Alumni Profiles

Irene Kaplow

  • Program Years: 2010-2014
  • Academic Institution: Stanford University
  • Field of Study: Computational Biology
  • Academic Advisor: Hunter Fraser
  • Practicum(s):
    Lawrence Berkeley National Laboratory (2011)
  • Degree(s):
    Ph.D. Computer Science, Stanford University, 2017
    M.S. Computer Science, Stanford University, 2014
    B.S. Mathematics, Massachusetts Institute of Technology, 2010

Current Status

Publications

Wirthlin ME*, Schmid TA*, Elie JE*, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Zoonomia Consortium, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science, 383(6686): abn3263, 2024.

Kaplow IM*, Lawler AJ*, Schaffer DE*, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Zoonomia Consortium, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science, 380(6643): eabm7993, 2023.

Christmas MJ*, Kaplow IM*, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira L, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morril KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schaffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Zoonomia Consortium, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer M, Teeling E, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science, 380(6643): eabn3943, 2023.

Lawler AJ, Ramamurthy E, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin M, Zhang X, Fox G, Wade K, He J, Ozturk BE, Byrne LC, Stauffer WR, Fish KN, Pfenning AR. Machine learning sequence prioritization for cell type-specific enhancer design. eLife, 11:e69571, 2022.

Kaplow IM*, Banerjee A, Foo CS*. Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2. BMC Genomics, 23: 295, 2022.

Kaplow IM*, Schaffer DE, Wirthlin ME, Lawler AJ, Brown AR, Kleyman M, Pfenning AR*. Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin. BMC Genomics, 23: 291, 2022.

Spix TA, Nanivadekar S, Toong N, Kaplow IM, Isett BR, Goksen Y, Pfenning AR, Gittis AH. Population-Specific Neuromodulation Prolongs Therapeutic Benefits of Deep Brain Stimulation. Science, 374(6564): 201-206, 2021.

Srinivasan C*, Phan BN*, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology. Journal of Neuroscience, 41(43): 9008-9030, 2021.

Zhang X*, Kaplow IM*, Wirthlin M, Park TY, Pfenning AR. HALPER facilitates the identification of regulatory element orthologs across species. Bioinformatics, 36(15): 4339-4340, 2020.

Tycko J*, Wainberg M*, Marinov G*, Ursu O, Hess G, Ego B, Aradhana A, Li A, Truong A, Trevino A, Spees K, Yao D, Kaplow IM, Greenside P, Morgens D, Phanstiel D, Snyder M, Bintu L, Greenleaf W, Kundaje A, Bassik M. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nature Communications, 10(1): 4063, 2019.

Tehranchi A, Hie B, Dacre M, Kaplow I, Pettie K, Combs P, Fraser HB. Fine-mapping cis-regulatory variants in diverse human populations. eLife, 8: e39595, 2019.

Kaplow IM, MacIsaac JL*, Mah SM*, McEwen LM, Kobor MS, Fraser HB. A pooling-based approach to mapping genetic variants associated with DNA methylation. Genome Research, 25(6): 907-917, 2015.

Dadiani M, van Dijk D, Segal B, Field Y, Ben-Artzi G, Raveh-Sadka T, Levo M, Kaplow I, Weinberger A, Segal E. Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Research, 23(6): 966-976, 2013.

Kaplow IM*, Singh R*, Friedman A, Bakal C, Perrimon N, Berger B. RNAiCut: Automated detection of significant genes from functional genomic screens. Nature Methods, 6(7): 476-477, 2009.

Schaub MA, Kaplow IM, Sirota M, Do CB, Butte AJ, Batzoglou S. A classifier-based approach to identify genetic similarities between diseases. Bioinformatics, 25(12): i21-29, 2009.

Awards

Carnegie Mellon Computational Biology Department Lane Postdoctoral Fellowship, awarded June 2017
Stanford Computational, Evolutionary, and Human Genomics Predoctoral Fellowship, awarded April 2015
National Science Foundation Graduate Research Fellowship, awarded April 2010 (deferred)
Stanford Graduate Fellowship, awarded April 2010 (deferred)
Department of Energy Computational Science Graduate Fellowship, awarded April 2010
Anna Pogosyants Undergraduate Research Opportunities Program Award, awarded May 2008
Phi Beta Kappa honors society, initiated May 2010
Order of Omega honors society, initiated May 2009