Maxim Shokhirev

Director / Staff Scientist

Integrative Genomics and Bioinformatics Core

Salk Institute for Biological Studies - Maxim Shokhirev

Maxim Shokhirev

Computer science and biology have been my passions for as long as I can remember. I immigrated to sunny Tucson, Arizona, from chilly Novosibirsk, Russia, in 1993, the youngest son of two Russian scientists, and grew up going with them to the Walker Lab in the old chemistry building at the University of Arizona (U of A). In high school, I started working in the lab alongside my parents, finding out about the chemical properties of nitrophorin proteins found in blood-sucking insects, learning how to run a nuclear magnetic resonance spectrometer, and experiencing the terrible odors coming from various organic compounds. As an undergraduate at the U of A, I double-majored in computer science and biochemistry and finished with honors, developing a coarse-grained molecular dynamics simulation tool. For graduate school, I joined the Bioinformatics and Systems Biology PhD program at UCSD, and worked with Dr. Alexander Hoffmann (now at UCLA), on a multi-scale understanding of the B-cell immune response. This entailed computational modeling, flow cytometry time-series experiments, live-cell time-lapse microscopy experiments, single-cell RNA-Seq, and (unfortunately) occasional mouse work.

A newly-minted Doctor of Philosophy, I moved across the street to the friendly world-renowned Salk Institute, working for Dr. Chris Benner (aka the Chuck Norris of Genomics), the founding director of the Salk Integrative Genomics and Bioinformatics Core (IGC). Under his tutelage, I learned very quickly about genomics analysis (RNA-Seq, ChIP-Seq, HiC, Bisulfite, and many others) and how to tell good data from the not-so-good data. After Chris started his own lab at UCSD, I worked with the Next Generation Sequencing Core, Salk IT, and the cores leadership to rebuild and expand the IGC. Since then, the core hired four excellent PhD-level bioinformatics analysts, instituted an internship program, developed an annual genomics/bioinformatics workshop, expanded computational and storage capacity, helped publish dozens of excellent scientific papers, and helped author numerous grant applications. I look forward to working with you on your next groundbreaking project!


  • PhD in Bioinformatics and Systems Biology, UCSD, San Diego, CA
  • BSc in Computer Science and Biochemistry, University of Arizona, Tucson, AZ


  • Computational biologist with a background in genomics, bioinformatics, systems biology, immunology, biochemistry, and computer science.
  • Directs a team of analysts and interns to ensure smooth core operation.
  • Works closely with over 30 labs and 100 scientists on diverse genomics projects.
  • Helps train Salk Scientists through regular workshops, one-on-one training, online website/knowledgebase.
  • Interfaces with other cores, information technology department, and institute leadership to help ensure long-term success of the IGC and Salk science.


  • R01 GM102491-07 (Saghatelian/Shokhirev, PI) 09/01/2017-04/30/2021
  • P30 CA014195-46 (McVicker, PI) 12/01/2018-11/30/2019

Selected Publications

Click here for a full list.
  1. Sanchez KK, Chen GY, Schieber AMP, Redford SE, Shokhirev MN, Leblanc M, Lee YM, Ayres JS. Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen. Cell. 2018;175(1):146-58 e15. Epub 2018/08/14. doi: 10.1016/j.cell.2018.07.016. PubMed PMID: 30100182.
  2. Ma J, Saghatelian A, Shokhirev MN. The influence of transcript assembly on the proteogenomics discovery of microproteins. PLoS One. 2018;13(3):e0194518. Epub 2018/03/28. doi: 10.1371/journal.pone.0194518. PubMed PMID: 29584760; PMCID: PMC5870951.
  3. Kurita M, Araoka T, Hishida T, O'Keefe DD, Takahashi Y, Sakamoto A, Sakurai M, Suzuki K, Wu J, Yamamoto M, Hernandez-Benitez R, Ocampo A, Reddy P, Shokhirev MN, Magistretti P, Nunez Delicado E, Eto H, Harii K, Izpisua Belmonte JC. In vivo reprogramming of wound-resident cells generates skin epithelial tissue. Nature. 2018;561(7722):243-7. Epub 2018/09/07. doi: 10.1038/s41586-018-0477-4. PubMed PMID: 30185909.
  4. Konermann S, Lotfy P, Brideau NJ, Oki J, Shokhirev MN, Hsu PD. Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors. Cell. 2018;173(3):665-76 e14. Epub 2018/03/20. doi: 10.1016/j.cell.2018.02.033. PubMed PMID: 29551272; PMCID: PMC5910255.
  5. Amaral ML, Erikson GA, Shokhirev MN. BART: bioinformatics array research tool. BMC Bioinformatics. 2018;19(1):296. Epub 2018/08/10. doi: 10.1186/s12859-018-2308-x. PubMed PMID: 30089462; PMCID: PMC6083570.
  6. Takahashi Y, Wu J, Suzuki K, Martinez-Redondo P, Li M, Liao HK, Wu MZ, Hernandez-Benitez R, Hishida T, Shokhirev MN, Esteban CR, Sancho-Martinez I, Belmonte JCI. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells. Science. 2017;356(6337):503-8. Epub 2017/05/06. doi: 10.1126/science.aag3260. PubMed PMID: 28473583; PMCID: PMC5654639.
  7. Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JA, Hoffmann A. A multi-scale approach reveals that NF-kappaB cRel enforces a B-cell decision to divide. Mol Syst Biol. 2015;11(1):783. Epub 2015/02/15. doi: 10.15252/msb.20145554. PubMed PMID: 25680807; PMCID: PMC4358656.
  8. Shokhirev MN, Johnson AA. Effects of extrinsic mortality on the evolution of aging: a stochastic modeling approach. PLoS One. 2014;9(1):e86602. Epub 2014/01/28. doi: 10.1371/journal.pone.0086602. PubMed PMID: 24466165; PMCID: PMC3897743.
  9. Shokhirev MN, Hoffmann A. FlowMax: A Computational Tool for Maximum Likelihood Deconvolution of CFSE Time Courses. PLoS One. 2013;8(6):e67620. Epub 2013/07/05. doi: 10.1371/journal.pone.0067620. PubMed PMID: 23826329; PMCID: PMC3694893.
  10. Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, Shin J, Lu S, Byron M, Kalantry S, Mercurio AM, Lawrence JB, Hoffmann A, Bach I. Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell. 2012;149(3):630-41. Epub 2012/05/01. doi: 10.1016/j.cell.2012.02.056. PubMed PMID: 22541433; PMCID: PMC3342660.