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.
Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons.
Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons. Cold Spring Harb Mol Case Stud. 2023 12; 9(4).
PMID: 38050021
Prostate Cancer Patient Stratification by Molecular Signatures in the Veterans Precision Oncology Data Commons.
Prostate Cancer Patient Stratification by Molecular Signatures in the Veterans Precision Oncology Data Commons. Cold Spring Harb Mol Case Stud. 2023 Nov 22.
PMID: 38050021
A deep-learning-based RNA-seq germline variant caller.
A deep-learning-based RNA-seq germline variant caller. Bioinform Adv. 2023; 3(1):vbad062.
PMID: 37416509
Multinucleotide mutations cause false inferences of lineage-specific positive selection.
Multinucleotide mutations cause false inferences of lineage-specific positive selection. Nat Ecol Evol. 2018 08; 2(8):1280-1288.
PMID: 29967485
Correlated evolution of male and female reproductive traits drive a cascading effect of reinforcement in Drosophila yakuba.
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).
PMID: 27440664
Evolutionary history inferred from the de novo assembly of a nonmodel organism, the blue-eyed black lemur.
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.
PMID: 26198179
Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.
Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science. 2015 Jun 05; 348(6239):1139-43.
PMID: 25977371
The genomes of two key bumblebee species with primitive eusocial organization.
The genomes of two key bumblebee species with primitive eusocial organization. Genome Biol. 2015 Apr 24; 16:76.
PMID: 25908251
The ABO blood group is a trans-species polymorphism in primates.
The ABO blood group is a trans-species polymorphism in primates. Proc Natl Acad Sci U S A. 2012 Nov 06; 109(45):18493-8.
PMID: 23091028
Revisiting an old riddle: what determines genetic diversity levels within species?
Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol. 2012; 10(9):e1001388.
PMID: 22984349