656.

Ochs MF, Karchin R, Ressom H, Gentleman R (2011) IDENTIFICATION OF ABERRANT PATHWAY AND NETWORK ACTIVITY FROM HIGH-THROUGHPUT DATA - Workshop Introduction Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing . PMID:21121064.

Leek JT, Taub MA, Pineda FJ (Nov 2011) Cooperation between referees and authors increases peer review accuracy PloS one 6 (11): e26895. doi:10.1371/journal.pone.0026895. PMID:22096506.

Rivera CG, Mellberg S, Claesson-Welsh L, Bader JS, Popel AS (Sep 2011) Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis PloS one 6 (9): e24887. doi:10.1371/journal.pone.0024887. PMID:21931866.

Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL (Jun 2011) Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies PloS one 6 (6): e21400. doi:10.1371/journal.pone.0021400. PMID:21731731.

Goes FS, Rongione M, Chen YC, Karchin R, Elhaik E, Potash JB (May 2011) Exonic DNA sequencing of ERBB4 in bipolar disorder PloS one 6 (5): e20242. doi:10.1371/journal.pone.0020242. PMID:21637803.

Hennessey PT, Ochs MF, Mydlarz WW, Hsueh W, Cope L, Yu W et al. (May 2011) Promoter methylation in head and neck squamous cell carcinoma cell lines is significantly different than methylation in primary tumors and xenografts PloS one 6 (5): e20584. doi:10.1371/journal.pone.0020584. PMID:21637785.

2010

Gangadharan S, Mularoni L, Fain-Thornton J, Wheelan SJ, Craig NL (Dec 2010) DNA transposon Hermes inserts into DNA in nucleosome-free regions in vivo Proceedings of the National Academy of Sciences of the United States of America 107 (51): 21966-72. doi:10.1073/pnas.1016382107. PMID:21131571.

Schreck KC, Taylor P, Marchionni L, Gopalakrishnan V, Bar EE, Gaiano N et al. (Dec 2010) The Notch target Hes1 directly modulates Gli1 expression and Hedgehog signaling: a potential mechanism of therapeutic resistance Clinical cancer research : an official journal of the American Association for Cancer Research 16 (24): 6060-70. doi:10.1158/1078-0432.CCR-10-1624. PMID:21169257.

Taub MA, Corrada Bravo H, Irizarry RA (Dec 2010) Overcoming bias and systematic errors in next generation sequencing data Genome medicine 2 (12): 87. doi:10.1186/gm208. PMID:21144010.

Hunninghake GM, Soto-Quiros ME, Avila L, Kim HP, Lasky-Su J, Rafaels N et al. (Dec 2010) TSLP polymorphisms are associated with asthma in a sex-specific fashion Allergy 65 (12): 1566-75. doi:10.1111/j.1398-9995.2010.02415.x. PMID:20560908.

Zou B, Yu H, Babcock JJ, Chanda P, Bader JS, McManus OB et al. (Dec 2010) Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-a-go-go related gene potassium channels Assay and drug development technologies 8 (6): 743-54. doi:10.1089/adt.2010.0339. PMID:21158688.

Langmead B (Dec 2010) Aligning short sequencing reads with Bowtie Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 11: Unit 11.7. doi:10.1002/0471250953.bi1107s32. PMID:21154709.

Noonan K, Marchionni L, Anderson J, Pardoll D, Roodman GD, Borrello I (Nov 2010) A novel role of IL-17-producing lymphocytes in mediating lytic bone disease in multiple myeloma Blood 116 (18): 3554-63. doi:10.1182/blood-2010-05-283895. PMID:20664052.

Assimes TL, Holm H, Kathiresan S, Reilly MP, Thorleifsson G, Voight BF et al. (Nov 2010) Lack of association between the Trp719Arg polymorphism in kinesin-like protein-6 and coronary artery disease in 19 case-control studies Journal of the American College of Cardiology 56 (19): 1552-63. doi:10.1016/j.jacc.2010.06.022. PMID:20933357.

Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S et al. (Nov 2010) Cross-platform Comparison of Two Pancreatic Cancer Phenotypes Cancer informatics 9: 257-64. doi:10.4137/CIN.S5755. PMID:21082040.

Morisot S, Wayne AS, Bohana-Kashtan O, Kaplan IM, Gocke CD, Hildreth R et al. (Nov 2010) High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K 24 (11): 1859-66. doi:10.1038/leu.2010.184. PMID:20739953.

Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U et al. (Nov 2010) Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains Protein science : a publication of the Protein Society 19 (11): 2110-21. doi:10.1002/pro.491. PMID:20799350.

Bozic I, Antal T, Ohtsuki H, Carter H, Kim D, Chen S et al. (Oct 2010) Accumulation of driver and passenger mutations during tumor progression Proceedings of the National Academy of Sciences of the United States of America 107 (43): 18545-50. doi:10.1073/pnas.1010978107. PMID:20876136.

Carvalho BS, Irizarry RA (Oct 2010) A framework for oligonucleotide microarray preprocessing Bioinformatics (Oxford, England) 26 (19): 2363-7. doi:10.1093/bioinformatics/btq431. PMID:20688976.

Lam TK, Ruczinski I, Helzlsouer KJ, Shugart YY, Caulfield LE, Alberg AJ (Oct 2010) Cruciferous vegetable intake and lung cancer risk: a nested case-control study matched on cigarette smoking Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 19 (10): 2534-40. doi:10.1158/1055-9965.EPI-10-0475. PMID:20841387.

Wu T, Liang KY, Hetmanski JB, Ruczinski I, Fallin MD, Ingersoll RG et al. (Oct 2010) Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate Human genetics 128 (4): 401-10. doi:10.1007/s00439-010-0863-y. PMID:20652317.

Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS et al. (Oct 2010) Temporal profiling of the secretome during adipogenesis in humans Journal of proteome research 9 (10): 5228-38. doi:10.1021/pr100521c. PMID:20707391.

Feinberg AP (Oct 2010) Epigenomics reveals a functional genome anatomy and a new approach to common disease Nature biotechnology 28 (10): 1049-52. doi:10.1038/nbt1010-1049. PMID:20944596.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE et al. (Oct 2010) Tackling the widespread and critical impact of batch effects in high-throughput data Nature reviews. Genetics 11 (10): 733-9. doi:10.1038/nrg2825. PMID:20838408.

Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P et al. (Sep 2010) Comprehensive methylome map of lineage commitment from haematopoietic progenitors Nature 467 (7313): 338-42. doi:10.1038/nature09367. PMID:20720541.

Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P et al. (Sep 2010) Epigenetic memory in induced pluripotent stem cells Nature 467 (7313): 285-90. doi:10.1038/nature09342. PMID:20644535.

Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T et al. (Sep 2010) Personalized epigenomic signatures that are stable over time and covary with body mass index Science translational medicine 2 (49): 49ra67. doi:10.1126/scitranslmed.3001262. PMID:20844285.

Fradin D, Cheslack-Postava K, Ladd-Acosta C, Newschaffer C, Chakravarti A, Arking DE et al. (Sep 2010) Parent-of-origin effects in autism identified through genome-wide linkage analysis of 16,000 SNPs PloS one 5 (9). doi:10.1371/journal.pone.0012513. PMID:20824079.

Bravo HC, Irizarry RA (Sep 2010) Model-based quality assessment and base-calling for second-generation sequencing data Biometrics 66 (3): 665-74. doi:10.1111/j.1541-0420.2009.01353.x. PMID:19912177.

Carter H, Samayoa J, Hruban RH, Karchin R (Sep 2010) Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM) Cancer biology & therapy 10 (6): 582-7. PMID:20581473.

Murray T, Beaty TH, Mathias RA, Rafaels N, Grant AV, Faruque MU et al. (Sep 2010) African and non-African admixture components in African Americans and an African Caribbean population Genetic epidemiology 34 (6): 561-8. doi:10.1002/gepi.20512. PMID:20717976.

Schatz MC, Delcher AL, Salzberg SL (Sep 2010) Assembly of large genomes using second-generation sequencing Genome research 20 (9): 1165-73. doi:10.1101/gr.101360.109. PMID:20508146.

Salzberg SL (Aug 2010) Recent advances in RNA sequence analysis F1000 biology reports 2: 64. doi:10.3410/B2-64. PMID:21173855.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ et al. (Aug 2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models Nature biotechnology 28 (8): 827-38. doi:10.1038/nbt.1665. PMID:20676074.

Huson HJ, Parker HG, Runstadler J, Ostrander EA (Jul 2010) A genetic dissection of breed composition and performance enhancement in the Alaskan sled dog BMC genetics 11: 71. doi:10.1186/1471-2156-11-71. PMID:20649949.

Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP (Jul 2010) Redefining CpG islands using hidden Markov models Biostatistics (Oxford, England) 11 (3): 499-514. doi:10.1093/biostatistics/kxq005. PMID:20212320.

Li Q, Fallin MD, Louis TA, Lasseter VK, McGrath JA, Avramopoulos D et al. (Jul 2010) Detection of SNP-SNP interactions in trios of parents with schizophrenic children Genetic epidemiology 34 (5): 396-406. doi:10.1002/gepi.20488. PMID:20568257.

Schatz MC, Langmead B, Salzberg SL (Jul 2010) Cloud computing and the DNA data race Nature biotechnology 28 (7): 691-3. doi:10.1038/nbt0710-691. PMID:20622843.

Huang CR, Schneider AM, Lu Y, Niranjan T, Shen P, Robinson MA et al. (Jun 2010) Mobile interspersed repeats are major structural variants in the human genome Cell 141 (7): 1171-82. doi:10.1016/j.cell.2010.05.026. PMID:20602999.

Seeber LM, Zweemer RP, Marchionni L, Massuger LF, Smit VT, van Baal WM et al. (Sep 2010) Methylation profiles of endometrioid and serous endometrial cancers Endocrine-related cancer 17 (3): 663-73. doi:10.1677/ERC-10-0014. PMID:20488783.

Kachhap SK, Rosmus N, Collis SJ, Kortenhorst MS, Wissing MD, Hedayati M et al. (Jun 2010) Downregulation of homologous recombination DNA repair genes by HDAC inhibition in prostate cancer is mediated through the E2F1 transcription factor PloS one 5 (6): e11208. doi:10.1371/journal.pone.0011208. PMID:20585447.

Schafer E, Irizarry R, Negi S, McIntyre E, Small D, Figueroa ME et al. (Jun 2010) Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting Blood 115 (23): 4798-809. doi:10.1182/blood-2009-09-243634. PMID:20215641.

Mathias RA, Kim Y, Sung H, Yanek LR, Mantese VJ, Hererra-Galeano JE et al. (Jun 2010) A combined genome-wide linkage and association approach to find susceptibility loci for platelet function phenotypes in European American and African American families with coronary artery disease BMC medical genomics 3: 22. doi:10.1186/1755-8794-3-22. PMID:20529293.

Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB et al. (Jun 2010) A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 Nature genetics 42 (6): 525-9. doi:10.1038/ng.580. PMID:20436469.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ et al. (May 2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature biotechnology 28 (5): 511-5. doi:10.1038/nbt.1621. PMID:20436464.

Wu H, Irizarry RA, Bravo HC (May 2010) Intensity normalization improves color calling in SOLiD sequencing Nature methods 7 (5): 336-7. doi:10.1038/nmeth0510-336. PMID:20431543.

McCall MN, Bolstad BM, Irizarry RA (Apr 2010) Frozen robust multiarray analysis (fRMA) Biostatistics (Oxford, England) 11 (2): 242-53. doi:10.1093/biostatistics/kxp059. PMID:20097884.

Ladd-Acosta C, Aryee MJ, Ordway JM, Feinberg AP (Apr 2010) Comprehensive high-throughput arrays for relative methylation (CHARM) Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.] Chapter 20: Unit 20.1.1-19. doi:10.1002/0471142905.hg2001s65. PMID:20373514.

Ji H, Liu XS (Apr 2010) Analyzing 'omics data using hierarchical models Nature biotechnology 28 (4): 337-40. doi:10.1038/nbt.1619. PMID:20379180.

Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA (Mar 2010) Performance evaluation of commercial miRNA expression array platforms BMC research notes 3: 80. doi:10.1186/1756-0500-3-80. PMID:20298588.

Lin MT, Tseng LH, Kamiyama H, Kamiyama M, Lim P, Hidalgo M et al. (Mar 2010) Quantifying the relative amount of mouse and human DNA in cancer xenografts using species-specific variation in gene length BioTechniques 48 (3): 211-8. doi:10.2144/000113363. PMID:20359302.

Louis TA, Ruczinski I (Feb 2010) Efficient evaluation of ranking procedures when the number of units is large, with application to SNP identification Biometrical journal. Biometrische Zeitschrift 52 (1): 34-49. doi:10.1002/bimj.200900044. PMID:20131327.

Mathias RA, Grant AV, Rafaels N, Hand T, Gao L, Vergara C et al. (Feb 2010) A genome-wide association study on African-ancestry populations for asthma The Journal of allergy and clinical immunology 125 (2): 336-346.e4. doi:10.1016/j.jaci.2009.08.031. PMID:19910028.

Salzberg SL (Feb 2010) Mind the gaps Nature methods 7 (2): 105-6. doi:10.1038/nmeth0210-105. PMID:20111034.

Feinberg AP, Irizarry RA (Jan 2010) Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease Proceedings of the National Academy of Sciences of the United States of America 107 Suppl 1: 1757-64. doi:10.1073/pnas.0906183107. PMID:20080672.

Lopez-Romero P, Gonzalez MA, Callejas S, Dopazo A, Irizarry RA (Jan 2010) Processing of Agilent microRNA array data BMC research notes 3: 18. doi:10.1186/1756-0500-3-18. PMID:20205787.

Carvalho BS, Louis TA, Irizarry RA (Jan 2010) Quantifying uncertainty in genotype calls Bioinformatics (Oxford, England) 26 (2): 242-9. doi:10.1093/bioinformatics/btp624. PMID:19906825.

Park Y, Moore C, Bader JS (Jan 2010) Dynamic networks from hierarchical bayesian graph clustering PloS one 5 (1): e8118. doi:10.1371/journal.pone.0008118. PMID:20084108.

Sleiman PM, Flory J, Imielinski M, Bradfield JP, Annaiah K, Willis-Owen SA et al. (Jan 2010) Variants of DENND1B associated with asthma in children The New England journal of medicine 362 (1): 36-44. doi:10.1056/NEJMoa0901867. PMID:20032318.

Schwender H, Ruczinski I (2010) Logic regression and its extensions Advances in genetics 72: 25-45. doi:10.1016/B978-0-12-380862-2.00002-3. PMID:21029847.

Parker HG, Shearin AL, Ostrander EA (2010) Man's best friend becomes biology's best in show: genome analyses in the domestic dog Annual review of genetics 44: 309-36. doi:10.1146/annurev-genet-102808-115200. PMID:21047261.

Kelley DR, Schatz MC, Salzberg SL (Nov 2010) Quake: quality-aware detection and correction of sequencing errors Genome biology 11 (11): R116. doi:10.1186/gb-2010-11-11-r116. PMID:21114842.

Salzberg SL, Pertea M (Oct 2010) Do-it-yourself genetic testing Genome biology 11 (10): 404. doi:10.1186/gb-2010-11-10-404. PMID:20932271.

Langmead B, Hansen KD, Leek JT (Aug 2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna Genome biology 11 (8): R83. doi:10.1186/gb-2010-11-8-r83. PMID:20701754.

Pertea M, Salzberg SL (May 2010) Between a chicken and a grape: estimating the number of human genes Genome biology 11 (5): 206. doi:10.1186/gb-2010-11-5-206. PMID:20441615.

Kelley DR, Salzberg SL (Mar 2010) Detection and correction of false segmental duplications caused by genome mis-assembly Genome biology 11 (3): R28. doi:10.1186/gb-2010-11-3-r28. PMID:20219098.

Scharpf RB, Ruczinski I (2010) R classes and methods for SNP array data Methods in molecular biology (Clifton, N.J.) 593: 67-79. doi:10.1007/978-1-60327-194-3_4. PMID:19957145.

2009

Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R et al. (Dec 2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts Nature genetics 41 (12): 1350-3. doi:10.1038/ng.471. PMID:19881528.

Irizarry RA, Wang C, Zhou Y, Speed TP (Dec 2009) Gene set enrichment analysis made simple Statistical methods in medical research 18 (6): 565-75. doi:10.1177/0962280209351908. PMID:20048385.

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD et al. (Nov 2009) Systems-level dynamic analyses of fate change in murine embryonic stem cells Nature 462 (7271): 358-62. doi:10.1038/nature08575. PMID:19924215.

Jorgensen TJ, Ruczinski I, Kessing B, Smith MW, Shugart YY, Alberg AJ (Oct 2009) Hypothesis-driven candidate gene association studies: practical design and analytical considerations American journal of epidemiology 170 (8): 986-93. doi:10.1093/aje/kwp242. PMID:19762372.

Gallicchio L, Chang HH, Christo DK, Thuita L, Huang HY, Strickland P et al. (Oct 2009) Single nucleotide polymorphisms in obesity-related genes and all-cause and cause-specific mortality: a prospective cohort study BMC medical genetics 10: 103. doi:10.1186/1471-2350-10-103. PMID:19818126.

Ritchie ME, Carvalho BS, Hetrick KN, Tavare S, Irizarry RA (Oct 2009) R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips Bioinformatics (Oxford, England) 25 (19): 2621-3. doi:10.1093/bioinformatics/btp470. PMID:19661241.

Wheless L, Ruczinski I, Alani RM, Clipp S, Hoffman-Bolton J, Jorgensen TJ et al. (Oct 2009) The association between skin characteristics and skin cancer prevention behaviors Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 18 (10): 2613-9. doi:10.1158/1055-9965.EPI-09-0383. PMID:19755654.

Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Muller-Reible C et al. (Oct 2009) Detecting species-site dependencies in large multiple sequence alignments Nucleic acids research 37 (18): 5959-68. doi:10.1093/nar/gkp634. PMID:19661281.

Phillippy AM, Deng X, Zhang W, Salzberg SL (Sep 2009) Efficient oligonucleotide probe selection for pan-genomic tiling arrays BMC bioinformatics 10: 293. doi:10.1186/1471-2105-10-293. PMID:19758451.

Irizarry RA, Wu H, Feinberg AP (Sep-Oct 2009) A species-generalized probabilistic model-based definition of CpG islands Mammalian genome : official journal of the International Mammalian Genome Society 20 (9-10): 674-80. doi:10.1007/s00335-009-9222-5. PMID:19777308.

Miller CL, Murakami P, Ruczinski I, Ross RG, Sinkus M, Sullivan B et al. (Sep 2009) Two complex genotypes relevant to the kynurenine pathway and melanotropin function show association with schizophrenia and bipolar disorder Schizophrenia research 113 (2-3): 259-67. doi:10.1016/j.schres.2009.05.014. PMID:19502010.

Roberson ED, Pevsner J (Aug 2009) Visualization of shared genomic regions and meiotic recombination in high-density SNP data PloS one 4 (8): e6711. doi:10.1371/journal.pone.0006711. PMID:19696932.

Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D et al. (Aug 2009) The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations BMC bioinformatics 10: 256. doi:10.1186/1471-2105-10-256. PMID:19695104.

Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW et al. (Aug 2009) Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations Cancer research 69 (16): 6660-7. doi:10.1158/0008-5472.CAN-09-1133. PMID:19654296.

Lam TK, Ruczinski I, Helzlsouer K, Shugart YY, Li KE, Clipp S et al. (Aug 2009) Copy number variants of GSTM1 and GSTT1 in relation to lung cancer risk in a prospective cohort study Annals of epidemiology 19 (8): 546-52. doi:10.1016/j.annepidem.2009.03.003. PMID:19394866.

Kingsford C, Nagarajan N, Salzberg SL (Jul 2009) 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates PloS one 4 (7): e6402. doi:10.1371/journal.pone.0006402. PMID:19636415.

Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC et al. (Jul 2009) The genome of the blood fluke Schistosoma mansoni Nature 460 (7253): 352-8. doi:10.1038/nature08160. PMID:19606141.

Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL (Jul 2009) Insignia: a DNA signature search web server for diagnostic assay development Nucleic acids research 37 (Web Server issue): W229-34. doi:10.1093/nar/gkp286. PMID:19417071.

He X, Marchionni L, Hansel DE, Yu W, Sood A, Yang J et al. (Jul 2009) Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma Stem cells (Dayton, Ohio) 27 (7): 1487-95. doi:10.1002/stem.92. PMID:19544456.

Ryan M, Diekhans M, Lien S, Liu Y, Karchin R (Jun 2009) LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures Bioinformatics (Oxford, England) 25 (11): 1431-2. doi:10.1093/bioinformatics/btp242. PMID:19369493.

Kottgen A, Glazer NL, Dehghan A, Hwang SJ, Katz R, Li M et al. (Jun 2009) Multiple loci associated with indices of renal function and chronic kidney disease Nature genetics 41 (6): 712-7. doi:10.1038/ng.377. PMID:19430482.

Zhou L, Pertea M, Delcher AL, Florea L (Jun 2009) Sim4cc: a cross-species spliced alignment program Nucleic acids research 37 (11): e80. doi:10.1093/nar/gkp319. PMID:19429899.

Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N, Ruczinski I et al. (Jun 2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations PLoS genetics 5 (6): e1000519. doi:10.1371/journal.pgen.1000519. PMID:19543370.

Himes BE, Hunninghake GM, Baurley JW, Rafaels NM, Sleiman P, Strachan DP et al. (May 2009) Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene American journal of human genetics 84 (5): 581-93. doi:10.1016/j.ajhg.2009.04.006. PMID:19426955.

Trapnell C, Pachter L, Salzberg SL (May 2009) TopHat: discovering splice junctions with RNA-Seq Bioinformatics (Oxford, England) 25 (9): 1105-11. doi:10.1093/bioinformatics/btp120. PMID:19289445.

Leek JT (May 2009) The tspair package for finding top scoring pair classifiers in R Bioinformatics (Oxford, England) 25 (9): 1203-4. doi:10.1093/bioinformatics/btp126. PMID:19276151.

Trapnell C, Salzberg SL (May 2009) How to map billions of short reads onto genomes Nature biotechnology 27 (5): 455-7. doi:10.1038/nbt0509-455. PMID:19430453.

Mankoo PK, Sukumar S, Karchin R (May 2009) PIK3CA somatic mutations in breast cancer: Mechanistic insights from Langevin dynamics simulations Proteins 75 (2): 499-508. doi:10.1002/prot.22265. PMID:18951408.

Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, Rudin CM et al. (Apr 2009) A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro Cancer research 69 (8): 3364-73. doi:10.1158/0008-5472.CAN-08-4210. PMID:19351829.

Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR et al. (Mar 2009) The 2008 update of the Aspergillus nidulans genome annotation: a community effort Fungal genetics and biology : FG & B 46 Suppl 1: S2-13. doi:10.1016/j.fgb.2008.12.003. PMID:19146970.

Salzberg SL, Puiu D, Sommer DD, Nene V, Lee NH (Mar 2009) Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB Journal of bacteriology 191 (5): 1725. doi:10.1128/JB.01731-08. PMID:19114486.

Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP (Feb 2009) Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells Nature genetics 41 (2): 246-50. doi:10.1038/ng.297. PMID:19151716.

Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P et al. (Feb 2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores Nature genetics 41 (2): 178-86. doi:10.1038/ng.298. PMID:19151715.

Ruczinski I, Plaxco KW (Feb 2009) Some recommendations for the practitioner to improve the precision of experimentally determined protein folding rates and phi values Proteins 74 (2): 461-74. doi:10.1002/prot.22155. PMID:18655053.

Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD et al. (Jan 2009) Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1 Mutation research 660 (1-2): 1-11. doi:10.1016/j.mrfmmm.2008.09.017. PMID:18992264.

Karchin R (Jan 2009) Next generation tools for the annotation of human SNPs Briefings in bioinformatics 10 (1): 35-52. doi:10.1093/bib/bbn047. PMID:19181721.

Irizarry R, Reiss A (2009) Beyond blood gases: making use of additional oxygenation parameters and plasma electrolytes in the emergency room Compendium (Yardley, PA) 31 (10): E1-5. PMID:20180211.

Irizarry R, Reiss A (2009) Arterial and venous blood gases Compendium (Yardley, PA) 31 (5): E1-E11. PMID:19517413.

Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D et al. (Apr 2009) A whole-genome assembly of the domestic cow, Bos taurus Genome biology 10 (4): R42. doi:10.1186/gb-2009-10-4-r42. PMID:19393038.

Langmead B, Trapnell C, Pop M, Salzberg SL (Mar 2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome biology 10 (3): R25. doi:10.1186/gb-2009-10-3-r25. PMID:19261174.

Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD et al. (Jan 2009) The complete genome sequence of Bacillus anthracis Ames "Ancestor" Journal of bacteriology 191 (1): 445-6. doi:10.1128/JB.01347-08. PMID:18952800.

Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL (Jan 2009) OperonDB: a comprehensive database of predicted operons in microbial genomes Nucleic acids research 37 (Database issue): D479-82. doi:10.1093/nar/gkn784. PMID:18948284.

Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT et al. (Jan 2009) MODBASE, a database of annotated comparative protein structure models and associated resources Nucleic acids research 37 (Database issue): D347-54. doi:10.1093/nar/gkn791. PMID:18948282.

Smith IM, Glazer CA, Mithani SK, Ochs MF, Sun W, Bhan S et al. (Mar 2009) Coordinated activation of candidate proto-oncogenes and cancer testes antigens via promoter demethylation in head and neck cancer and lung cancer PloS one 4 (3): e4961. doi:10.1371/journal.pone.0004961. PMID:19305507.

2008

Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D et al. (Dec 2008) nGASP--the nematode genome annotation assessment project BMC bioinformatics 9: 549. doi:10.1186/1471-2105-9-549. PMID:19099578.

Schaeffer EM, Marchionni L, Huang Z, Simons B, Blackman A, Yu W et al. (Dec 2008) Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer Oncogene 27 (57): 7180-91. doi:10.1038/onc.2008.327. PMID:18794802.

Leek JT, Storey JD (Dec 2008) A general framework for multiple testing dependence Proceedings of the National Academy of Sciences of the United States of America 105 (48): 18718-23. doi:10.1073/pnas.0808709105. PMID:19033188.

Katzman S, Barrett C, Thiltgen G, Karchin R, Karplus K (Nov 2008) PREDICT-2ND: a tool for generalized protein local structure prediction Bioinformatics (Oxford, England) 24 (21): 2453-9. doi:10.1093/bioinformatics/btn438. PMID:18757875.

Yegnasubramanian S, Haffner MC, Zhang Y, Gurel B, Cornish TC, Wu Z et al. (Nov 2008) DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity Cancer research 68 (21): 8954-67. doi:10.1158/0008-5472.CAN-07-6088. PMID:18974140.

Wen B, Wu H, Bjornsson H, Green RD, Irizarry R, Feinberg AP (Nov 2008) Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification Genome research 18 (11): 1806-13. doi:10.1101/gr.067587.108. PMID:18849526.

Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH (Nov 2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data Nature biotechnology 26 (11): 1293-300. doi:10.1038/nbt.1505. PMID:18978777.

Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E et al. (Oct 2008) Comparative genomics of the neglected human malaria parasite Plasmodium vivax Nature 455 (7214): 757-63. doi:10.1038/nature07327. PMID:18843361.

McCall MN, Irizarry RA (Oct 2008) Consolidated strategy for the analysis of microarray spike-in data Nucleic acids research 36 (17): e108. doi:10.1093/nar/gkn430. PMID:18676452.

Salzberg SL, Sommer DD, Puiu D, Lee VT (Sep 2008) Gene-boosted assembly of a novel bacterial genome from very short reads PLoS computational biology 4 (9): e1000186. doi:10.1371/journal.pcbi.1000186. PMID:18818729.

Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P et al. (Sep 2008) Core signaling pathways in human pancreatic cancers revealed by global genomic analyses Science (New York, N.Y.) 321 (5897): 1801-6. doi:10.1126/science.1164368. PMID:18772397.

Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P et al. (Sep 2008) An integrated genomic analysis of human glioblastoma multiforme Science (New York, N.Y.) 321 (5897): 1807-12. doi:10.1126/science.1164382. PMID:18772396.

Chen J, Ruczinski I, Jorgensen TJ, Yenokyan G, Yao Y, Alani R et al. (Sep 2008) Nonmelanoma skin cancer and risk for subsequent malignancy Journal of the National Cancer Institute 100 (17): 1215-22. doi:10.1093/jnci/djn260. PMID:18728282.

Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park J et al. (Sep 2008) Differential parental transmission of markers in RUNX2 among cleft case-parent trios from four populations Genetic epidemiology 32 (6): 505-12. doi:10.1002/gepi.20323. PMID:18357615.

Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA (Sep 2008) Estimating genome-wide copy number using allele-specific mixture models Journal of computational biology : a journal of computational molecular cell biology 15 (7): 857-66. doi:10.1089/cmb.2007.0148. PMID:18707534.

Kingsford C, Salzberg SL (Sep 2008) What are decision trees? Nature biotechnology 26 (9): 1011-3. doi:10.1038/nbt0908-1011. PMID:18779814.

Pattaro C, Ruczinski I, Fallin DM, Parmigiani G (Aug 2008) Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies BMC genomics 9: 405. doi:10.1186/1471-2164-9-405. PMID:18759977.

Nguyen P, Cui H, Bisht KS, Sun L, Patel K, Lee RS et al. (Jul 2008) CTCFL/BORIS is a methylation-independent DNA-binding protein that preferentially binds to the paternal H19 differentially methylated region Cancer research 68 (14): 5546-51. doi:10.1158/0008-5472.CAN-08-1005. PMID:18632606.

Wheelan SJ, Martinez Murillo F, Boeke JD (Jul 2008) The incredible shrinking world of DNA microarrays Molecular bioSystems 4 (7): 726-32. doi:10.1039/b706237k. PMID:18563246.

Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H et al. (Jun 2008) Intra-individual change over time in DNA methylation with familial clustering JAMA : the journal of the American Medical Association 299 (24): 2877-83. doi:10.1001/jama.299.24.2877. PMID:18577732.

Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I (Jun 2008) Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays The annals of applied statistics 2 (2): 687-713. doi:10.1214/07-AOAS155. PMID:19609370.

Miller RA, Christoforou N, Pevsner J, McCallion AS, Gearhart JD (May 2008) Efficient array-based identification of novel cardiac genes through differentiation of mouse ESCs PloS one 3 (5): e2176. doi:10.1371/journal.pone.0002176. PMID:18478100.

Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S et al. (May 2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A BMC genomics 9: 204. doi:10.1186/1471-2164-9-204. PMID:18452608.

Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM et al. (May 2008) SNP-specific array-based allele-specific expression analysis Genome research 18 (5): 771-9. doi:10.1101/gr.073254.107. PMID:18369178.

Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA et al. (May 2008) Comprehensive high-throughput arrays for relative methylation (CHARM) Genome research 18 (5): 780-90. doi:10.1101/gr.7301508. PMID:18316654.

Sun L, Huang L, Nguyen P, Bisht KS, Bar-Sela G, Ho AS et al. (Apr 2008) DNA methyltransferase 1 and 3B activate BAG-1 expression via recruitment of CTCFL/BORIS and modulation of promoter histone methylation Cancer research 68 (8): 2726-35. doi:10.1158/0008-5472.CAN-07-6654. PMID:18413740.

Lin S, Carvalho B, Cutler DJ, Arking DE, Chakravarti A, Irizarry RA (Apr 2008) Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays Genome biology 9 (4): R63. doi:10.1186/gb-2008-9-4-r63. PMID:18387188.

Gallicchio L, Chang H, Christo DK, Thuita L, Huang HY, Strickland P et al. (Apr 2008) Single nucleotide polymorphisms in inflammation-related genes and mortality in a community-based cohort in Washington County, Maryland American journal of epidemiology 167 (7): 807-13. doi:10.1093/aje/kwm378. PMID:18263601.

Feinberg AP (Mar 2008) Epigenetics at the epicenter of modern medicine JAMA : the journal of the American Medical Association 299 (11): 1345-50. doi:10.1001/jama.299.11.1345. PMID:18349095.

Bengtsson H, Irizarry R, Carvalho B, Speed TP (Mar 2008) Estimation and assessment of raw copy numbers at the single locus level Bioinformatics (Oxford, England) 24 (6): 759-67. doi:10.1093/bioinformatics/btn016. PMID:18204055.

Marchionni L, Wilson RF, Wolff AC, Marinopoulos S, Parmigiani G, Bass EB et al. (Mar 2008) Systematic review: gene expression profiling assays in early-stage breast cancer Annals of internal medicine 148 (5): 358-69. PMID:18252678.

Pop M, Salzberg SL (Mar 2008) Bioinformatics challenges of new sequencing technology Trends in genetics : TIG 24 (3): 142-9. doi:10.1016/j.tig.2007.12.006. PMID:18262676.

Rodriguez-Quinones JF, Irizarry RA, Diaz-Blanco NL, Rivera-Molina FE, Gomez-Garzon D, Rodriguez-Medina JR (Jan 2008) Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions BMC genomics 9: 34. doi:10.1186/1471-2164-9-34. PMID:18215314.

Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J et al. (Jan 2008) Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments Genome biology 9 (1): R7. doi:10.1186/gb-2008-9-1-r7. PMID:18190707.

Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP et al. (Jan 2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA Nature 451 (7175): 202-6. doi:10.1038/nature06468. PMID:18185590.

Potash JB, Buervenich S, Cox NJ, Zandi PP, Akula N, Steele J et al. (Jan 2008) Gene-based SNP mapping of a psychotic bipolar affective disorder linkage region on 22q12.3: association with HMG2L1 and TOM1 American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 147B (1): 59-67. doi:10.1002/ajmg.b.30574. PMID:17671966.

Schulze KJ, Christian P, Ruczinski I, Ray AL, Nath A, Wu LS et al. (2008) Hepcidin and iron status among pregnant women in Bangladesh Asia Pacific journal of clinical nutrition 17 (3): 451-6. PMID:18818166.

Karchin R, Agarwal M, Sali A, Couch F, Beattie MS (Apr 2008) Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios Cancer informatics 6: 203-16. PMID:19043619.

Peyser BD, Irizarry R, Spencer FA (2008) Statistical analysis of fitness data determined by TAG hybridization on microarrays Methods in molecular biology (Clifton, N.J.) 416: 369-81. doi:10.1007/978-1-59745-321-9_25. PMID:18392981.

Meluh PB, Pan X, Yuan DS, Tiffany C, Chen O, Sookhai-Mahadeo S et al. (2008) Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray Methods in molecular biology (Clifton, N.J.) 416: 221-47. doi:10.1007/978-1-59745-321-9_15. PMID:18392971.

Puiu D, Salzberg SL (Oct 2008) Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18 PloS one 3 (10): e3427. doi:10.1371/journal.pone.0003427. PMID:18927608.

2007

Marchionni L, Wilson RF, Marinopoulos SS, Wolff AC, Parmigiani G, Bass EB et al. (Dec 2007) Impact of gene expression profiling tests on breast cancer outcomes Evidence report/technology assessment . PMID:18457476.

Ting JC, Roberson ED, Miller ND, Lysholm-Bernacchi A, Stephan DA, Capone GT et al. (Dec 2007) Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio Human mutation 28 (12): 1225-35. doi:10.1002/humu.20583. PMID:17661425.

Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ et al. (Nov 2007) The genomic landscapes of human breast and colorectal cancers Science (New York, N.Y.) 318 (5853): 1108-13. doi:10.1126/science.1145720. PMID:17932254.

Zilliox MJ, Irizarry RA (Nov 2007) A gene expression bar code for microarray data Nature methods 4 (11): 911-3. doi:10.1038/nmeth1102. PMID:17906632.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J et al. (Sep 2007) Draft genome of the filarial nematode parasite Brugia malayi Science (New York, N.Y.) 317 (5845): 1756-60. doi:10.1126/science.1145406. PMID:17885136.

Kingsford C, Delcher AL, Salzberg SL (Sep 2007) A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes Molecular biology and evolution 24 (9): 2091-8. doi:10.1093/molbev/msm145. PMID:17642473.

Leek JT, Storey JD (Sep 2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis PLoS genetics 3 (9): 1724-35. doi:10.1371/journal.pgen.0030161. PMID:17907809.

Akey JM, Biswas S, Leek JT, Storey JD (Jul 2007) On the design and analysis of gene expression studies in human populations Nature genetics 39 (7): 807-8; author reply 808-9. doi:10.1038/ng0707-807. PMID:17597765.

Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ et al. (Jun 2007) Genome sequence of Aedes aegypti, a major arbovirus vector Science (New York, N.Y.) 316 (5832): 1718-23. doi:10.1126/science.1138878. PMID:17510324.

Feinberg AP (May 2007) Phenotypic plasticity and the epigenetics of human disease Nature 447 (7143): 433-40. doi:10.1038/nature05919. PMID:17522677.

Pertea M, Mount SM, Salzberg SL (May 2007) A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana BMC bioinformatics 8: 159. doi:10.1186/1471-2105-8-159. PMID:17517127.

Salzberg SL, Kingsford C, Cattoli G, Spiro DJ, Janies DA, Aly MM et al. (May 2007) Genome analysis linking recent European and African influenza (H5N1) viruses Emerging infectious diseases 13 (5): 713-8. doi:10.3201/eid1305.070013. PMID:17553249.

Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A et al. (May 2007) Comprehensive DNA signature discovery and validation PLoS computational biology 3 (5): e98. doi:10.1371/journal.pcbi.0030098. PMID:17511514.

Loyo-Berrios NI, Irizarry R, Hennessey JG, Tao XG, Matanoski G (Apr 2007) Air pollution sources and childhood asthma attacks in Catano, Puerto Rico American journal of epidemiology 165 (8): 927-35. doi:10.1093/aje/kwk088. PMID:17308332.

Carvalho B, Bengtsson H, Speed TP, Irizarry RA (Apr 2007) Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data Biostatistics (Oxford, England) 8 (2): 485-99. doi:10.1093/biostatistics/kxl042. PMID:17189563.

Storey JD, Dai JY, Leek JT (Apr 2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments Biostatistics (Oxford, England) 8 (2): 414-32. doi:10.1093/biostatistics/kxl019. PMID:16928955.

Delcher AL, Bratke KA, Powers EC, Salzberg SL (Mar 2007) Identifying bacterial genes and endosymbiont DNA with Glimmer Bioinformatics (Oxford, England) 23 (6): 673-9. doi:10.1093/bioinformatics/btm009. PMID:17237039.

Visvanathan K, Crum RM, Strickland PT, You X, Ruczinski I, Berndt SI et al. (Mar 2007) Alcohol dehydrogenase genetic polymorphisms, low-to-moderate alcohol consumption, and risk of breast cancer Alcoholism, clinical and experimental research 31 (3): 467-76. doi:10.1111/j.1530-0277.2006.00334.x. PMID:17295732.

Scharpf RB, Ting JC, Pevsner J, Ruczinski I (Mar 2007) SNPchip: R classes and methods for SNP array data Bioinformatics (Oxford, England) 23 (5): 627-8. doi:10.1093/bioinformatics/btl638. PMID:17204461.

Sommer DD, Delcher AL, Salzberg SL, Pop M (Feb 2007) Minimus: a fast, lightweight genome assembler BMC bioinformatics 8: 64. doi:10.1186/1471-2105-8-64. PMID:17324286.

Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A (Feb 2007) Functional impact of missense variants in BRCA1 predicted by supervised learning PLoS computational biology 3 (2): e26. doi:10.1371/journal.pcbi.0030026. PMID:17305420.

Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF et al. (Feb 2007) Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis Cancer research 67 (4): 1494-501. doi:10.1158/0008-5472.CAN-06-3297. PMID:17308087.

Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q et al. (Jan 2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis Science (New York, N.Y.) 315 (5809): 207-12. doi:10.1126/science.1132894. PMID:17218520.

Clark TG, De Iorio M, Griffiths RC (Jan 2007) Bayesian logistic regression using a perfect phylogeny Biostatistics (Oxford, England) 8 (1): 32-52. doi:10.1093/biostatistics/kxj030. PMID:16556611.

Jorgensen TJ, Visvanathan K, Ruczinski I, Thuita L, Hoffman S, Helzlsouer KJ (Jan 2007) Breast cancer risk is not associated with polymorphic forms of xeroderma pigmentosum genes in a cohort of women from Washington County, Maryland Breast cancer research and treatment 101 (1): 65-71. doi:10.1007/s10549-006-9263-3. PMID:16823510.

Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL (2007) Hawkeye: an interactive visual analytics tool for genome assemblies Genome biology 8 (3): R34. doi:10.1186/gb-2007-8-3-r34. PMID:17349036.

Kingsford CL, Ayanbule K, Salzberg SL (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake Genome biology 8 (2): R22. doi:10.1186/gb-2007-8-2-r22. PMID:17313685.

Salzberg SL (2007) Genome re-annotation: a wiki solution? Genome biology 8 (1): 102. doi:10.1186/gb-2007-8-1-102. PMID:17274839.

Kelly L, Karchin R, Sali A (2007) Protein interactions and disease phenotypes in the ABC transporter superfamily Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing . PMID:17990484.

2006

Yuan DS, Irizarry RA (Dec 2006) High-resolution spatial normalization for microarrays containing embedded technical replicates Bioinformatics (Oxford, England) 22 (24): 3054-60. doi:10.1093/bioinformatics/btl542. PMID:17060357.

An W, Han JS, Wheelan SJ, Davis ES, Coombes CE, Ye P et al. (Dec 2006) Active retrotransposition by a synthetic L1 element in mice Proceedings of the National Academy of Sciences of the United States of America 103 (49): 18662-7. doi:10.1073/pnas.0605300103. PMID:17124176.

Dai JY, Ruczinski I, LeBlanc M, Kooperberg C (Dec 2006) Imputation methods to improve inference in SNP association studies Genetic epidemiology 30 (8): 690-702. doi:10.1002/gepi.20180. PMID:16986162.

Wheelan SJ, Scheifele LZ, Martinez-Murillo F, Irizarry RA, Boeke JD (Nov 2006) Transposon insertion site profiling chip (TIP-chip) Proceedings of the National Academy of Sciences of the United States of America 103 (47): 17632-7. doi:10.1073/pnas.0605450103. PMID:17101968.

Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E et al. (Nov 2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB BMC bioinformatics 7: 489. doi:10.1186/1471-2105-7-489. PMID:17087822.

Wheelan SJ, Martinez-Murillo F, Irizarry RA, Boeke JD (Nov 2006) Stacking the deck: double-tiled DNA microarrays Nature methods 3 (11): 903-7. doi:10.1038/nmeth951. PMID:17060914.

Katz S, Irizarry RA, Lin X, Tripputi M, Porter MW (Oct 2006) A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database BMC bioinformatics 7: 464. doi:10.1186/1471-2105-7-464. PMID:17059591.

Ruczinski I, Sosnick TR, Plaxco KW (Oct 2006) Methods for the accurate estimation of confidence intervals on protein folding phi-values Protein science : a publication of the Protein Society 15 (10): 2257-64. doi:10.1110/ps.062230106. PMID:17008714.

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR et al. (Sep 2006) Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote PLoS biology 4 (9): e286. doi:10.1371/journal.pbio.0040286. PMID:16933976.

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Allen JE, Salzberg SL (Aug 2006) A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons Algorithms for molecular biology : AMB 1: 14. doi:10.1186/1748-7188-1-14. PMID:16934144.

Takahashi H, McCaffery JM, Irizarry RA, Boeke JD (Jul 2006) Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription Molecular cell 23 (2): 207-17. doi:10.1016/j.molcel.2006.05.040. PMID:16857587.

DiPietro JA, Caulfield LE, Irizarry RA, Chen P, Merialdi M, Zavaleta N (Jun 2006) Prenatal development of intrafetal and maternal-fetal synchrony Behavioral neuroscience 120 (3): 687-701. doi:10.1037/0735-7044.120.3.687. PMID:16768620.

Brown EE, Fallin D, Ruczinski I, Hutchinson A, Staats B, Vitale F et al. (May 2006) Associations of classic Kaposi sarcoma with common variants in genes that modulate host immunity Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 15 (5): 926-34. doi:10.1158/1055-9965.EPI-05-0791. PMID:16702372.

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Richardson SM, Wheelan SJ, Yarrington RM, Boeke JD (Apr 2006) GeneDesign: rapid, automated design of multikilobase synthetic genes Genome research 16 (4): 550-6. doi:10.1101/gr.4431306. PMID:16481661.

Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W et al. (Mar 2006) Top-down standards will not serve systems biology Nature 440 (7080): 24. doi:10.1038/440024a. PMID:16511469.

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Leek JT, Monsen E, Dabney AR, Storey JD (Feb 2006) EDGE: extraction and analysis of differential gene expression Bioinformatics (Oxford, England) 22 (4): 507-8. doi:10.1093/bioinformatics/btk005. PMID:16357033.

Cope L, Hartman SM, Gohlmann HW, Tiesman JP, Irizarry RA (Feb 2006) Analysis of Affymetrix GeneChip data using amplified RNA BioTechniques 40 (2): 165-6, 168, 170. PMID:16526405.

Malek RL, Wang HY, Kwitek AE, Greene AS, Bhagabati N, Borchardt G et al. (Feb 2006) Physiogenomic resources for rat models of heart, lung and blood disorders Nature genetics 38 (2): 234-9. doi:10.1038/ng1693. PMID:16415889.

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Zeger SL, Irizarry R, Peng RD (2006) On time series analysis of public health and biomedical data Annual review of public health 27: 57-79. doi:10.1146/annurev.publhealth.26.021304.144517. PMID:16533109.

Brewster AM, Jorgensen TJ, Ruczinski I, Huang HY, Hoffman S, Thuita L et al. (Jan 2006) Polymorphisms of the DNA repair genes XPD (Lys751Gln) and XRCC1 (Arg399Gln and Arg194Trp): relationship to breast cancer risk and familial predisposition to breast cancer Breast cancer research and treatment 95 (1): 73-80. doi:10.1007/s10549-005-9045-3. PMID:16319991.

Irizarry RA, Cope LM, Wu Z (2006) Feature-level exploration of a published Affymetrix GeneChip control dataset Genome biology 7 (8): 404. doi:10.1186/gb-2006-7-8-404. PMID:16953902.

Allen JE, Majoros WH, Pertea M, Salzberg SL (Aug 2006) JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions Genome biology 7 Suppl 1: S9.1-13. doi:10.1186/gb-2006-7-s1-s9. PMID:16925843.

Feinberg AP, Ohlsson R, Henikoff S (Jan 2006) The epigenetic progenitor origin of human cancer Nature reviews. Genetics 7 (1): 21-33. doi:10.1038/nrg1748. PMID:16369569.

Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A et al. (Jan 2006) MODBASE: a database of annotated comparative protein structure models and associated resources Nucleic acids research 34 (Database issue): D291-5. doi:10.1093/nar/gkj059. PMID:16381869.

Lechtzin N, John M, Irizarry R, Merlo C, Diette GB, Boyle MP (Aug 2006) Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa Respiration; international review of thoracic diseases 73 (1): 27-33. doi:10.1159/000087686. PMID:16113513.

Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS et al. (Jan 2006) Global synthetic-lethality analysis and yeast functional profiling Trends in genetics : TIG 22 (1): 56-63. doi:10.1016/j.tig.2005.11.003. PMID:16309778.

2005

Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J et al. (Dec 2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus Nature 438 (7071): 1151-6. doi:10.1038/nature04332. PMID:16372009.

Karplus K, Karchin R, Shackelford G, Hughey R (Nov 2005) Calibrating E-values for hidden Markov models using reverse-sequence null models Bioinformatics (Oxford, England) 21 (22): 4107-15. doi:10.1093/bioinformatics/bti629. PMID:16123115.

Ghedin E, Sengamalay NA, Shumway M, Zaborsky J, Feldblyum T, Subbu V et al. (Oct 2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution Nature 437 (7062): 1162-6. doi:10.1038/nature04239. PMID:16208317.

Peng S, Trimble C, Ji H, He L, Tsai YC, Macaes B et al. (Oct 2005) Characterization of HPV-16 E6 DNA vaccines employing intracellular targeting and intercellular spreading strategies Journal of biomedical science 12 (5): 689-700. doi:10.1007/s11373-005-9012-3. PMID:16200349.

Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J et al. (Oct 2005) The External RNA Controls Consortium: a progress report Nature methods 2 (10): 731-4. doi:10.1038/nmeth1005-731. PMID:16179916.

McCarney ER, Werner JH, Bernstein SL, Ruczinski I, Makarov DE, Goodwin PM et al. (Sep 2005) Site-specific dimensions across a highly denatured protein; a single molecule study Journal of molecular biology 352 (3): 672-82. doi:10.1016/j.jmb.2005.07.015. PMID:16095607.

Allen JE, Salzberg SL (Sep 2005) JIGSAW: integration of multiple sources of evidence for gene prediction Bioinformatics (Oxford, England) 21 (18): 3596-603. doi:10.1093/bioinformatics/bti609. PMID:16076884.

Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD et al. (Sep 2005) Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools Nucleic acids research 33 (16): e140. doi:10.1093/nar/gni138. PMID:16166654.

Storey JD, Xiao W, Leek JT, Tompkins RG, Davis RW (Sep 2005) Significance analysis of time course microarray experiments Proceedings of the National Academy of Sciences of the United States of America 102 (36): 12837-42. doi:10.1073/pnas.0504609102. PMID:16141318.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N et al. (Sep 2005) The transcriptional landscape of the mammalian genome Science (New York, N.Y.) 309 (5740): 1559-63. doi:10.1126/science.1112014. PMID:16141072.

Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A et al. (Sep 2005) Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species Genome research 15 (9): 1284-91. doi:10.1101/gr.3869505. PMID:16109971.

Wheelan SJ, Aizawa Y, Han JS, Boeke JD (Aug 2005) Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution Genome research 15 (8): 1073-8. doi:10.1101/gr.3688905. PMID:16024818.

Kittleson MM, Minhas KM, Irizarry RA, Ye SQ, Edness G, Breton E et al. (Jul 2005) Gene expression in giant cell myocarditis: Altered expression of immune response genes International journal of cardiology 102 (2): 333-40. doi:10.1016/j.ijcard.2005.03.075. PMID:15982506.

Wu Z, Irizarry RA (Jul-Aug 2005) Stochastic models inspired by hybridization theory for short oligonucleotide arrays Journal of computational biology : a journal of computational molecular cell biology 12 (6): 882-93. doi:10.1089/cmb.2005.12.882. PMID:16108723.

Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA et al. (Jul 2005) Improved microarray methods for profiling the Yeast Knockout strain collection Nucleic acids research 33 (12): e103. doi:10.1093/nar/gni105. PMID:15994458.

Sheridan T, Askin FB, Ji H (Jul-Aug 2005) Multinucleated foreign body giant cells in placental membrane Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society 8 (4): 493-6. doi:10.1007/s10024-005-0027-6. PMID:16211455.

Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N et al. (Jul 2005) Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes Science (New York, N.Y.) 309 (5731): 134-7. doi:10.1126/science.1110439. PMID:15994558.

Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N et al. (Jun 2005) LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources Bioinformatics (Oxford, England) 21 (12): 2814-20. doi:10.1093/bioinformatics/bti442. PMID:15827081.

Dalla E, Mignone F, Verardo R, Marchionni L, Marzinotto S, Lazarevic D et al. (Jun 2005) Discovery of 342 putative new genes from the analysis of 5'-end-sequenced full-length-enriched cDNA human transcripts Genomics 85 (6): 739-51. doi:10.1016/j.ygeno.2005.02.009. PMID:15885500.

Kittleson MM, Minhas KM, Irizarry RA, Ye SQ, Edness G, Breton E et al. (May 2005) Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure Physiological genomics 21 (3): 299-307. doi:10.1152/physiolgenomics.00255.2004. PMID:15769906.

Grigoryev DN, Ma SF, Simon BA, Irizarry RA, Ye SQ, Garcia JG (May 2005) In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology BMC genomics 6: 62. doi:10.1186/1471-2164-6-62. PMID:15871745.

Majoros WH, Pertea M, Salzberg SL (May 2005) Efficient implementation of a generalized pair hidden Markov model for comparative gene finding Bioinformatics (Oxford, England) 21 (9): 1782-8. doi:10.1093/bioinformatics/bti297. PMID:15691859.

Hansel NN, Hilmer SC, Georas SN, Cope LM, Guo J, Irizarry RA et al. (May 2005) Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma The Journal of laboratory and clinical medicine 145 (5): 263-74. doi:10.1016/j.lab.2005.02.010. PMID:15902098.

Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC et al. (May 2005) Multiple-laboratory comparison of microarray platforms Nature methods 2 (5): 345-50. doi:10.1038/nmeth756. PMID:15846361.

Hernandez EA, Posada B, Irizarry R, Castro ME (Apr 2005) Role of hydrogen bonding interactions in directing one-dimensional thiol-assisted growth of silver-based nanofibers The journal of physical chemistry. B 109 (15): 7251-7. doi:10.1021/jp044242n. PMID:16851829.

Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN (Mar 2005) On the utility of pooling biological samples in microarray experiments Proceedings of the National Academy of Sciences of the United States of America 102 (12): 4252-7. doi:10.1073/pnas.0500607102. PMID:15755808.

Maxwell KL, Wildes D, Zarrine-Afsar A, De Los Rios MA, Brown AG, Friel CT et al. (Mar 2005) Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins Protein science : a publication of the Protein Society 14 (3): 602-16. doi:10.1110/ps.041205405. PMID:15689503.

Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D et al. (Feb 2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans Science (New York, N.Y.) 307 (5713): 1321-4. doi:10.1126/science.1103773. PMID:15653466.

Kooperberg C, Ruczinski I (Feb 2005) Identifying interacting SNPs using Monte Carlo logic regression Genetic epidemiology 28 (2): 157-70. doi:10.1002/gepi.20042. PMID:15532037.

Majoros WH, Pertea M, Delcher AL, Salzberg SL (Jan 2005) Efficient decoding algorithms for generalized hidden Markov model gene finders BMC bioinformatics 6: 16. doi:10.1186/1471-2105-6-16. PMID:15667658.

Feinberg AP (2005) A genetic approach to cancer epigenetics Cold Spring Harbor symposia on quantitative biology 70: 335-41. doi:10.1101/sqb.2005.70.027. PMID:16869770.

Mao R, Wang X, Spitznagel EL Jr, Frelin LP, Ting JC, Ding H et al. (Dec 2005) Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart Genome biology 6 (13): R107. doi:10.1186/gb-2005-6-13-r107. PMID:16420667.

Florea L, Di Francesco V, Miller J, Turner R, Yao A, Harris M et al. (Jan 2005) Gene and alternative splicing annotation with AIR Genome research 15 (1): 54-66. doi:10.1101/gr.2889405. PMID:15632090.

Mao R, Pevsner J (2005) The use of genomic microarrays to study chromosomal abnormalities in mental retardation Mental retardation and developmental disabilities research reviews 11 (4): 279-85. doi:10.1002/mrdd.20082. PMID:16240409.

Karchin R, Kelly L, Sali A (2005) Improving functional annotation of non-synonomous SNPs with information theory Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing . PMID:15759645.

2004

Kittleson MM, Ye SQ, Irizarry RA, Minhas KM, Edness G, Conte JV et al. (Nov 2004) Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy Circulation 110 (22): 3444-51. doi:10.1161/01.CIR.0000148178.19465.11. PMID:15557369.

Fannjiang Y, Cheng WC, Lee SJ, Qi B, Pevsner J, McCaffery JM et al. (Nov 2004) Mitochondrial fission proteins regulate programmed cell death in yeast Genes & development 18 (22): 2785-97. doi:10.1101/gad.1247904. PMID:15520274.

Keles S, van der Laan MJ, Vulpe C (Nov 2004) Regulatory motif finding by logic regression Bioinformatics (Oxford, England) 20 (16): 2799-811. doi:10.1093/bioinformatics/bth333. PMID:15166027.

Majoros WH, Pertea M, Salzberg SL (Nov 2004) TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders Bioinformatics (Oxford, England) 20 (16): 2878-9. doi:10.1093/bioinformatics/bth315. PMID:15145805.

(Oct 2004) The ENCODE (ENCyclopedia Of DNA Elements) Project Science (New York, N.Y.) 306 (5696): 636-40. doi:10.1126/science.1105136. PMID:15499007.

De Cecco L, Marchionni L, Gariboldi M, Reid JF, Lagonigro MS, Caramuta S et al. (Oct 2004) Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2 Oncogene 23 (49): 8171-83. doi:10.1038/sj.onc.1207979. PMID:15377994.

Ward N, Larsen O, Sakwa J, Bruseth L, Khouri H, Durkin AS et al. (Oct 2004) Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath) PLoS biology 2 (10): e303. doi:10.1371/journal.pbio.0020303. PMID:15383840.

Salzberg SL, Church D, DiCuccio M, Yaschenko E, Ostell J (Sep 2004) The genome Assembly Archive: a new public resource PLoS biology 2 (9): E285. doi:10.1371/journal.pbio.0020285. PMID:15367931.

Kohn JE, Millett IS, Jacob J, Zagrovic B, Dillon TM, Cingel N et al. (Aug 2004) Random-coil behavior and the dimensions of chemically unfolded proteins Proceedings of the National Academy of Sciences of the United States of America 101 (34): 12491-6. doi:10.1073/pnas.0403643101. PMID:15314214.

Dipietro JA, Irizarry RA, Costigan KA, Gurewitsch ED (Jul 2004) The psychophysiology of the maternal-fetal relationship Psychophysiology 41 (4): 510-20. doi:10.1111/j.1469-8986.2004.00187.x. PMID:15189474.

Wu Z, Irizarry RA (Jun 2004) Preprocessing of oligonucleotide array data Nature biotechnology 22 (6): 656-8; author reply 658. doi:10.1038/nbt0604-656b. PMID:15175677.

Karchin R, Cline M, Karplus K (May 2004) Evaluation of local structure alphabets based on residue burial Proteins 55 (3): 508-18. doi:10.1002/prot.20008. PMID:15103615.

Pain A, Woodward J, Quail MA, Anderson MJ, Clark R, Collins M et al. (Apr 2004) Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster Fungal genetics and biology : FG & B 41 (4): 443-53. doi:10.1016/j.fgb.2003.12.003. PMID:14998527.

Warren CD, Eckley DM, Lee MS, Hanna JS, Hughes A, Peyser B et al. (Apr 2004) S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion Molecular biology of the cell 15 (4): 1724-35. doi:10.1091/mbc.E03-09-0637. PMID:14742710.

Monte M, Benetti R, Collavin L, Marchionni L, Del Sal G, Schneider C (Mar 2004) hGTSE-1 expression stimulates cytoplasmic localization of p53 The Journal of biological chemistry 279 (12): 11744-52. doi:10.1074/jbc.M311123200. PMID:14707141.

Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP (Feb 2004) A benchmark for Affymetrix GeneChip expression measures Bioinformatics (Oxford, England) 20 (3): 323-31. doi:10.1093/bioinformatics/btg410. PMID:14960458.

Gautier L, Cope L, Bolstad BM, Irizarry RA (Feb 2004) affy--analysis of Affymetrix GeneChip data at the probe level Bioinformatics (Oxford, England) 20 (3): 307-15. doi:10.1093/bioinformatics/btg405. PMID:14960456.

Feinberg AP, Tycko B (Feb 2004) The history of cancer epigenetics Nature reviews. Cancer 4 (2): 143-53. doi:10.1038/nrc1279. PMID:14732866.

Cummings DA, Irizarry RA, Huang NE, Endy TP, Nisalak A, Ungchusak K et al. (Jan 2004) Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand Nature 427 (6972): 344-7. doi:10.1038/nature02225. PMID:14737166.

Bjornsson HT, Cui H, Gius D, Fallin MD, Feinberg AP (2004) The new field of epigenomics: implications for cancer and other common disease research Cold Spring Harbor symposia on quantitative biology 69: 447-56. doi:10.1101/sqb.2004.69.447. PMID:16117680.

Irizarry R (Winter 2004) LARES: an artificial chemical process approach for optimization Evolutionary computation 12 (4): 435-59. doi:10.1162/1063656043138897. PMID:15768524.

Chen H, Irizarry RA, Luo L, Zirkin BR (Jan 2004) Leydig cell gene expression: effects of age and caloric restriction Experimental gerontology 39 (1): 31-43. PMID:14724062.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S et al. (Sep 2004) Bioconductor: open software development for computational biology and bioinformatics Genome biology 5 (10): R80. doi:10.1186/gb-2004-5-10-r80. PMID:15461798.

Grigoryev DN, Ma SF, Irizarry RA, Ye SQ, Quackenbush J, Garcia JG (Apr 2004) Orthologous gene-expression profiling in multi-species models: search for candidate genes Genome biology 5 (5): R34. doi:10.1186/gb-2004-5-5-r34. PMID:15128448.

Pop M, Kosack DS, Salzberg SL (Jan 2004) Hierarchical scaffolding with Bambus Genome research 14 (1): 149-59. doi:10.1101/gr.1536204. PMID:14707177.

Allen JE, Pertea M, Salzberg SL (Jan 2004) Computational gene prediction using multiple sources of evidence Genome research 14 (1): 142-8. doi:10.1101/gr.1562804. PMID:14707176.

Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP (2004) Experimental design and low-level analysis of microarray data International review of neurobiology 60: 25-58. doi:10.1016/S0074-7742(04)60002-X. PMID:15474586.

Bader JS, Chaudhuri A, Rothberg JM, Chant J (Jan 2004) Gaining confidence in high-throughput protein interaction networks Nature biotechnology 22 (1): 78-85. doi:10.1038/nbt924. PMID:14704708.

2003

Sidransky D, Irizarry R, Califano JA, Li X, Ren H, Benoit N et al. (Nov 2003) Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer patients from control subjects Journal of the National Cancer Institute 95 (22): 1711-7. PMID:14625262.

Dalla E, Verardo R, Lazarevic D, Marchionni L, Reid JF, Bahar N et al. (Oct-Nov 2003) LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome Comptes rendus biologies 326 (10-11): 967-70. PMID:14744102.

Scharfstein DO, Irizarry RA (Sep 2003) Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data Biometrics 59 (3): 601-13. PMID:14601761.

Ha PK, Benoit NE, Yochem R, Sciubba J, Zahurak M, Sidransky D et al. (Aug 2003) A transcriptional progression model for head and neck cancer Clinical cancer research : an official journal of the American Association for Cancer Research 9 (8): 3058-64. PMID:12912957.

Majoros WH, Pertea M, Antonescu C, Salzberg SL (Jul 2003) GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders Nucleic acids research 31 (13): 3601-4. PMID:12824375.

Cappola TP, Cope L, Cernetich A, Barouch LA, Minhas K, Irizarry RA et al. (Jun 2003) Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy Physiological genomics 14 (1): 25-34. doi:10.1152/physiolgenomics.00156.2002. PMID:12709511.

(Jun 2003) In-depth view of structure, activity, and evolution of rice chromosome 10 Science (New York, N.Y.) 300 (5625): 1566-9. doi:10.1126/science.1083523. PMID:12791992.

Volfovsky N, Haas BJ, Salzberg SL (Jun 2003) Computational discovery of internal micro-exons Genome research 13 (6A): 1216-21. doi:10.1101/gr.677503. PMID:12799353.

Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K (Jun 2003) Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry Proteins 51 (4): 504-14. doi:10.1002/prot.10369. PMID:12784210.

Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE et al. (May 2003) The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria Nature 423 (6935): 81-6. doi:10.1038/nature01586. PMID:12721629.

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U et al. (Apr 2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics (Oxford, England) 4 (2): 249-64. doi:10.1093/biostatistics/4.2.249. PMID:12925520.

Tankersley CG, Irizarry R, Flanders SE, Rabold R, Frank R (Mar 2003) Unstable heart rate and temperature regulation predict mortality in AKR/J mice American journal of physiology. Regulatory, integrative and comparative physiology 284 (3): R742-50. doi:10.1152/ajpregu.00416.2002. PMID:12388436.

Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (Feb 2003) Summaries of Affymetrix GeneChip probe level data Nucleic acids research 31 (4): e15. PMID:12582260.

Delcher AL, Salzberg SL, Phillippy AM (Feb 2003) Using MUMmer to identify similar regions in large sequence sets Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 10: Unit 10.3. doi:10.1002/0471250953.bi1003s00. PMID:18428693.

Bolstad BM, Irizarry RA, Astrand M, Speed TP (Jan 2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics (Oxford, England) 19 (2): 185-93. PMID:12538238.

Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D et al. (Jan 2003) Sequence variations in the public human genome data reflect a bottlenecked population history Proceedings of the National Academy of Sciences of the United States of America 100 (1): 376-81. doi:10.1073/pnas.222673099. PMID:12502794.

Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M et al. (2003) Combining local-structure, fold-recognition, and new fold methods for protein structure prediction Proteins 53 Suppl 6: 491-6. doi:10.1002/prot.10540. PMID:14579338.

Irizarry RA, Ooi SL, Wu Z, Boeke JD (Mar 2003) Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants Statistical applications in genetics and molecular biology 2: Article1. doi:10.2202/1544-6115.1002. PMID:16646779.

2002

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S et al. (Dec 2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs Nature 420 (6915): 563-73. doi:10.1038/nature01266. PMID:12466851.

Fraser CM, Eisen JA, Nelson KE, Paulsen IT, Salzberg SL (Dec 2002) The value of complete microbial genome sequencing (you get what you pay for) Journal of bacteriology 184 (23): 6403-5; discusion 6405. PMID:12426324.

Feinberg AP, Oshimura M, Barrett JC (Nov 2002) Epigenetic mechanisms in human disease Cancer research 62 (22): 6784-7. PMID:12438281.

Cui H, Onyango P, Brandenburg S, Wu Y, Hsieh CL, Feinberg AP (Nov 2002) Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2 Cancer research 62 (22): 6442-6. PMID:12438232.

Pertea M, Salzberg SL (Nov 2002) Using GlimmerM to find genes in eukaryotic genomes Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 4: Unit 4.4. doi:10.1002/0471250953.bi0404s00. PMID:18792941.

Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A et al. (Oct 2002) Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 Nature 419 (6906): 531-4. doi:10.1038/nature01094. PMID:12368868.

Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC et al. (Oct 2002) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii Nature 419 (6906): 512-9. doi:10.1038/nature01099. PMID:12368865.

Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW et al. (Oct 2002) Genome sequence of the human malaria parasite Plasmodium falciparum Nature 419 (6906): 498-511. doi:10.1038/nature01097. PMID:12368864.

Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J et al. (Oct 2002) Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains Journal of bacteriology 184 (19): 5479-90. PMID:12218036.

Bonneau R, Ruczinski I, Tsai J, Baker D (Aug 2002) Contact order and ab initio protein structure prediction Protein science : a publication of the Protein Society 11 (8): 1937-44. doi:10.1110/ps.3790102. PMID:12142448.

Ruczinski I, Kooperberg C, Bonneau R, Baker D (Jul 2002) Distributions of beta sheets in proteins with application to structure prediction Proteins 48 (1): 85-97. doi:10.1002/prot.10123. PMID:12012340.

Delcher AL, Phillippy A, Carlton J, Salzberg SL (Jun 2002) Fast algorithms for large-scale genome alignment and comparison Nucleic acids research 30 (11): 2478-83. PMID:12034836.

Rhee I, Bachman KE, Park BH, Jair KW, Yen RW, Schuebel KE et al. (Apr 2002) DNMT1 and DNMT3b cooperate to silence genes in human cancer cells Nature 416 (6880): 552-6. doi:10.1038/416552a. PMID:11932749.

Poole LJ, Yu Y, Kim PS, Zheng QZ, Pevsner J, Hayward GS (Apr 2002) Altered patterns of cellular gene expression in dermal microvascular endothelial cells infected with Kaposi's sarcoma-associated herpesvirus Journal of virology 76 (7): 3395-420. PMID:11884566.

Larson SM, Ruczinski I, Davidson AR, Baker D, Plaxco KW (Feb 2002) Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation Journal of molecular biology 316 (2): 225-33. doi:10.1006/jmbi.2001.5344. PMID:11851333.

Tankersley CG, Irizarry R, Flanders S, Rabold R (Feb 2002) Circadian rhythm variation in activity, body temperature, and heart rate between C3H/HeJ and C57BL/6J inbred strains Journal of applied physiology (Bethesda, Md. : 1985) 92 (2): 870-7. doi:10.1152/japplphysiol.00904.2001. PMID:11796704.

Karchin R, Karplus K, Haussler D (Jan 2002) Classifying G-protein coupled receptors with support vector machines Bioinformatics (Oxford, England) 18 (1): 147-59. PMID:11836223.

Pertea M, Salzberg SL (Jan 2002) Computational gene finding in plants Plant molecular biology 48 (1-2): 39-48. PMID:11860211.

2001

Crone NE, Hao L, Hart J Jr, Boatman D, Lesser RP, Irizarry R et al. (Dec 2001) Electrocorticographic gamma activity during word production in spoken and sign language Neurology 57 (11): 2045-53. PMID:11739824.

Dipietro JA, Irizarry RA, Hawkins M, Costigan KA, Pressman EK (Dec 2001) Cross-correlation of fetal cardiac and somatic activity as an indicator of antenatal neural development American journal of obstetrics and gynecology 185 (6): 1421-8. doi:10.1067/mob.2001.119108. PMID:11744919.

Irizarry RA, Tankersley C, Frank R, Flanders S (Dec 2001) Assessing homeostasis through circadian patterns Biometrics 57 (4): 1228-37. PMID:11764264.

Purcell AE, Jeon OH, Pevsner J (Dec 2001) The abnormal regulation of gene expression in autistic brain tissue Journal of autism and developmental disorders 31 (6): 545-9. PMID:11814264.

Wheelan SJ, Church DM, Ostell JM (Nov 2001) Spidey: a tool for mRNA-to-genomic alignments Genome research 11 (11): 1952-7. doi:10.1101/gr.195301. PMID:11691860.

Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S (Oct 2001) Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence Genome research 11 (10): 1641-50. doi:10.1101/gr.190201. PMID:11591641.

Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V et al. (Oct 2001) Gene expression profiling in postmortem Rett Syndrome brain: differential gene expression and patient classification Neurobiology of disease 8 (5): 847-65. doi:10.1006/nbdi.2001.0428. PMID:11592853.

Bouton CM, Hossain MA, Frelin LP, Laterra J, Pevsner J (Oct 2001) Microarray analysis of differential gene expression in lead-exposed astrocytes Toxicology and applied pharmacology 176 (1): 34-53. doi:10.1006/taap.2001.9274. PMID:11578147.

Bonneau R, Tsai J, Ruczinski I, Baker D (May-Jun 2001) Functional inferences from blind ab initio protein structure predictions Journal of structural biology 134 (2-3): 186-90. doi:10.1006/jsbi.2000.4370. PMID:11551178.

Pertea M, Lin X, Salzberg SL (Mar 2001) GeneSplicer: a new computational method for splice site prediction Nucleic acids research 29 (5): 1185-90. PMID:11222768.

Yuan Q, Quackenbush J, Sultana R, Pertea M, Salzberg SL, Buell CR (Mar 2001) Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species Plant physiology 125 (3): 1166-74. PMID:11244096.

Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y et al. (Feb 2001) Functional annotation of a full-length mouse cDNA collection Nature 409 (6821): 685-90. doi:10.1038/35055500. PMID:11217851.

Kooperberg C, Ruczinski I, LeBlanc ML, Hsu L (2001) Sequence analysis using logic regression Genetic epidemiology 21 Suppl 1: S626-31. PMID:11793751.

Ostell JM, Wheelan SJ, Kans JA (2001) The NCBI data model Methods of biochemical analysis 43: 19-43. PMID:11449725.

Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE et al. (2001) Rosetta in CASP4: progress in ab initio protein structure prediction Proteins Suppl 5: 119-26. PMID:11835488.

Lesk AM, Lo Conte L, Hubbard TJ (2001) Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts Proteins Suppl 5: 98-118. PMID:11835487.

Karplus K, Karchin R, Barrett C, Tu S, Cline M, Diekhans M et al. (2001) What is the value added by human intervention in protein structure prediction? Proteins Suppl 5: 86-91. PMID:11835485.

2000

(Dec 2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 (6814): 796-815. doi:10.1038/35048692. PMID:11130711.

Onyango P, Miller W, Lehoczky J, Leung CT, Birren B, Wheelan S et al. (Nov 2000) Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain Genome research 10 (11): 1697-710. PMID:11076855.

Plaxco KW, Simons KT, Ruczinski I, Baker D (Sep 2000) Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics Biochemistry 39 (37): 11177-83. PMID:10985762.

Wheelan SJ, Marchler-Bauer A, Bryant SH (Jul 2000) Domain size distributions can predict domain boundaries Bioinformatics (Oxford, England) 16 (7): 613-8. PMID:11038331.

Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B et al. (Apr 2000) Evolutionary conservation in protein folding kinetics Journal of molecular biology 298 (2): 303-12. doi:10.1006/jmbi.1999.3663. PMID:10764599.

Pertea M, Salzberg SL, Gardner MJ (Mar 2000) Finding genes in Plasmodium falciparum Nature 404 (6773): 34; discussion 34-5. doi:10.1038/35003643. PMID:10716431.

Wheelan S, Makalowski W (Jan 2000) Genome research: the second decade. A report on the XI Cold Spring Harbor Laboratory Meeting on Genome Mapping and Sequencing, May 13-17, 1998, Cold Spring Harbor, NY Computers & chemistry 24 (1): 125-7. PMID:10642884.

1999

Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D (Nov 1999) Experiment and theory highlight role of native state topology in SH3 folding Nature structural biology 6 (11): 1016-24. doi:10.1038/14901. PMID:10542092.

Wheelan SJ, Boguski MS, Duret L, Makalowski W (Sep 1999) Human and nematode orthologs--lessons from the analysis of 1800 human genes and the proteome of Caenorhabditis elegans Gene 238 (1): 163-70. PMID:10570994.

Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H (Jul 1999) Interpolated Markov models for eukaryotic gene finding Genomics 59 (1): 24-31. doi:10.1006/geno.1999.5854. PMID:10395796.

Simons KT, Bonneau R, Ruczinski I, Baker D (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins Suppl 3: 171-6. PMID:10526365.

Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D (Jan 1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Proteins 34 (1): 82-95. PMID:10336385.

1998

Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV et al. (Nov 1998) Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum Science (New York, N.Y.) 282 (5391): 1126-32. PMID:9804551.

Salzberg SL, Salzberg AJ, Kerlavage AR, Tomb JF (Sep 1998) Skewed oligomers and origins of replication Gene 217 (1-2): 57-67. PMID:9795135.

Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R et al. (Jul 1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete Science (New York, N.Y.) 281 (5375): 375-88. PMID:9665876.

Wheelan SJ, Boguski MS (Mar 1998) Late-night thoughts on the sequence annotation problem Genome research 8 (3): 168-9. PMID:9521919.

Salzberg SL, Delcher AL, Kasif S, White O (Jan 1998) Microbial gene identification using interpolated Markov models Nucleic acids research 26 (2): 544-8. PMID:9421513.

Karchin R, Hughey R (1998) Weighting hidden Markov models for maximum discrimination Bioinformatics (Oxford, England) 14 (9): 772-82. PMID:9918947.

Salzberg S, Delcher AL, Fasman KH, Henderson J (Winter 1998) A decision tree system for finding genes in DNA Journal of computational biology : a journal of computational molecular cell biology 5 (4): 667-80. PMID:10072083.

1997

Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R et al. (Dec 1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi Nature 390 (6660): 580-6. doi:10.1038/37551. PMID:9403685.

Salzberg SL (Aug 1997) A method for identifying splice sites and translational start sites in eukaryotic mRNA Computer applications in the biosciences : CABIOS 13 (4): 365-76. PMID:9283751.

1992

Salzberg S, Cost S (Sep 1992) Predicting protein secondary structure with a nearest-neighbor algorithm Journal of molecular biology 227 (2): 371-4. PMID:1404357.