Yana Bromberg - Publications

Affiliations: 
Rutgers University, New Brunswick, New Brunswick, NJ, United States 
Area:
Bioinformatics, Metagenomics, Genetics, Molecular Biology

64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Zhu C, Miller M, Lusskin N, Mahlich Y, Wang Y, Zeng Z, Bromberg Y. Fingerprinting cities: differentiating subway microbiome functionality. Biology Direct. 14: 19. PMID 31666099 DOI: 10.1186/s13062-019-0252-y  1
2019 Zeng Z, Bromberg Y. Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives. Frontiers in Genetics. 10: 914. PMID 31649718 DOI: 10.3389/fgene.2019.00914  0.4
2019 Miller M, Vitale D, Kahn PC, Rost B, Bromberg Y. funtrp: identifying protein positions for variation driven functional tuning. Nucleic Acids Research. PMID 31584091 DOI: 10.1093/nar/gkz818  1
2019 Wang Y, Miller M, Astrakhan Y, Petersen BS, Schreiber S, Franke A, Bromberg Y. Identifying Crohn's disease signal from variome analysis. Genome Medicine. 11: 59. PMID 31564248 DOI: 10.1186/s13073-019-0670-6  1
2019 Bromberg Y, El-Mabrouk N, Radivojac P. ISMB/ECCB 2019 Proceedings. Bioinformatics (Oxford, England). 35: i1-i2. PMID 31510708 DOI: 10.1093/bioinformatics/btz439  1
2019 Clark WT, Kasak L, Bakolitsa C, Hu Z, Andreoletti G, Babbi G, Bromberg Y, Casadio R, Dunbrack R, Folkman L, Ford CT, Jones D, Katsonis P, Kundu K, Lichtarge O, et al. Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016. Human Mutation. PMID 31342580 DOI: 10.1002/humu.23875  1
2019 Bromberg Y, Capriotti E, Carter H. VarI-COSI 2018: a forum for research advances in variant interpretation and diagnostics. Bmc Genomics. 20: 550. PMID 31307380 DOI: 10.1186/s12864-019-5862-3  1
2019 Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, et al. Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants. Human Mutation. PMID 31301157 DOI: 10.1002/humu.23868  1
2019 Miller M, Wang Y, Bromberg Y. What went wrong with variant effect predictor performance for the PCM1 challenge. Human Mutation. PMID 31268618 DOI: 10.1002/humu.23832  1
2019 Monzon AM, Carraro M, Chiricosta L, Reggiani F, Han J, Ozturk K, Wang Y, Miller M, Bromberg Y, Capriotti E, Savojardo C, Babbi G, Martelli PL, Casadio R, Katsonis P, et al. Performance of computational methods for the evaluation of Pericentriolar Material 1 missense variants in CAGI-5. Human Mutation. PMID 31260570 DOI: 10.1002/humu.23856  1
2019 Voskanian A, Katsonis P, Lichtarge O, Pejaver V, Radivojac P, Mooney SD, Capriotti E, Bromberg Y, Wang Y, Miller M, Martelli PL, Savojardo C, Babbi G, Casadio R, Cao Y, et al. Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Human Mutation. PMID 31241222 DOI: 10.1002/humu.23849  1
2019 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, et al. Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Human Mutation. PMID 31184403 DOI: 10.1002/humu.23838  1
2019 Wang Y, Bromberg Y. Identifying mutation-driven changes in gene functionality that lead to venous thromboembolism. Human Mutation. PMID 31144782 DOI: 10.1002/humu.23824  0.4
2019 McInnes G, Daneshjou R, Katsonis P, Lichtarge O, Srinivasan RG, Rana S, Radivojac P, Mooney SD, Pagel KA, Stamboulian M, Jiang Y, Capriotti E, Wang Y, Bromberg Y, Bovo S, et al. Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation. PMID 31140652 DOI: 10.1002/humu.23825  1
2018 Bromberg Y, Radivojac P. ISMB 2018 proceedings. Bioinformatics (Oxford, England). 34: i2-i3. PMID 29950022 DOI: 10.1093/bioinformatics/bty413  1
2018 Mahlich Y, Steinegger M, Rost B, Bromberg Y. HFSP: high speed homology-driven function annotation of proteins. Bioinformatics (Oxford, England). 34: i304-i312. PMID 29950013 DOI: 10.1093/bioinformatics/bty262  1
2018 McDermott JE, Partridge M, Bromberg Y. Ten simple rules for drawing scientific comics. Plos Computational Biology. 14: e1005845. PMID 29300733 DOI: 10.1371/journal.pcbi.1005845  0.04
2017 Beerenwinkel N, Bromberg Y. ISMB/ECCB 2017 proceedings. Bioinformatics (Oxford, England). 33: i1-i2. PMID 29547916 DOI: 10.1093/bioinformatics/btx321  0.01
2017 Zhu C, Miller M, Marpaka S, Vaysberg P, Rühlemann MC, Wu G, Heinsen FA, Tempel M, Zhao L, Lieb W, Franke A, Bromberg Y. Functional sequencing read annotation for high precision microbiome analysis. Nucleic Acids Research. PMID 29194524 DOI: 10.1093/nar/gkx1209  1
2017 Zhu C, Mahlich Y, Miller M, Bromberg Y. fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks. Nucleic Acids Research. PMID 29194481 DOI: 10.1093/nar/gkx1212  1
2017 Daneshjou R, Wang Y, Bromberg Y, Bovo S, Martelli PL, Babbi G, Lena PD, Casadio R, Edwards M, Gifford D, Jones DT, Sundaram L, Bhat R, Li X, Pal LR, et al. Working towards precision medicine: predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation. PMID 28634997 DOI: 10.1002/humu.23280  1
2017 Liu J, Lopez N, Ahn YB, Goldberg T, Bromberg Y, Kerkhof LJ, Häggblom MM. Novel Reductive Dehalogenases from the Marine Sponge Associated Bacterium Desulfoluna spongiiphila. Environmental Microbiology Reports. PMID 28618195 DOI: 10.1111/1758-2229.12556  1
2017 Miller M, Zhu C, Bromberg Y. clubber: removing the bioinformatics bottleneck in big data analyses. Journal of Integrative Bioinformatics. PMID 28609295 DOI: 10.1515/jib-2017-0020  1
2017 Mahlich Y, Reeb J, Hecht M, Schelling M, De Beer TAP, Bromberg Y, Rost B. Common sequence variants affect molecular function more than rare variants? Scientific Reports. 7: 1608. PMID 28487536 DOI: 10.1038/s41598-017-01054-2  1
2017 Carraro M, Minervini G, Giollo M, Bromberg Y, Capriotti E, Casadio R, Dunbrack R, Elefanti L, Fariselli P, Ferrari C, Gough J, Katsonis P, Leonardi E, Lichtarge O, Menin C, et al. Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Human Mutation. PMID 28440912 DOI: 10.1002/humu.23235  1
2016 Bromberg Y, Hahn MW, Radivojac P. COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 1-2. PMID 27896956  1
2016 Goldberg T, Rost B, Bromberg Y. Computational prediction shines light on type III secretion origins. Scientific Reports. 6: 34516. PMID 27713481 DOI: 10.1038/srep34516  1
2016 Reeb J, Hecht M, Mahlich Y, Bromberg Y, Rost B. Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. Plos Computational Biology. 12: e1005047. PMID 27536940 DOI: 10.1371/journal.pcbi.1005047  1
2016 Rost B, Radivojac P, Bromberg Y. Protein function in precision medicine: deep understanding with machine learning. Febs Letters. PMID 27423136 DOI: 10.1002/1873-3468.12307  1
2016 Bromberg Y, Capriotti E, Carter H. VarI-SIG 2015: methods for personalized medicine - the role of variant interpretation in research and diagnostics. Bmc Genomics. 17: 425. PMID 27357578 DOI: 10.1186/s12864-016-2721-3  1
2016 Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 21: 557-67. PMID 26776218  0.01
2016 Bruse S, Moreau M, Bromberg Y, Jang JH, Wang N, Ha H, Picchi M, Lin Y, Langley RJ, Qualls C, Klensney-Tait J, Zabner J, Leng S, Mao J, Belinsky SA, et al. Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility. Human Genomics. 10: 1. PMID 26744305 DOI: 10.1186/s40246-015-0058-7  1
2015 Zhu C, Delmont TO, Vogel TM, Bromberg Y. Functional Basis of Microorganism Classification. Plos Computational Biology. 11: e1004472. PMID 26317871 DOI: 10.1371/journal.pcbi.1004472  1
2015 Hecht M, Bromberg Y, Rost B. Better prediction of functional effects for sequence variants. Bmc Genomics. 16: S1. PMID 26110438 DOI: 10.1186/1471-2164-16-S8-S1  1
2015 Bromberg Y, Capriotti E. VarI-SIG 2014--From SNPs to variants: interpreting different types of genetic variants. Bmc Genomics. 16: I1. PMID 26110281 DOI: 10.1186/1471-2164-16-S8-I1  1
2014 Bromberg Y, Capriotti E. SNP-SIG 2013: from coding to non-coding--new approaches for genomic variant interpretation. Bmc Genomics. 15: S1. PMID 25056427 DOI: 10.1186/1471-2164-15-S4-S1  1
2014 Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, et al. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Research. 42: W337-43. PMID 24799431 DOI: 10.1093/nar/gku366  1
2014 Harel A, Bromberg Y, Falkowski PG, Bhattacharya D. Evolutionary history of redox metal-binding domains across the tree of life. Proceedings of the National Academy of Sciences of the United States of America. 111: 7042-7. PMID 24778258 DOI: 10.1073/pnas.1403676111  1
2014 Senn S, Nanda V, Falkowski P, Bromberg Y. Function-based assessment of structural similarity measurements using metal co-factor orientation. Proteins. 82: 648-56. PMID 24127252 DOI: 10.1002/prot.24442  1
2013 de Ridder J, Bromberg Y, Michaut M, Satagopam VP, Corpas M, MacIntyre G, Alexandrov T. The young PI buzz: learning from the organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013. Plos Computational Biology. 9: e1003350. PMID 24244148 DOI: 10.1371/journal.pcbi.1003350  1
2013 Ren X, Graham JC, Jing L, Mikheev AM, Gao Y, Lew JP, Xie H, Kim AS, Shang X, Friedman C, Vail G, Fang MZ, Bromberg Y, Zarbl H. Mapping of Mcs30, a new mammary carcinoma susceptibility quantitative trait locus (QTL30) on rat chromosome 12: identification of fry as a candidate Mcs gene. Plos One. 8: e70930. PMID 24023717 DOI: 10.1371/journal.pone.0070930  1
2013 Bromberg Y, Kahn PC, Rost B. Neutral and weakly nonneutral sequence variants may define individuality. Proceedings of the National Academy of Sciences of the United States of America. 110: 14255-60. PMID 23940345 DOI: 10.1073/pnas.1216613110  1
2013 Hecht M, Bromberg Y, Rost B. News from the protein mutability landscape. Journal of Molecular Biology. 425: 3937-48. PMID 23896297 DOI: 10.1016/j.jmb.2013.07.028  1
2013 Capriotti E, Altman RB, Bromberg Y. Collective judgment predicts disease-associated single nucleotide variants. Bmc Genomics. 14: S2. PMID 23819846 DOI: 10.1186/1471-2164-14-S3-S2  1
2013 Bromberg Y, Capriotti E. Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations. Bmc Genomics. 14: S1. PMID 23819751 DOI: 10.1186/1471-2164-14-S3-S1  1
2013 Bromberg Y. Chapter 15: disease gene prioritization. Plos Computational Biology. 9: e1002902. PMID 23633938 DOI: 10.1371/journal.pcbi.1002902  0.01
2013 Ellinghaus D, Zhang H, Zeissig S, Lipinski S, Till A, Jiang T, Stade B, Bromberg Y, Ellinghaus E, Keller A, Rivas MA, Skieceviciene J, Doncheva NT, Liu X, Liu Q, et al. Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. Gastroenterology. 145: 339-47. PMID 23624108 DOI: 10.1053/j.gastro.2013.04.040  1
2012 Schaefer C, Bromberg Y, Achten D, Rost B. Disease-related mutations predicted to impact protein function. Bmc Genomics. 13: S11. PMID 22759649 DOI: 10.1186/1471-2164-13-S4-S11  1
2012 Bromberg Y, Capriotti E. SNP-SIG Meeting 2011: identification and annotation of SNPs in the context of structure, function, and disease. Bmc Genomics. 13: S1. PMID 22759647 DOI: 10.1186/1471-2164-13-S4-S1  1
2012 Rawat SR, Männistö MK, Bromberg Y, Häggblom MM. Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils. Fems Microbiology Ecology. 82: 341-55. PMID 22486608 DOI: 10.1111/j.1574-6941.2012.01381.x  1
2012 Harel A, Falkowski P, Bromberg Y. TrAnsFuSE refines the search for protein function: oxidoreductases. Integrative Biology : Quantitative Biosciences From Nano to Macro. 4: 765-77. PMID 22481248 DOI: 10.1039/c2ib00131d  1
2012 Capriotti E, Nehrt NL, Kann MG, Bromberg Y. Bioinformatics for personal genome interpretation. Briefings in Bioinformatics. 13: 495-512. PMID 22247263 DOI: 10.1093/bib/bbr070  1
2012 Schaefer C, Meier A, Rost B, Bromberg Y. SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics (Oxford, England). 28: 601-2. PMID 22210871 DOI: 10.1093/bioinformatics/btr705  1
2010 Wainreb G, Ashkenazy H, Bromberg Y, Starovolsky-Shitrit A, Haliloglu T, Ruppin E, Avraham KB, Rost B, Ben-Tal N. MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Research. 38: W523-8. PMID 20542913 DOI: 10.1093/nar/gkq528  1
2010 Zaghloul NA, Liu Y, Gerdes JM, Gascue C, Oh EC, Leitch CC, Bromberg Y, Binkley J, Leibel RL, Sidow A, Badano JL, Katsanis N. Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet-Biedl syndrome. Proceedings of the National Academy of Sciences of the United States of America. 107: 10602-7. PMID 20498079 DOI: 10.1073/pnas.1000219107  1
2010 Sester M, Koebernick K, Owen D, Ao M, Bromberg Y, May E, Stock E, Andrews L, Groh V, Spies T, Steinle A, Menz B, Burgert HG. Conserved amino acids within the adenovirus 2 E3/19K protein differentially affect downregulation of MHC class I and MICA/B proteins. Journal of Immunology (Baltimore, Md. : 1950). 184: 255-67. PMID 19949079 DOI: 10.4049/jimmunol.0902343  0.01
2009 Bromberg Y, Rost B. Correlating protein function and stability through the analysis of single amino acid substitutions. Bmc Bioinformatics. 10: S8. PMID 19758472 DOI: 10.1186/1471-2105-10-S8-S8  1
2009 Bromberg Y, Overton J, Vaisse C, Leibel RL, Rost B. In silico mutagenesis: a case study of the melanocortin 4 receptor. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. 23: 3059-69. PMID 19417090 DOI: 10.1096/fj.08-127530  1
2009 Bromberg Y, Yachdav G, Ofran Y, Schneider R, Rost B. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. Current Opinion in Drug Discovery & Development. 12: 408-19. PMID 19396742  1
2009 Calton MA, Ersoy BA, Zhang S, Kane JP, Malloy MJ, Pullinger CR, Bromberg Y, Pennacchio LA, Dent R, McPherson R, Ahituv N, Vaisse C. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Human Molecular Genetics. 18: 1140-7. PMID 19091795 DOI: 10.1093/hmg/ddn431  1
2008 Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics (Oxford, England). 24: 2397-8. PMID 18757876 DOI: 10.1093/bioinformatics/btn435  1
2008 Bromberg Y, Rost B. Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics (Oxford, England). 24: i207-12. PMID 18689826 DOI: 10.1093/bioinformatics/btn268  1
2008 Dokmanovic-Chouinard M, Chung WK, Chevre JC, Watson E, Yonan J, Wiegand B, Bromberg Y, Wakae N, Wright CV, Overton J, Ghosh S, Sathe GM, Ammala CE, Brown KK, Ito R, et al. Positional cloning of "Lisch-Like", a candidate modifier of susceptibility to type 2 diabetes in mice. Plos Genetics. 4: e1000137. PMID 18654634 DOI: 10.1371/journal.pgen.1000137  1
2007 Bromberg Y, Rost B. SNAP: Predict effect of non-synonymous polymorphisms on function Nucleic Acids Research. 35: 3823-3835. PMID 17526529 DOI: 10.1093/nar/gkm238  1
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