| Center for Computational Biology Department of Computer Science |
|---|
Email: rsherman [at] jhu [dot] edu
Twitter: @rshermanjhu
Pronouns: she/her
Google Scholar
Curriculum Vitae
Rachel Sherman
Ph.D., Computer Science, Salzberg Lab, Johns Hopkins University
About me:
I completed my Ph.D. in Computer Science at Johns Hopkins University in January 2021. I was advised by Steven Salzberg, and my research involved considerable collaboration with Mike Schatz's lab. I recently started a new job at Illumina, as a Bioinformatics Support Scientist 2.
My PhD research focused on structural variant discovery and analyses in human genomic data, using both alignment and assembly based approaches. I have worked with short and long read data sets, developing and applying novel WGS analysis pipelines.
My recent research on discovering 300 Mb of long novel insertion sequences in 910 individuals of African-ancestry has received attention in the popular press, including in The Atlantic, Inverse, and Genetic Engineering and Biotech News. I gave an interview on the subject on Ireland's Newstalk radio show Futureproof (interview begins at 24:00), and was a guest on the podcast Conversations on Science.
Prior to beginning my PhD in 2015, I received a B.S. from Harvey Mudd College in Mathematical and Computational Biology. During my undergraduate I participated in several research projects, including a NSF REU at Cold Spring Harbor Laboratory where I examined genomic structural variation detection methods in Mike Schatz's lab, and a collaborative senior capstone project with Anne Condon at University of British Columbia studying RNA folding energies and pathways.
In addition to my research, I have sought out opportunities to develop my teaching skills. I have completed the Johns Hopkins Teaching Academy Certificate Program, through which I attended classes and workshops to strengthen my teaching skills and learn to think pedagogically. In January 2019, I taught a 3-week intersession course on dog DNA sequencing analyses, which I designed and taught as the sole instructor. In Fall 2019 I taught Introduction to Computer Science at Mount St Mary's University as an adjunct faculty member.
In my spare time I enjoy volunteering at my local animal shelter, the Maryland SPCA, where I both walk dogs and co-teach a volunteer class on handling behaviorally challenging dogs by employing force-free and positive reinforcent based training and management techniques. I also love hanging out with my own rescue pup, playing volleyball and board games, and cooking and baking.
Publications and Presented Work:
- Peer-Reviewed Publications
- Ramos, A. P., Leonhard, S. E., Halstead, S. K., Cuba, M. A., Castañeda, C. C., Dioses, J. A., ... , Sherman, R. M., ... & Pardo, C. A. (2021). Guillain-Barré syndrome outbreak in Peru 2019 associated with Campylobacter jejuni infection. Neurology-Neuroimmunology Neuroinflammation, 8(2).
- Aganezov, S., Goodwin, S., Sherman, R. M., Sedlazeck, F. J., Arun, G., Bhatia, S., ... & Schatz, M. C. (2020). Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Research.
- Shumate, A.*, Zimin, A. V.*, Sherman, R. M., Puiu, D., Wagner, J. M., Olson, N. D., ..., & Salzberg, S. L. (2020). Assembly and Annotation of an Ashkenazi Human Reference Genome. Genome Biology 21, 129.
- Sherman, R. M. & Salzberg, S. L. (2020). Pan-genomics in the human genome era. Nature Reviews Genetics 21, 243-254.
- Chen, S.*, Krusche, P.*, Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., ... & Eberle, M. A. (2019). Paragraph: A graph-based structural variant genotyper for short-read sequence data. Genome Biology 20, 291.
- Sherman, R. M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., ... & Salzberg, S. L. (2019). Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nature Genetics, 51(1), 30.
- Sork, V. L., Fitz-Gibbon, S. T., Puiu, D., Crepeau, M., Gugger, P. F., Sherman, R., ... & Salzberg, S. L. (2016). First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Nee (Fagaceae). G3: Genes | Genomes | Genetics, g3-116.
- Cannon, J.G.D., Sherman, R. M., Wang, V.M.Y., & Newman, G.A. (2015). Cross-species conservation of complementary amino acid-ribonucleobase interactions and their potential for ribosome-free encoding. Scientific Reports, 5, 18054.
- Preprints
- Yan, S. M., Sherman, R. M., Taylor, D. J., Nair, D. R., Bortvin, A. N., Schatz, M. C., & McCoy, R. C. (2021). Local adaptation and archaic introgression shape global diversity at human structural variant loci. bioRxiv.
- Presentations
- Discovering non-reference sequences to assemble a pan-genome of 910 African-ancestry individuals. Personal Genomics and International Cooperation Conference., Shanghai, China. October 2019.
- Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Research in Computational Molecular Biology (RECOMB), Washington D.C., May 2019.
- Diversifying Genomics: Identifying large variations in genomes of African ancestry individuals. Baltimore Underground Science Space, Baltimore, MD. March 2019.
- Analyzing structural variation in breast cancer with long read sequencing of patient-derived organoids. Biological Data Science, Cold Spring Harbor, NY. November 2018.
- Presented Posters
- Sherman, R.M., and Salzberg, S.L.. Evidence of transcription of novel human genomic sequences. RECOMB. Washington, DC. May 2019.
- Sherman, R.M., Antonescu, V., Rasika M.A.., Taub, M.A., Beaty, T.H., Ruczinski, I., Barnes, K.C., Salzberg, S.L.. Discovery of long novel insertions in African descent populations. The Biology of Genomes. Cold Spring Harbor, NY. May 2017.
- Agwamba, K.*, Heinen, S.*, Ramsden, C.*, Sherman, R.*, Sweedyk, E., & Condon, A.. Designing and analyzing RNA molecules with long and diverse folding pathways. 21st International Conference on DNA Computing and Molecular Programming. Boston, MA. August 2015.
For an up to date list of publications, please visit my Google Scholar profile.
Teaching:
-
Fall 2019 - Introduction to Computer Science, CMSCI 120, Mount Saint Mary's University
Adjunct faculty/sole instructor of a 3-credit intro computer science course (taught in Python) intended for freshman computer science majors and interested non-majors. I designed all lectures and assignments for the course (basing the material covered on learning goals outlined in previous CMSCI 120 syllabi). Students learned about fundamentals of programming including designing algorithms and writing modular programs, and practiced these techniques in lab and homework assignments and a final project.
-
Winter 2019 - What's in a Mutt: An Intro to Dog DNA Analysis, Johns Hopkins University
Sole instructor. Designed and taught as a 1-credit, 3-week course. Students learned computational methods used to examine SNP array data to determine dog breed of a mutt and applied these methods to mutt data given a reference panel of purebreds. If you're interested in teaching a course on this topic, feel free to contact me for additional materials.
Course Materials:
-
Spring 2017 - Introduction to Genomic Research, Johns Hopkins University
Teaching Assistant. Course taught by Steven Salzberg. Created assignments and held office hours. Course was project based, with students completing three projects on the topics of genome assembly, RNA-seq analysis, and metagenomics sequencing.
