We are excited to welcome back a familiar face from UCLA! Jeremy Rotman recently joined Mangul Lab at USC as a software engineer. Jeremy will be constructing tools and pipelines that will help us study large, noisy biological datasets on a high performance computing cluster.

Jeremy earned a Master’s degree and a Bachelor’s degree in Computer Science from UCLA. While an undergraduate and graduate student, and while Serghei was a postdoctoral scholar at UCLA, Jeremy worked in Eleazar Eskin’s computational genomics lab. He has contributed to the development of the ImReP tool for RNA sequencing analysis, lay-friendly reviews of clinical metagenomics and read alignment, and the release of our lab’s first publication:

Alser, Mohammed; Rotman, Jeremy; Taraszka, Kodi; Shi, Huwenbo; Baykal, Pelin Icer; Yang, Harry Taegyun; Xue, Victor; Knyazev, Sergey; Singer, Benjamin D; Balliu, Brunilda; Koslicki, David; Skums, Pavel; Zelikovsky, Alex; Alkan, Can; Mutlu, Onur; Mangul, Serghei

Technology dictates algorithms: Recent developments in read alignment Journal Article

arXiv, 2020.

Abstract | Links | BibTeX

Brito, Jaqueline J; Mosqueiro, Thiago; Rotman, Jeremy; Xue, Victor; Chapski, Douglas J; la Hoz, Juan De; Matias, Paulo; Martin, Lana S; Zelikovsky, Alex; Pellegrini, Matteo; Mangul, Serghei

Telescope: an interactive tool for managing large scale analysis from mobile devices Journal Article

GigaScience, 9 (1), pp. giz163, 2020.

Abstract | Links | BibTeX

Loeffler, Caitlin; Gibson, Keylie M; Martin, Lana S; Chang, Yutong; Rotman, Jeremy; Toma, Ian V; Mason, Christopher E; Eskin, Eleazar; Zackular, Joseph P; Crandall, Keith A; Koslicki, David; Mangul, Serghei

Unlocking the diagnostic and therapeutic potential of metagenomics Journal Article

arXiv, 2019.

Abstract | Links | BibTeX

Mandric, Igor; Rotman, Jeremy; Yang, Harry Taegyun; Strauli, Nicolas; Montoya, Dennis; Rotman, Jeremy; der Lay, Will Van; Ronas, Jiem R; Statz, Benjamin; Yao, Douglas; Petrova, Velislava; Zelikovsky, Alex; Spreafico, Roberto; Shifman, Sagiv; Zaitlen, Noah; Rossetti, Maura; Ansel, Mark K; Eskin, Eleazar; Mangul, Serghei

Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing Journal Article

bioRxiv; under consideration at Nature Communications, 2019.

Abstract | Links | BibTeX

Thomas, Brandon; Karimzada, Mohammed; Spreafico, Roberto; Mangul, Serghei; Botten, Jason W; Rotman, Jeremy; Wesel, Kevin; Binder, Pratibha S; Gharavi, Nima; Chesnut, Robert W

104 Lack of human papilloma virus transcription in cutaneous squamous cell carcinoma stratified by histological grade and host immune status Journal Article

Journal of Investigative Dermatology, 137 (5), pp. S18, 2017.

Abstract | Links | BibTeX

Interested in developing and applying bioinformatics methods for big data? Join our lab!