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 am currently on the job market, with a particular
interest in teaching, training, and outreach focused positions in genomics.
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
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
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.
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.
- 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.
- 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.
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.
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.