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portfolio
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publications
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
Published in Science, 2010
Recommended citation: 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.
Gene cluster prediction and its application to genome annotation
Published in Protein function prediction for omics era, 2011
Recommended citation: Pejaver VR, Lee H, Kim S (2011) Gene cluster prediction and its application to genome annotation. Protein function prediction for omics era 35-54.
Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters
Published in BMC Genomics, 2011
Recommended citation: 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.
GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis
Published in Bioinformatics, 2012
Recommended citation: 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.
The structural and functional signatures of proteins that undergo multiple events of post-translational modification
Published in Protein Sci., 2014
Recommended citation: 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.
Intrinsic size parameters for palmitoylated and carboxyamidomethylated peptides
Published in Int. J. Mass Spectrom., 2014
Recommended citation: 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.
Position of proline mediates the reactivity of S-palmitoylation
Published in ACS Chem. Biol., 2015
Recommended citation: 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.
Draft genome sequence of Caedibacter varicaedens, a Kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia
Published in Genome Announc., 2015
Recommended citation: 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.
The loss and gain of functional amino acid residues is a frequent mechanism causing human inherited disease
Published in PLoS Comput. Biol., 2016
Recommended citation: 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.
REVEL: an ensemble score for predicting the pathogenicity of rare non synonymous variants
Published in Am. J. Hum. Genet., 2016
Recommended citation: *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.
MutPred2: inferring the molecular and phenotypic impact of amino acid variants
Published in bioRxiv, 2017
Recommended citation: 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 .
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants
Published in Bioinformatics, 2017
Recommended citation: 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.
Physicochemical sequence characteristics that influence S-palmitoylation propensity
Published in J. Biomol. Struct. Dyn., 2017
Recommended citation: 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.
Working toward precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges
Published in Hum. Mutat., 2017
Recommended citation: 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.
Missense variant pathogenicity predictors generalize well across a range of function-specific prediction challenges
Published in Hum. Mutat., 2017
Recommended citation: 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.
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
Published in Genome Med., 2017
Recommended citation: 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) .
Big data in public health: terminology, machine learning, and privacy
Published in Annu. Rev. Public Health, 2018
Recommended citation: Mooney SJ, Pejaver V (2018) Big data in public health: terminology, machine learning, and privacy. Annu. Rev. Public Health 39 95-112.
Target site specificity and in vivo complexity of the mammalian arginylome
Published in Sci. Rep., 2018
Recommended citation: *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.
The sequencing and interpretation of the genome obtained from a Serbian individual
Published in PLoS One, 2018
Recommended citation: *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.
The comparative genomics and complex population history of Papio baboons
Published in Sci. Adv., 2019
Recommended citation: 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.
Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016
Published in Hum. Mutat., 2019
Recommended citation: 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.
Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants
Published in Hum. Mutat., 2019
Recommended citation: 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 methods for predicting the effects of PTEN and TPMT protein variants
Published in Hum. Mutat., 2019
Recommended citation: ^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.
Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer
Published in Hum. Mutat., 2019
Recommended citation: 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.
Evaluation of the secondary use of electronic health records to detect seasonal, holiday-related, and rare events related to traumatic injury and poisoning
Published in BMC Public Health, 2020
Recommended citation: 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.
A survey-based analysis of the academic job market
Published in eLife, 2020
Recommended citation: 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) .
A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results
Published in J. Clin. Virol., 2020
Recommended citation: 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.
Piloting a model-to-data approach to enable predictive analytics in healthcare through patient mortality prediction
Published in J. Am. Med. Inform. Assoc., 2020
Recommended citation: *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.
talks
Tutorial on GeneclusterViz for visualization of microbial genomes
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MutPred2: predicting the pathogenicity and molecular consequences of missense variants
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Predicting the in vitro functional effects of natural and synthetic missense mutations
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Probabilistic prediction of the different notions of missense variant impact
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Predicting the molecular mechanisms of disease-associated amino acid substitutions
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Reproducibility in bioinformatics
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A performance-based approach to establish standards for missense variant impact prediction tools
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Machine learning on secondary data for rare genetic diseases
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Machine learning on secondary data for the interpretation of genetic variants
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Reproducibility in bioinformatics
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Machine learning on secondary data for rare genetic diseases
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teaching
Teaching Assistant, Introduction to Bioinformatics
Graduate course, School of Informatics and Computing, Indiana University, 2010
Designed and taught lab sessions, graded assignments and held office hours on topics related to biological sequence analysis and Python programming.
Teaching Assistant, Information Representation
Undergraduate course, School of Informatics and Computing, Indiana University, 2011
Co-designed lab sessions, assignments and exams, taught lab sessions and held office hours. The course introduced students to the different ways in which computers accept and interpret information.
Teaching Assistant, Machine Learning
Graduate course, School of Informatics and Computing, Indiana University, 2011
Delivered guest lectures, graded assignments and held office hours on topics in machine learning including linear regression, logistic regression, neural networks, and ensemble methods.
Teaching Assistant, Data Visualization
Undergraduate and graduate course, School of Informatics and Computing, Indiana University, 2013
Designed and taught lab sessions on D3.js, delivered guest lectures on the principles of visualization, and graded assignments.
Teaching Assistant, Human-centered Research Methods
Graduate course, School of Informatics and Computing, Indiana University, 2014
Led class discussions and graded assignments on qualitative methods for informatics research.
Teaching Assistant, Data Visualization
Undergraduate and graduate course, School of Informatics and Computing, Indiana University, 2014
Designed and taught lab sessions on D3.js, delivered guest lectures on the principles of visualization, and graded assignments.
Instructor, The Carpentries
Workshop, The eScience Institute, University of Washington, 2018
Taught session on the Unix shell as a certified Carpentries Instructor.