Publications

Yana Bromberg (2022). Tightening the (neural) net for protein structure prediction. Nature Reviews Genetics.

Yana Bromberg, Ariel Aptekmann, Yannick Mahlich, Linda Cook, Stefan Senn, ..., Paul Falkowski (2022). Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer. Science Advances.

Siqi Sun, Maximilian Miller, Yanran Wang, Katarzyna Tyc, Xiaolong Cao, ..., Jinchuan Xing (2022). Predicting embryonic aneuploidy rate in IVF patients using whole-exome sequencing. Human Genetics.

A Aptekmann, J Buongiorno, D Giovannelli, M Glamoclija, D Ferreiro, Y Bromberg (2022). mebipred : identifying metal-binding potential in protein sequence. Bioinformatics.

Zishuo Zeng, Yana Bromberg (2022). Inferring Potential Cancer Driving Synonymous Variants. Genes.

Joseph Lubin, Christine Zardecki, Elliott Dolan, Changpeng Lu, Zhuofan Shen, ..., Stephen Burley (2022). Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Proteins: Structure, Function, and Bioinformatics.

A. Hoarfrost, A. Aptekmann, G. Farfañuk, Y. Bromberg (2022). Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter. Nature Communications.

Yana Bromberg, Predrag Radivojac (2022). Computational interpretation of human genetic variation. Human Genetics.

Michael Bernhofer, Christian Dallago, Tim Karl, Venkata Satagopam, Michael Heinzinger, ..., Burkhard Rost (2021). PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research.

Yannick Mahlich, Maximillian Miller, Zishuo Zeng, Yana Bromberg (2021). Low Diversity of Human Variation Despite Mostly Mild Functional Impact of De Novo Variants. Frontiers in Molecular Biosciences.

Maryam Honarbakhsh, Aaron Ericsson, Guo Zhong, Nina Isoherranen, Chengsheng Zhu, ..., Loredana Quadro (2021). Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions. Journal of Lipid Research.

Zishuo Zeng, Ariel Aptekmann, Yana Bromberg (2021). Decoding the effects of synonymous variants. Nucleic Acids Research.

Chengsheng Zhu, Maximilian Miller, Nicholas Lusskin, Benoı̂t Bergk Pinto, Lorrie Maccario, ..., Yana Bromberg (2020). Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds. MicrobiologyOpen.

Javiera Norambuena, Maximilian Miller, Jeffrey M Boyd, Tamar Barkay (2020). Expression and regulation of the mer operon in Thermus thermophilus. Environmental Microbiology.

Chengsheng Zhu, Maximilian Miller, Zishuo Zeng, Yanran Wang, Yannick Mahlich, ..., Yana Bromberg (2020). Computational Approaches for Unraveling the Effects of Variation in the Human Genome and Microbiome. Annual Review of Biomedical Data Science.

Hesham ElAbd, Yana Bromberg, Adrienne Hoarfrost, Tobias Lenz, Andre Franke, Mareike Wendorff (2020). Amino acid encoding for deep learning applications. BMC bioinformatics.

Chengsheng Zhu, Maximilian Miller, Nick Lusskin, Yannick Mahlich, Yanran Wang, ..., Yana Bromberg (2019). Fingerprinting cities: differentiating subway microbiome functionality. Biology Direct.

Maximilian Miller, Yanran Wang, Yana Bromberg (2019). What went wrong with variant effect predictor performance for the PCM1 challenge. Human Mutation.

Alexander Miguel Monzon, Marco Carraro, Luigi Chiricosta, Francesco Reggiani, James Han, ..., Silvio C. E. Tosatto (2019). Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5. Human Mutation.

Yanran Wang, Maximilian Miller, Yuri Astrakhan, Britt-Sabina Petersen, Stefan Schreiber, ..., Yana Bromberg (2019). Identifying Crohn's disease signal from variome analysis. Genome Medicine.

Maximilian Miller, Daniel Vitale, Peter C Kahn, Burkhard Rost, Yana Bromberg (2019). funtrp: identifying protein positions for variation driven functional tuning. Nucleic Acids Research.

Vikas Pejaver, Giulia Babbi, Rita Casadio, Lukas Folkman, Panagiotis Katsonis, ..., Yana Bromberg (2019). Assessment of methods for predicting the effects of PTEN and TPMT protein variants. Human Mutation.

Alin Voskanian, Panagiotis Katsonis, Olivier Lichtarge, Vikas Pejaver, Predrag Radivojac, ..., Maricel G. Kann (2019). 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.

Yogesh Kumar, Montana T. Morris, Jeffrey D. Mandell Nawei Sun Sheng Wang Dongmei Yu (2018). De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Reports.

Yana Bromberg, Predrag Radivojac (2018). ISMB 2018 proceedings. Bioinformatics.

Yannick Mahlich, Martin Steinegger, Burkhard Rost, Yana Bromberg (2018). HFSP: high speed homology-driven function annotation of proteins. Bioinformatics.

Jason E. McDermott, Matthew Partridge, Yana Bromberg (2018). Ten simple rules for drawing scientific comics. PLOS Computational Biology.

Chengsheng Zhu, Yannick Mahlich, Maximilian Miller, Yana Bromberg (2017). fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks. Nucleic Acids Research.

Chengsheng Zhu, Maximilian Miller, Srinayani Marpaka, Pavel Vaysberg, Malte C Rühlemann, ..., Yana Bromberg (2017). Functional sequencing read annotation for high precision microbiome analysis. Nucleic Acids Research.

Roxana Daneshjou, Yanran Wang, Yana Bromberg, Samuele Bovo, Pier L Martelli, ..., Alexander A. Morgan (2017). Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges. Human Mutation.

Jie Liu, Nora Lopez, Youngbeom Ahn, Tatyana Goldberg, Yana Bromberg, ..., Max M. Häggblom (2017). Novel reductive dehalogenases from the marine sponge associated bacterium Desulfoluna spongiiphila. Environmental Microbiology Reports.

Niko Beerenwinkel, Yana Bromberg (2017). ISMB/ECCB 2017 proceedings. Bioinformatics.

Maximilian Miller, Chengsheng Zhu, Yana Bromberg (2017). clubber: removing the bioinformatics bottleneck in big data analyses. Journal of Integrative Bioinformatics.

Marco Carraro, Giovanni Minervini, Manuel Giollo, Yana Bromberg, Emidio Capriotti, ..., Silvio C. E. Tosatto (2017). Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI. Human Mutation.

Andrea Dietrich Thomas V. Fernandez A. Jeremy Willsey Robert A. King Dongmei Yu (2017). De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron.

Yannick Mahlich, Jonas Reeb, Maximilian Hecht, Maria Schelling, Tjaart Andries Petrus De Beer, ..., Burkhard Rost (2017). Common sequence variants affect molecular function more than rare variants?. Scientific Reports.

Maximilian Miller, Yana Bromberg, Liskin Swint-Kruse (2017). Computational predictors fail to identify amino acid substitution effects at rheostat positions. Scientific Reports.

Yana Bromberg, Matthew W. Hahn, Predrag Radivojac (2016). COMPUTATIONAL APPROACHES TO UNDERSTANDING THE EVOLUTION OF MOLECULAR FUNCTION. Biocomputing 2017.

Tatyana Goldberg, Burkhard Rost, Yana Bromberg (2016). Computational prediction shines light on type III secretion origins. Scientific Reports.

Burkhard Rost, Predrag Radivojac, Yana Bromberg (2016). Protein function in precision medicine: deep understanding with machine learning. FEBS Letters.

Jonas Reeb, Maximilian Hecht, Yannick Mahlich, Yana Bromberg, Burkhard Rost (2016). Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLOS Computational Biology.

Yana Bromberg, Emidio Capriotti, Hannah Carter (2016). VarI-SIG 2015: methods for personalized medicine – the role of variant interpretation in research and diagnostics. BMC Genomics.

Shannon Bruse, Michael Moreau, Yana Bromberg, Jun-Ho Jang, Nan Wang, ..., Toru Nyunoya (2016). Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility. Human Genomics.

Casey S Greene, James A Foster, Bruce A Stanton, Deborah A Hogan, Yana Bromberg (2016). COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES.. Pac Symp Biocomput.

Weimin Sun, Guangwei Yu, Tiffany Louie, Tong Liu, Chengsheng Zhu, ..., Pin Gao (2015). From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples. Applied microbiology and biotechnology.

Chengsheng Zhu, Tom O. Delmont, Timothy M. Vogel, Yana Bromberg (2015). Functional Basis of Microorganism Classification. PLOS Computational Biology.

Yana Bromberg, Emidio Capriotti (2015). VarI-SIG 2014 - From SNPs to variants: interpreting different types of genetic variants. BMC Genomics.

Maximilian Hecht, Yana Bromberg, Burkhard Rost (2015). Better prediction of functional effects for sequence variants. BMC Genomics.

Yana Bromberg, Emidio Capriotti (2014). SNP-SIG 2013: from coding to non-coding - new approaches for genomic variant interpretation. BMC Genomics.

Guy Yachdav, Edda Kloppmann, Laszlo Kajan, Maximilian Hecht, Tatyana Goldberg, ..., Burkhard Rost (2014). PredictProtein—an open resource for online prediction of protein structural and functional features. Nucleic Acids Research.

A. Harel, Y. Bromberg, P. G. Falkowski, D. Bhattacharya (2014). Evolutionary history of redox metal-binding domains across the tree of life. Proceedings of the National Academy of Sciences.

Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P. Satagopam, Manuel Corpas, ..., Theodore Alexandrov (2013). The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013. PLoS Computational Biology.

Maximilian Hecht, Yana Bromberg, Burkhard Rost (2013). News from the Protein Mutability Landscape. Journal of Molecular Biology.

Stefan Senn, Vikas Nanda, Paul Falkowski, Yana Bromberg (2013). Function-based assessment of structural similarity measurements using metal co-factor orientation. Proteins: Structure, Function, and Bioinformatics.

Yana Bromberg (2013). Building a Genome Analysis Pipeline to Predict Disease Risk and Prevent Disease. Journal of Molecular Biology.

Xuefeng Ren, Jessica C. Graham, Lichen Jing, Andrei M. Mikheev, Yuan Gao, ..., Helmut Zarbl (2013). 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.

Yana Bromberg, Peter C Kahn, Burkhard Rost (2013). Neutral and weakly nonneutral sequence variants may define individuality. Proceedings of the National Academy of Sciences.

David Ellinghaus, Hu Zhang, Sebastian Zeissig, Simone Lipinski, Andreas Till, ..., Andre Franke (2013). Association Between Variants of PRDM1 and NDP52 and Crohn′s Disease, Based on Exome Sequencing and Functional Studies. Gastroenterology.

Yana Bromberg, Emidio Capriotti (2013). Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations.. BMC Genomics.

Yana Bromberg (2013). Chapter 15: Disease Gene Prioritization. PLoS Computational Biology.

Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, ..., Burkhard Rost (2013). Homology-based inference sets the bar high for protein function prediction. BMC Bioinformatics.

Emidio Capriotti, Russ B Altman, Yana Bromberg (2013). Collective judgment predicts disease-associated single nucleotide variants. BMC Genomics.

Predrag Radivojac, Wyatt T. Clark, Tal Ronnen Oron, Alexandra M. Schnoes, Tobias Wittkop, ..., others (2013). A large-scale evaluation of computational protein function prediction. Nature methods.

Zachary Freedman, Chengsheng Zhu, Tamar Barkay (2012). Mercury resistance and mercuric reductase activities and expression among chemotrophic thermophilic Aquificae. Appl. Environ. Microbiol..

Arye Harel, Paul Falkowski, Yana Bromberg (2012). TrAnsFuSE refines the search for protein function: oxidoreductases. Integrative Biology.

Suman R. Rawat, Minna K. Männistö, Yana Bromberg, Max M. Häggblom (2012). Comparative genomic and physiological analysis provides insights into the role ofAcidobacteriain organic carbon utilization in Arctic tundra soils. FEMS Microbiology Ecology.

Yana Bromberg, Emidio Capriotti (2012). SNP-SIG Meeting 2011: Identification and annotation of SNPs in the context of structure, function, and disease. BMC Genomics.

Christian Schaefer, Yana Bromberg, Dominik Achten, Burkhard Rost (2012). Disease-related mutations predicted to impact protein function. BMC Genomics.

E. Capriotti, N. L. Nehrt, M. G. Kann, Y. Bromberg (2012). Bioinformatics for personal genome interpretation. Briefings in Bioinformatics.

C. Schaefer, A. Meier, B. Rost, Y. Bromberg (2011). SNPdbe: constructing an nsSNP functional impacts database. Bioinformatics.

Gilad Wainreb, Haim Ashkenazy, Yana Bromberg, Alina Starovolsky-Shitrit, Turkan Haliloglu, ..., Nir Ben-Tal (2010). MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Research.

N. A. Zaghloul, Y. Liu, J. M. Gerdes, C. Gascue, E. C. Oh, ..., N. Katsanis (2010). 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.

Martina Sester, Katja Koebernick, Douglas Owen, Minghui Ao, Yana Bromberg, ..., Hans-Gerhard Burgert (2009). Conserved Amino Acids within the Adenovirus 2 E3/19K Protein Differentially Affect Downregulation of MHC Class I and MICA/B Proteins. The Journal of Immunology.

Yana Bromberg, John Overton, Christian Vaisse, Rudolph L. Leibel, Burkhard Rost (2009). In silico mutagenesis: a case study of the melanocortin 4 receptor. The FASEB Journal.

Yana Bromberg, Burkhard Rost (2009). Correlating protein function and stability through the analysis of single amino acid substitutions. BMC Bioinformatics.

Yana Bromberg, Guy Yachdav, Yanay Ofran, Reinhard Schneider, Burkhard Rost (2009). New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.. Curr Opin Drug Discov Devel.

M. A. Calton, B. A. Ersoy, S. Zhang, J. P. Kane, M. J. Malloy, ..., C. Vaisse (2009). 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.

Yana Bromberg, Guy Yachdav, Burkhard Rost (2008). SNAP predicts effect of mutations on protein function. Bioinformatics.

Y. Bromberg, B. Rost (2008). Comprehensive in silico mutagenesis highlights functionally important residues in proteins. Bioinformatics.

Marija Dokmanovic-Chouinard, Wendy K. Chung, Jean-Claude Chevre, Elizabeth Watson, Jason Yonan, ..., Rudolph L. Leibel (2008). Positional Cloning of “Lisch-like”, a Candidate Modifier of Susceptibility to Type 2 Diabetes in Mice. PLoS Genetics.

Y. Bromberg, B. Rost (2007). SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Research.