Selected Publications

Note: we are no longer keeping this list up to date. Please see the webpages of individual CCB faculty for current lists of publications.


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.


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.


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.


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.


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.

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