CV

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Education

• B.E. in Biotechnology, P.E.S. Institute of Technology, Visveswaraya Technological University, 2008
• M.S. in Bioinformatics, Indiana University Bloomington, 2010
• Ph.D. in Informatics (Bioinformatics), Indiana University Bloomington, 2016
  • Dissertation: Computational methods for understanding the impact of amino acid substitutions in protein function
  • Advisor: Predrag Radivojac

Work experience

• 2017-Present: Postdoctoral Scholar
  • Department of Biomedical Informatics and Medical Education, University of Washington
  • Developing data science approaches for genomic and electronic health record data
  • Supervisor: Dr. Sean D. Mooney
• 2012-2013, 2015-2017: Research Assistant
  • School of Informatics and Computing, Indiana University Bloomington
  • Developed methods for the prediction of pathogenicity of genetic variants and their effects on protein structure and function
  • Supervisor: Dr. Predrag Radivojac
• Summer 2011: Research Intern
  • Department of Bioinformatics and Computational Biology, Genentech
  • Integrated ChIP-Seq and microarray data for the identification of transcription factor targets relevant to autoimmune diseases
• Summer 2010: Research Intern
  • Center for Genomics and Bioinformatics, Indiana University Bloomington
  • Refined gene models in the Nasonia vitripennis genome through the integration of RNA-Seq, EST and tiling array data
• 2008-2010: Research Assistant
  • School of Informatics and Computing, Indiana University Bloomington
  • Designed and developed methods and software for the detection, visualization and analysis of conserved and functionally related gene clusters across multiple microbial genomes
  • Supervisors: Dr. Sun Kim and Dr. Yves Brun

Awards and honors

• 2019: Travel Fellowship from CAGI* Workshop: Assessing the Future of Genome Interpretation
• 2019: NIH Pathway to Independence Award (K99/R00)
• 2016: Moore/Sloan and Washington Research Foundation Innovation in Data Science Postdoctoral Fellowship, eScience Institute, University of Washington
• 2014: ISCB Student Council Travel Fellowship
• 2004-2008: Certificate of distinction, P.E.S. Institute of Technology

Service and leadership

• Grant reviewer: Advanced Scientific Computing Research Program, Department of Energy, 2020
• Chair/organizer:
  • CAGI Trainee Salon, CAGI* Workshop: Assessing the Future of Genome Interpretation, 2019
  • Breakout session - To what extent can biomedical and health data be made FAIR?, Moore-Sloan Data Science Environment Annual Summit, 2018
  • Gordon Research Seminar on Human Genetic Variation and Disease, 2018
• Panelist: Future of genome interpretation and vision for CAGI panel, CAGI* Workshop: Assessing the Future of Genome Interpretation, 2019
• Program committee member: International Conference on Intelligent Systems for Molecular Biology, 2018
• Reviewer:
  • AMIA Annual Symposium, 2020
  • BioData Mining
  • Bioinformatics
  • BMC Bioinformatics
  • Genetics and Molecular Biology
  • Human Mutation
  • IEEE/ACM Transactions on Computational Biology and Bioinformatics
  • IEEE Journal of Biomedical and Health Informatics
  • International Journal of Epidemiology
  • Intrinsically Disordered Proteins
  • Nature Computational Science
  • Nucleic Acids Research
  • Pacific Symposium on Biocomputing (specific sessions)
    • 2019: Precision medicine: improving health through high-resolution analysis of personal data
    • 2017: Computational approaches to understanding the evolution of molecular function
  • Patterns
  • PeerJ
  • PLOS Computational Biology
  • PLOS Genetics
  • PLOS ONE
  • Proceedings of the National Academy of Sciences
  • SSM - Population Health
  • Translational Research
• Member:
  • Academic Data Science Alliance (ADSA)
  • American Medical Informatics Association (AMIA)
  • American Society of Human Genetics (ASHG)
  • International Society for Computational Biology (ISCB)

Teaching

Teaching Assistant, Introduction to Bioinformatics

Teaching Assistant, Information Representation

Teaching Assistant, Machine Learning

Teaching Assistant, Data Visualization

Teaching Assistant, Human-centered Research Methods

Teaching Assistant, Data Visualization

Instructor, The Carpentries

Publications

* Equal contribution     ^ Co-corresponding author

Piloting a model-to-data approach to enable predictive analytics in healthcare through patient mortality prediction

*Bergquist T, *Yan Y, Schaffter T, Yu T, Pejaver V, Hammarlund N, Prosser J, Guinney J, Mooney SD (2020) Piloting a model-to-data approach to enable predictive analytics in healthcare through patient mortality prediction. J. Am. Med. Inform. Assoc. 27(9) 1393-1400.

A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results

Joshi R, Pejaver V, Hammarlund N, Sung H, Lee SK, Lee H, Scott G, Gombar S, Shah N, Shen S, Mooney SD, Pinsky B (2020) A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results. J. Clin. Virol. 129 104502.

A survey-based analysis of the academic job market

Fernandes JD, Sarabipour S, Smith CT, Niemi NM, Jadavji NM, Kozik AJ, Holehouse AS, Pejaver V, Symmons O, Filho AW, Haage A (2020) A survey-based analysis of the academic job market. eLife 9(e54097) .

Evaluation of the secondary use of electronic health records to detect seasonal, holiday-related, and rare events related to traumatic injury and poisoning

Bergquist T, Pejaver V, Hammarlund N, Mooney SD, Mooney SJ (2020) Evaluation of the secondary use of electronic health records to detect seasonal, holiday-related, and rare events related to traumatic injury and poisoning. BMC Public Health 20(1) 46.

Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, ..., Neuhausen S, Ziv E, Pal LR, Andreoletti G, Brenner S, Kann MG (2019) Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Hum. Mutat. 40(9) 1612-1622.

Assessment of methods for predicting the effects of PTEN and TPMT protein variants

^Pejaver V, Babbi G, Casadio R, Folkman L, Katsonis P, Kundu K, Lichtarge O, Martelli PL, Miller M, Moult J, Pal LR, Savojardo C, Yin Y, Zhou Y, Radivojac P, Bromberg Y (2019) Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Hum. Mutat. 40(9) 1495-1506.

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

Cline M, Babbi G, Bonache S, Cao Y, Casadio R, Cruz X, ..., Pejaver V, ..., Sun Y, Topper S, Parsons MT, Spurdle AB, Goldgar DE, ENIGMA Consortium (2019) Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Hum. Mutat. 40(9) 1546-1556.

Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016

Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, ..., Pejaver V, Wang M, Wei L, Moult J, Yu GK, Brenner SE, LeBowitz JH (2019) Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016. Hum. Mutat. 40(9) 1519-1529.

The comparative genomics and complex population history of Papio baboons

Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä, Athanasiadis G, ..., Zinner D, Roos C, Jolly CJ, Gibbs RA, Worley KC, Consortium BG (2019) The comparative genomics and complex population history of Papio baboons. Sci. Adv. 5(1) eaau6947.

The sequencing and interpretation of the genome obtained from a Serbian individual

*Ismail WA, *Pagel KA, Pejaver V, Zhang SV, Casasa S, Mort M, Cooper DN, Hahn MW, Radivojac P (2018) The sequencing and interpretation of the genome obtained from a Serbian individual. PLoS One 13(12) e0208901.

Target site specificity and in vivo complexity of the mammalian arginylome

*Wang J, *Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A (2018) Target site specificity and in vivo complexity of the mammalian arginylome. Sci. Rep. 8(1) 16177.

Big data in public health: terminology, machine learning, and privacy

Mooney SJ, Pejaver V (2018) Big data in public health: terminology, machine learning, and privacy. Annu. Rev. Public Health 39 95-112.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Glusman G, Rose PW, Prlic A, Dougherty J, Duarte JM, Hoffman AS, ..., Pejaver V, ..., Reynolds S, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW (2017) Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med. 9(113) .

Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges

Pejaver V, Mooney SD, Radivojac P (2017) Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges. Hum. Mutat. 38(9) 1092-1108.

Working toward precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, ..., Pejaver V, ..., Altman R, Klein TE, Hoskins RA, Repo S, Brenner SE, Morgan AA (2017) Working toward precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Hum. Mutat. 38(9) 1182-1192.

Physicochemical sequence characteristics that influence S-palmitoylation propensity

Reddy KD, Malipeddi J, DeForte S, Pejaver V, Radivojac P, Uversky VN, Deschenes RJ (2017) Physicochemical sequence characteristics that influence S-palmitoylation propensity. J. Biomol. Struct. Dyn. 35(11) 2337-2350.

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants

Pagel KA, Pejaver V, Lin GN, Nam H, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P (2017) When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics 33(14) i389-i398.

MutPred2: inferring the molecular and phenotypic impact of amino acid variants

Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam H, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P (2017) MutPred2: inferring the molecular and phenotypic impact of amino acid variants. bioRxiv 134981 .

REVEL: an ensemble score for predicting the pathogenicity of rare non synonymous variants

*Ioannidis NM, *Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, ..., Ostrander E, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W (2016) REVEL: an ensemble score for predicting the pathogenicity of rare non synonymous variants. Am. J. Hum. Genet. 99(4) 877-885.

The loss and gain of functional amino acid residues is a frequent mechanism causing human inherited disease

Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P (2016) The loss and gain of functional amino acid residues is a frequent mechanism causing human inherited disease. PLoS Comput. Biol. 12(8) e10005091.

Draft genome sequence of Caedibacter varicaedens, a Kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia

Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR (2015) Draft genome sequence of Caedibacter varicaedens, a Kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia. Genome Announc. 3(6) e01310-15.

Position of proline mediates the reactivity of S-palmitoylation

Khanal N, Pejaver V, Li Z, Radivojac P, Clemmer DE, Mukhopadhyay S (2015) Position of proline mediates the reactivity of S-palmitoylation. ACS Chem. Biol. 10(11) 2529-2536.

Intrinsic size parameters for palmitoylated and carboxyamidomethylated peptides

Li Z, Dilger JM, Pejaver V, Smiley D, Arnold RJ, Mooney SD, Mukhopadhyay S, Radivojac P, Clemmer DE (2014) Intrinsic size parameters for palmitoylated and carboxyamidomethylated peptides. Int. J. Mass Spectrom. 368 6-14.

The structural and functional signatures of proteins that undergo multiple events of post-translational modification

Pejaver V, Hsu W, Xin F, Dunker AK, Uversky VN, Radivojac P (2014) The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci. 23(8) 1077-1093.

GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis

Pejaver VR, An J, Rhee S, Bhan A, Choi J, Liu B, Lee H, Brown PJ, Kysela D, Brun YV, Kim S (2012) GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis. Bioinformatics 28(11) 1527-1529.

Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters

Pejaver VR, Kim S (2011) Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters. BMC Genomics 12(Suppl 2 - IEEE International Conference on Bioinformatics and Biomedicine 2010) S2.

Gene cluster prediction and its application to genome annotation

Pejaver VR, Lee H, Kim S (2011) Gene cluster prediction and its application to genome annotation. Protein function prediction for omics era 35-54.

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, ..., Pejaver V, ..., Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA (2010) Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science 327(5963) 343-348.

Talks

Tutorial on GeneclusterViz for visualization of microbial genomes

2011

Tutorial at the Center for Genomics and Bioinformatics Workshop on Microbial Analysis, Indiana University, Bloomington, Indiana

MutPred2: predicting the pathogenicity and molecular consequences of missense variants

2014

Talk at ISCB Student Council Symposium, Boston, Massachussetts

Predicting the in vitro functional effects of natural and synthetic missense mutations

2017

Talk at QBI/Convergence Zone Symposium, San Francisco, California

Probabilistic prediction of the different notions of missense variant impact

2017

Talk at Human Genome Variation Society Meeting, Orlando, Florida

Predicting the molecular mechanisms of disease-associated amino acid substitutions

2017

Talk at Moore-Sloan Data Science Environment Summit, New Orleans, Louisiana

Reproducibility in bioinformatics

2018

Guest lecture at the ITHS KL2-TL1 Seminar Series, University of Washington, Seattle, Washington

A performance-based approach to establish standards for missense variant impact prediction tools

2019

Talk at CAGI* Workshop: Assessing the Future of Genome Interpretation, San Francisco, California

Machine learning on secondary data for rare genetic diseases

2020

Talk at the Department of Biostatistics and Informatics, University of Colorado Anschutz, Aurora, Colorado

Machine learning on secondary data for the interpretation of genetic variants

2020

Talk at the Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, New York

Reproducibility in bioinformatics

2020

Guest lecture at the ITHS KL2-TL1 Seminar Series, University of Washington, Seattle, Washington

Machine learning on secondary data for rare genetic diseases

2020

Talk at the Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York