Publications

2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | other




2017


2017 | Nucleic Acids Research

Functional sequencing read annotation for high precision microbiome analysis

C Zhu, M Miller, S Marpaka, P Vaysberg, MC Rühlemann, G Wu, ...

PubMed: 29194524

#Citations: 0

2017 | Human Mutation

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

R Daneshjou, Y Wang, Y Bromberg, S Bovo, PL Martelli, G Babbi, ...

#Citations: 0

2017 | BIOINFORMATICS 33 (14), I1-I2

ISMB/ECCB 2017 proceedings

Y Bromberg, N Beerenwinkel

#Citations: 0

2017 | Bioinformatics 33 (14), i1-i2

ismb/eccb 2017 proceedings

N Beerenwinkel, Y Bromberg

#Citations: 0

2017 | Environmental Microbiology Reports

Novel Reductive Dehalogenases from the Marine Sponge Associated Bacterium Desulfoluna spongiiphila

J Liu, N Lopez, YB Ahn, T Goldberg, Y Bromberg, LJ Kerkhof, ...

#Citations: 0

2017 | Human Mutation

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI

M Carraro, G Minervini, M Giollo, Y Bromberg, E Capriotti, R Casadio, ...

PubMed: 28440912

#Citations: 1

2017 | Scientific Reports 7, 41329

Computational predictors fail to identify amino acid substitution effects at rheostat positions

M Miller, Y Bromberg, L Swint-Kruse

PubMed: 28134345

#Citations: 3

2017 | bioRxiv, 216432

Identifying Crohns disease signal from variome analysis

Y Wang, Y Astrakhan, BS Petersen, S Schreiber, A Franke, Y Bromberg

#Citations: 0

2017 | Scientific Reports 7

Common sequence variants affect molecular function more than rare variants?

Y Mahlich, J Reeb, M Hecht, M Schelling, TAP De Beer, Y Bromberg, ...

PubMed: 28487536

#Citations: 3

2017 | PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017, 1-2

COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION

Y Bromberg, MW Hahn, P Radivojac

PubMed: 27896956

#Citations: 0


2016


2016 | PLoS computational biology 12 (8), e1005047

Predicted molecular effects of sequence variants link to system level of disease

J Reeb, M Hecht, Y Mahlich, Y Bromberg, B Rost

#Citations: 6

2016 | FEBS letters 590 (15), 2327-2341

Protein function in precision medicine: deep understanding with machine learning

B Rost, P Radivojac, Y Bromberg

PubMed: 27423136

#Citations: 14

2016 | BMC genomics 17 (2), 425

VarI-SIG 2015: methods for personalized medicine–the role of variant interpretation in research and diagnostics

Y Bromberg, E Capriotti, H Carter

PubMed: 27357578

#Citations: 1

2016 | Human genomics 10 (1), 1

Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility

S Bruse, M Moreau, Y Bromberg, JH Jang, N Wang, H Ha, M Picchi, Y Lin, ...

PubMed: 26744305

#Citations: 6

2016 | Scientific reports 6

Computational prediction shines light on type III secretion origins

T Goldberg, B Rost, Y Bromberg

PubMed: 27713481

#Citations: 5

2016 | bioRxiv, 035923

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks

C Zhu, Y Mahlich, Y Bromberg

PubMed: 29194481

#Citations: 0

2016 | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 21, 557

Computational Approaches to Study Microbes and Microbiomes

CS Greene, JA Foster, BA Stanton, DA Hogan, Y Bromberg

PubMed: 26776218

#Citations: 4


2015


2015 | BMC genomics 16 (S8), S1

Better prediction of functional effects for sequence variants

M Hecht, Y Bromberg, B Rost

PubMed: 26110438

#Citations: 57

2015 | BMC genomics 16 (S8), I1

VarI-SIG 2014-From SNPs to variants: interpreting different types of genetic variants

Y Bromberg, E Capriotti

#Citations: 2

2015 | PLoS computational biology 11 (8), e1004472

Functional basis of microorganism classification

C Zhu, TO Delmont, TM Vogel, Y Bromberg

PubMed: 26317871

#Citations: 5

2015 | Bioinformatics 31 (3), 449-450

SNP-SIG 2013: the state of the art of genomic variant interpretation

Y Bromberg, E Capriotti

#Citations: 0


2014


2014 | Proceedings of the National Academy of Sciences 111 (19), 7042-7047

Evolutionary history of redox metal-binding domains across the tree of life

A Harel, Y Bromberg, PG Falkowski, D Bhattacharya

PubMed: 24778258

#Citations: 24

2014 | Nucleic acids research 42 (W1), W337-W343

PredictProtein—an open resource for online prediction of protein structural and functional features

G Yachdav, E Kloppmann, L Kajan, M Hecht, T Goldberg, T Hamp, ...

#Citations: 208

2014 | BMC genomics 15 (S4), S1

SNP-SIG 2013: from coding to non-coding-new approaches for genomic variant interpretation

Y Bromberg, E Capriotti

PubMed: 25056427

#Citations: 3

2014 | Proteins: Structure, Function, and Bioinformatics 82 (4), 648-656

Function‐based assessment of structural similarity measurements using metal co‐factor orientation

S Senn, V Nanda, P Falkowski, Y Bromberg

PubMed: 24127252

#Citations: 4

2014 | JOURNAL OF MOLECULAR BIOLOGY 426 (2), 501-501

News from the Protein Mutability Landscape (vol 425, pg 3937, 2013)

M Hecht, Y Bromberg, B Rost

#Citations: 0

2014 | Nucleic Acids Research, 1

PredictProtein-An open resource for online prediction of protein structural and functional

E Kloppmann, Y Bromberg, R Schneider, N Ben-Tal

PubMed: 24799431

#Citations: 0

2014 | Journal of Molecular Biology 2 (426), 501

Erratum for “News from the Protein Mutability Landscape”[J. Mol. Biol. 425 (2013) 3937–3948]

M Hecht, Y Bromberg, B Rost

#Citations: 0


2013


2013 | PLoS computational biology 9 (11), e1003350

The young PI buzz: learning from the organizers of the junior principal investigator meeting at ISMB-ECCB 2013

J de Ridder, Y Bromberg, M Michaut, VP Satagopam, M Corpas, ...

#Citations: 1

2013 | Journal of molecular biology 425 (21), 3993-4005

Building a genome analysis pipeline to predict disease risk and prevent disease

Y Bromberg

PubMed: 23928561

#Citations: 32

2013 | Journal of molecular biology 425 (21), 3937-3948

News from the protein mutability landscape

M Hecht, Y Bromberg, B Rost

PubMed: 23896297

#Citations: 43

2013 | PloS one 8 (9), e70930

Mapping of Mcs30, a new mammary carcinoma susceptibility quantitative trait locus (QTL30) on rat chromosome 12: identification of Fry as a candidate Mcs gene

X Ren, JC Graham, L Jing, AM Mikheev, Y Gao, JP Lew, H Xie, AS Kim, ...

#Citations: 3

2013 | Gastroenterology 145 (2), 339-347

Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies

D Ellinghaus, H Zhang, S Zeissig, S Lipinski, A Till, T Jiang, B Stade, ...

#Citations: 80

2013 | Proceedings of the National Academy of Sciences 110 (35), 14255-14260

Neutral and weakly nonneutral sequence variants may define individuality

Y Bromberg, PC Kahn, B Rost

PubMed: 23940345

#Citations: 18

2013 | studies 145 (2), 339-47

PMCID: PMC3143657.

Y Bromberg, E Ellinghaus, A Keller, MA Rivas, J Skieceviciene, ...

#Citations: 0

2013 | BMC genomics 14 (3), S1

Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations

Y Bromberg, E Capriotti

PubMed: 23819751

#Citations: 3

2013 | BMC genomics 14 (3), S2

Collective judgment predicts disease-associated single nucleotide variants

E Capriotti, RB Altman, Y Bromberg

PubMed: 23819846

#Citations: 73

2013 | Elsevier

Association Between Variants of PRDM1 and NDP52 and Crohn's Disease, Based on Exome Sequencing and Functional Studies

H Zhang, S Zeissig, S Lipinski, A Till, T Jiang, B Stade, Y Bromberg, ...

#Citations: 0

2013 | PLoS computational biology 9 (4), e1002902

Disease gene prioritization

Y Bromberg

PubMed: 27995669

#Citations: 39


2012


2012 | FEMS microbiology ecology 82 (2), 341-355

Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils

SR Rawat, MK Männistö, Y Bromberg, MM Häggblom

PubMed: 22486608

#Citations: 62

2012 | BMC genomics 13 (4), S1

SNP-SIG Meeting 2011: identification and annotation of SNPs in the context of structure, function, and disease

Y Bromberg, E Capriotti

PubMed: 22759647

#Citations: 6

2012 | BMC genomics 13 (S4), S11

Disease-related mutations predicted to impact protein function

C Schaefer, Y Bromberg, D Achten, B Rost

PubMed: 22759649

#Citations: 18

2012 | Briefings in bioinformatics 13 (4), 495-512

Bioinformatics for personal genome interpretation

E Capriotti, NL Nehrt, MG Kann, Y Bromberg

PubMed: 22247263

#Citations: 56

2012 | Integrative Biology 4 (7), 765-777

TrAnsFuSE refines the search for protein function: oxidoreductases

A Harel, P Falkowski, Y Bromberg

PubMed: 22481248

#Citations: 9


2011


2011 | Bioinformatics 28 (4), 601-602

SNPdbe: constructing an nsSNP functional impacts database

C Schaefer, A Meier, B Rost, Y Bromberg

PubMed: 22210871

#Citations: 50

2011 | Cancer Research 71 (8 Supplement), 2118-2118

Phenotypic diversity of disease-associated transforming growth factor-β (TGF-β) type I receptor gene (TGFBR1) mutants

DS Rosman, Y Bromberg, A Weinstein, M Reiss

#Citations: 1


2010


2010 | Nucleic acids research 38 (suppl_2), W523-W528

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data

G Wainreb, H Ashkenazy, Y Bromberg, A Starovolsky-Shitrit, T Haliloglu, ...

PubMed: 20542913

#Citations: 31

2010 | Proceedings of the National Academy of Sciences 107 (23), 10602-10607

Functional analyses of variants reveal a significant role for dominant negative and common alleles in oligogenic Bardet–Biedl syndrome

NA Zaghloul, Y Liu, JM Gerdes, C Gascue, EC Oh, CC Leitch, Y Bromberg, ...

PubMed: 20498079

#Citations: 88

2010 |

ISMB 2010 ORGANIZATION

RF Murphy, A Bateman, UK Hinxton, T Lengauer, Y Moreau, D Durand, ...

#Citations: 0

2010 | The journal of immunology 184 (1), 255-267

Conserved amino acids within the adenovirus 2 E3/19K protein differentially affect downregulation of MHC class I and MICA/B proteins

M Sester, K Koebernick, D Owen, M Ao, Y Bromberg, E May, E Stock, ...

PubMed: 19949079

#Citations: 19


2009


2009 | The FASEB Journal 23 (9), 3059-3069

In silico mutagenesis: a case study of the melanocortin 4 receptor

Y Bromberg, J Overton, C Vaisse, RL Leibel, B Rost

PubMed: 25163632

#Citations: 36

2009 | Bmc Bioinformatics 10 (S8), S8

Correlating protein function and stability through the analysis of single amino acid substitutions

Y Bromberg, B Rost

PubMed: 19758472

#Citations: 29

2009 | Biochem Biophys Res Commun 380 (4), 736-41

PMC3759375.

D Krex, Z Arlier, N Nayak, YM Ruigrok, M Niemelä, A Tajima, B Schoch, ...

#Citations: 0

2009 | Current opinion in drug discovery & development 12 (3), 408-419

New in protein structure and function annotation: Hotspots, single nucleotide polymorphisms and the'Deep Web'

Y Bromberg, G Yachdav, Y Ofran, R Schneider, B Rost

#Citations: 7


2008


2008 | Human molecular genetics 18 (6), 1140-1147

Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case–control study

MA Calton, BA Ersoy, S Zhang, JP Kane, MJ Malloy, CR Pullinger, ...

PubMed: 19091795

#Citations: 104

2008 | Bioinformatics 24 (20), 2397-2398

SNAP predicts effect of mutations on protein function

Y Bromberg, G Yachdav, B Rost

PubMed: 18757876

#Citations: 153

2008 | Bioinformatics 24 (16), i207-i212

Comprehensive in silico mutagenesis highlights functionally important residues in proteins

Y Bromberg, B Rost

PubMed: 18689826

#Citations: 44

2008 | PLoS Genet 4 (7), e1000137

1: Papatheodorou P, Hornuss D, Nölke T, Hemmasi S, Castonguay J, Picchianti M, Aktories K. Clostridium difficile binary toxin CDT induces clustering of the lipolysis...

JB Dumas, O Guerassimenko, BE Bihain, MS Hildebrand, ZM Ahmed, ...

#Citations: 0

2008 | PLoS genetics 4 (7), e1000137

Positional cloning of “Lisch-Like”, a candidate modifier of susceptibility to type 2 diabetes in mice

M Dokmanovic-Chouinard, WK Chung, JC Chevre, E Watson, J Yonan, ...

#Citations: 45


2007


2007 | Nucleic acids research 35 (11), 3823-3835

SNAP: predict effect of non-synonymous polymorphisms on function

Y Bromberg, B Rost

#Citations: 518

2007 | Columbia University

Prediction and Analysis of Effects of Non-synonymous Single Nucleotide Polymorphisms on Protein Function

Y Bromberg

PubMed: 18393868

#Citations: 0


other


| Journal of Integrative Bioinformatics

clubber: removing the bioinformatics bottleneck in big data analyses

M Miller, C Zhu, Y Bromberg

PubMed: 28609295

#Citations: 1

|

Supporting online material (SOM) for

Y Mahlich, J Reeb, M Hecht, TAP De Beer, Y Bromberg, B Rost

#Citations: 0

|

Supporting online material for: Better prediction of functional effects for sequence variants

M Hecht, Y Bromberg, B Rost

#Citations: 0

|

Mapping The Electronic Blueprint of Life.

P Falkowski, D Bhattacharya, Y Bromberg, V Nanda, N Yee, D Case, ...

#Citations: 0

|

WSA05–Fc Receptors

HG Burgert, M Sester, K Koebernick, D Owen, M Ao, Y Bromberg, E May, ...

#Citations: 0

| Detail:

Bioinformatics (Oxford, England) Volume: 24 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2008 Oct

Y Bromberg, G Yachdav, B Rost

#Citations: 0