| Year |
Citation |
Score |
| 2025 |
Prabakaran R, Bromberg Y. Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools. Bioinformatics (Oxford, England). 41. PMID 39854283 DOI: 10.1093/bioinformatics/btaf035 |
0.377 |
|
| 2024 |
Chung HC, Friedberg I, Bromberg Y. Assembling bacterial puzzles: piecing together functions into microbial pathways. Nar Genomics and Bioinformatics. 6: lqae109. PMID 39184378 DOI: 10.1093/nargab/lqae109 |
0.357 |
|
| 2024 |
Bromberg Y, Prabakaran R, Kabir A, Shehu A. Variant Effect Prediction in the Age of Machine Learning. Cold Spring Harbor Perspectives in Biology. PMID 38621825 DOI: 10.1101/cshperspect.a041467 |
0.304 |
|
| 2023 |
Mahlich Y, Zhu C, Chung H, Velaga PK, De Paolis Kaluza MC, Radivojac P, Friedberg I, Bromberg Y. Learning from the unknown: exploring the range of bacterial functionality. Nucleic Acids Research. 51: 10162-10175. PMID 37739408 DOI: 10.1093/nar/gkad757 |
0.791 |
|
| 2022 |
Zeng Z, Bromberg Y. Inferring Potential Cancer Driving Synonymous Variants. Genes. 13. PMID 35627162 DOI: 10.3390/genes13050778 |
0.766 |
|
| 2022 |
Sun S, Miller M, Wang Y, Tyc KM, Cao X, Scott RT, Tao X, Bromberg Y, Schindler K, Xing J. Predicting embryonic aneuploidy rate in IVF patients using whole-exome sequencing. Human Genetics. PMID 35347416 DOI: 10.1007/s00439-022-02450-z |
0.672 |
|
| 2022 |
Bromberg Y, Aptekmann AA, Mahlich Y, Cook L, Senn S, Miller M, Nanda V, Ferreiro DU, Falkowski PG. Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. Science Advances. 8: eabj3984. PMID 35030025 DOI: 10.1126/sciadv.abj3984 |
0.744 |
|
| 2021 |
Zeng Z, Aptekmann AA, Bromberg Y. Decoding the effects of synonymous variants. Nucleic Acids Research. PMID 34850938 DOI: 10.1093/nar/gkab1159 |
0.814 |
|
| 2021 |
Bernhofer M, Dallago C, Karl T, Satagopam V, Heinzinger M, Littmann M, Olenyi T, Qiu J, Schütze K, Yachdav G, Ashkenazy H, Ben-Tal N, Bromberg Y, Goldberg T, Kajan L, et al. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research. PMID 33999203 DOI: 10.1093/nar/gkab354 |
0.746 |
|
| 2021 |
Mahlich Y, Miller M, Zeng Z, Bromberg Y. Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants. Frontiers in Molecular Biosciences. 8: 635382. PMID 33816556 DOI: 10.3389/fmolb.2021.635382 |
0.803 |
|
| 2021 |
Honarbakhsh M, Ericsson A, Zhong G, Isoherranen N, Zhu C, Bromberg Y, Van Buiten C, Malta K, Joseph L, Sampath H, Lakey A, Storch J, Vetriani C, Chikindas ML, Breslin P, et al. Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions. Journal of Lipid Research. 100046. PMID 33587919 DOI: 10.1016/j.jlr.2021.100046 |
0.735 |
|
| 2020 |
Zhu C, Miller M, Lusskin N, Bergk Pinto B, Maccario L, Häggblom M, Vogel T, Larose C, Bromberg Y. Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds. Microbiologyopen. e1100. PMID 32762019 DOI: 10.1002/mbo3.1100 |
0.765 |
|
| 2020 |
Zhu C, Miller M, Zeng Z, Wang Y, Mahlich Y, Aptekmann A, Bromberg Y. Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome Annual Review of Biomedical Data Science. 3: 411-432. DOI: 10.1146/annurev-biodatasci-030320-041014 |
0.755 |
|
| 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 |
0.739 |
|
| 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 |
0.816 |
|
| 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 |
0.601 |
|
| 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 |
0.65 |
|
| 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 |
0.412 |
|
| 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 |
0.443 |
|
| 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 |
0.746 |
|
| 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 |
0.715 |
|
| 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 |
0.71 |
|
| 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 |
0.421 |
|
| 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 |
0.721 |
|
| 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 |
0.698 |
|
| 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 |
0.808 |
|
| 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 |
0.82 |
|
| 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 |
0.801 |
|
| 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 |
0.798 |
|
| 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 |
0.323 |
|
| 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 |
0.777 |
|
| 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 |
0.817 |
|
| 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 |
0.429 |
|
| 2017 |
Miller M, Bromberg Y, Swint-Kruse L. Computational predictors fail to identify amino acid substitution effects at rheostat positions. Scientific Reports. 7: 41329. PMID 28134345 DOI: 10.1038/Srep41329 |
0.364 |
|
| 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 |
0.58 |
|
| 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 |
0.812 |
|
| 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 |
0.552 |
|
| 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 |
0.443 |
|
| 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 |
0.349 |
|
| 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 |
0.802 |
|
| 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 |
0.618 |
|
| 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 |
0.434 |
|
| 2015 |
Bromberg Y, Capriotti E. SNP-SIG 2013: the state of the art of genomic variant interpretation Bioinformatics. 31: 449-450. DOI: 10.1093/Bioinformatics/Btu415 |
0.475 |
|
| 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 |
0.429 |
|
| 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 |
0.763 |
|
| 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 |
0.34 |
|
| 2014 |
Hecht M, Bromberg Y, Rost B. Erratum for “News from the Protein Mutability Landscape” [J. Mol. Biol. 425 (2013) 3937–3948] Journal of Molecular Biology. 426: 501. DOI: 10.1016/J.Jmb.2013.11.016 |
0.463 |
|
| 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 |
0.3 |
|
| 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 |
0.32 |
|
| 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 |
0.673 |
|
| 2013 |
Bromberg Y. Building a genome analysis pipeline to predict disease risk and prevent disease. Journal of Molecular Biology. 425: 3993-4005. PMID 23928561 DOI: 10.1016/J.Jmb.2013.07.038 |
0.467 |
|
| 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 |
0.596 |
|
| 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 |
0.467 |
|
| 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 |
0.405 |
|
| 2013 |
Bromberg Y. Chapter 15: disease gene prioritization. Plos Computational Biology. 9: e1002902. PMID 23633938 DOI: 10.1371/Journal.Pcbi.1002902 |
0.308 |
|
| 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 |
0.408 |
|
| 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 |
0.573 |
|
| 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 |
0.409 |
|
| 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 |
0.375 |
|
| 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 |
0.398 |
|
| 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 |
0.467 |
|
| 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 |
0.617 |
|
| 2011 |
Bromberg Y, Daniels C, Yachdav G, Marks D, Rost B. Improved manuscript search through PubSeq F1000research. 2. DOI: 10.7490/F1000Research.797.1 |
0.44 |
|
| 2011 |
Rosman DS, Bromberg Y, Weinstein A, Reiss M. Abstract 2118: Phenotypic diversity of disease-associated transforming growth factor-β (TGF-β) type I receptor gene (TGFBR1) mutants Cancer Research. 71: 2118-2118. DOI: 10.1158/1538-7445.Am2011-2118 |
0.314 |
|
| 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/Gkq1208 |
0.6 |
|
| 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 |
0.404 |
|
| 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 |
0.553 |
|
| 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 |
0.583 |
|
| 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 |
0.766 |
|
| 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 |
0.581 |
|
| 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 |
0.493 |
|
| 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 |
0.58 |
|
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