Background

Dr. Venkat has fourteen years of computational experience in genomics and bioinformatics for a wide range of applications, from evolutionary genetics to oncology. She obtained her Ph.D. in Human Genetics from the University of Chicago in 2018, and subsequently worked at Tempus labs, a precision oncology company in Chicago where she was the Associate Director of Bioinformatics. At Tempus, she managed a team of bioinformatics scientists and worked on developing clinical bioinformatics pipelines and algorithms for copy number detection, tumor purity and tumor ploidy estimation, identification of exon level deletion and duplication events, identifying the sets of patients that will respond to PARP inhibitor treatment, and identification of germline variants from tumor RNA using Deep Learning. She currently serves two roles at the University of Chicago, one as the Assistant Professor of Medicine, and two as the Directory of Clinical Informatics at the Center for Translational Data Science (CTDS). In these roles, she is continuing to work on her research interests in oncology, specifically i) developing bioinformatics and machine learning methods for improving cancer diagnosis and prognosis, and ii) building data meshes, systems that researchers can use to perform federated search and learning. She is Co-PI for the Biomedical Research Hub, a leading example of a data mesh for biomedical research.

Research Interests

• Multiomic integration and AI for cancer research

• Immunology and AI for disease

• Bioinformatics and computational genomics 

• Cancer biology and evolution

• Viruses and evolution

• Reproducibility of research

Education

• B.S. - Life Sciences and Biochemistry - St.Xavier’s College, Mumbai, India

• M.S. - Biochemistry - K.E.M. Hospital, Mumbai, India

• M.S. - Bioinformatics - University of Illinois, Champaign-Urbana

• Ph.D. -  Human Genetics - University of Chicago

Positions

• 2008-2008 Cancer Internship, Advanced Center for Treatment, Research and Education in Cancer

• 2011-2012 Bioinformatics Programmer, Howard Hughes Medical institute

• 2018-2020 Bioinformatics Scientist, Tempus

• 2020-2021 Senior Bioinformatics Scientist, Tempus

• 2021-2022 Associate Director of Bioinformatics, Tempus

• 2022-present Assistant Professor of Medicine & Director of Clinical Informatics, Center for Translational Data Science, University of Chicago

Honors

• 2022 Integrated machine-learning framework to estimate homologous recombination deficiency, US PTO 10975445

• 2016 Doctoral Dissertation Improvement Grant, National Science Foundation

Other Sites

• http://med-faculty.bsd.uchicago.edu/Default/Details/17975

PUblications

• Daniel E. Cook, Aarti Venkat, Dennis Yelizarov, Yannick Pouliot, Pi-Chuan Chang,  Andrew Carroll, Francisco M. De La Vega. A Deep-learning based RNA-seq Germline Variant Caller. bioRxiv. 2022 Oct 20 doi: https://doi.org/10.1101/2022.10.16.512451

• Venkat A, Hahn MW, Thornton JW. Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nat Ecol Evol. 2018 Aug;2(8):1280-1288. PubMed Central PMCID:PMC6093625

• Ségurel L, Thompson EE, Flutre T, Lovstad J, Venkat A, Margulis SW, Moyse J, Ross S, Gamble K, Sella G, Ober C, Przeworski M. The ABO blood group is a trans-species polymorphism in primates. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18493-8. PubMed Central PMCID: PMC3494955.

• Leffler EM, Bullaughey K, Matute DR, Meyer WK, Ségurel L, Venkat A, Andolfatto P, Przeworski M. Revisiting an old riddle: what determines genetic diversity levels within species?. PLoS Biol. 2012;10(9):e1001388. PubMed Central PMCID: PMC3439417.

• Auton A, Fledel-Alon A, Pfeifer S, Venn O, Ségurel L, Street T, Leffler EM, Bowden R, Aneas I,Broxholme J, Humburg P, Iqbal Z, Lunter G, Maller J, Hernandez RD, Melton C, Venkat A, Nobrega MA, Bontrop R, Myers S, Donnelly P, Przeworski M, McVean G. A fine-scale chimpanzee genetic map from population sequencing. Science. 2012 Apr 13;336(6078):193-8. PubMed Central PMCID: PMC3532813.

• Comeault AA, Venkat A, Matute DR. Correlated evolution of male and female reproductive traits drive a cascading effect of reinforcement in Drosophila yakuba. Proc Biol Sci. 2016 Jul 27;283(1835) PubMed Central PMCID: PMC4971202.

• Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science. 2015 Jun 5;348(6239):1139-43. PubMed Central PMCID: PMC5471836.

• Woodard SH, Fischman BJ, Venkat A, Hudson ME, Varala K, Cameron SA, Clark AG, Robinson GE. Genes involved in convergent evolution of eusociality in bees. Proc Natl Acad Sci U S A. 2011 May 3;108(18):7472-7. PubMed Central PMCID: PMC3088614.

• Meyer WK, Venkat A, Kermany AR, van de Geijn B, Zhang S, Przeworski M. Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur. Mol Ecol. 2015 Sep;24(17):4392-405. PubMed Central PMCID: PMC4557055.

• Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol. 2015 Apr 24;16:76. PubMed Central PMCID: PMC4414376.