Comprehensive in silico mutagenesis highlights functionally important residues in proteins. - Yana Bromberg; Burkhard Rost (ECCB, 2008)

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

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

MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. - Gilad Wainreb; Haim Ashkenazy; Yana Bromberg; Alina Starovolsky-Shitrit; Turkan Haliloglu; Eytan Ruppin; Karen B. Avraham; Burkhard Rost; Nir Ben-Tal (Nucleic Acids Res., 2010)

Bioinformatics for personal genome interpretation. - Emidio Capriotti; Nathan L. Nehrt; Maricel G. Kann; Yana Bromberg (Briefings Bioinform., 2012)

SNPdbe: constructing an nsSNP functional impacts database. - Christian Schaefer; Alice Meier; Burkhard Rost; Yana Bromberg (Bioinform., 2012)

Chapter 15: Disease Gene Prioritization. - Yana Bromberg (PLoS Comput. Biol., 2013)

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

PredictProtein - an open resource for online prediction of protein structural and functional features. - Guy Yachdav; Edda Kloppmann; László Kaján; Maximilian Hecht; Tatyana Goldberg; Tobias Hamp; Peter Hönigschmid; Andrea Schafferhans; Manfred Roos; Michael Bernhofer; Lothar Richter; Haim Ashkenazy; et al. (Nucleic Acids Res., 2014)

Editor's Choice: SNP-SIG 2013: the state of the art of genomic variant interpretation. - Yana Bromberg; Emidio Capriotti (Bioinform., 2015)

Functional Basis of Microorganism Classification. - Chengsheng Zhu; Tom O. Delmont; Timothy M. Vogel; Yana Bromberg (PLoS Comput. Biol., 2015)

Computational Approaches to Study Microbes and Microbiomes. - Casey S. Greene; James A. Foster; Bruce A. Stanton; Deborah A. Hogan; Yana Bromberg (PSB, 2016)

Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. - Jonas Reeb; Maximilian Hecht; Yannick Mahlich; Yana Bromberg; Burkhard Rost (PLoS Comput. Biol., 2016)

Session Introduction. - Yana Bromberg; Matthew W. Hahn; Predrag Radivojac (PSB, 2017)

ISMB/ECCB 2017 proceedings. - Niko Beerenwinkel; Yana Bromberg (Bioinform., 2017)

clubber: removing the bioinformatics bottleneck in big data analyses. - Maximilian Miller; Chengsheng Zhu; Yana Bromberg (J. Integr. Bioinform., 2017)

ISMB 2018 proceedings. - Yana Bromberg; Predrag Radivojac (Bioinform., 2018)

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

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks. - Chengsheng Zhu; Yannick Mahlich; Maximilian Miller; Yana Bromberg (Nucleic Acids Res., 2018)

Ten simple rules for drawing scientific comics. - Jason E. McDermott; Matthew Partridge; Yana Bromberg (PLoS Comput. Biol., 2018)

ISMB/ECCB 2019 Proceedings. - Yana Bromberg; Nadia El-Mabrouk; Predrag Radivojac (Bioinform., 2019)

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

PredictProtein - Predicting Protein Structure and Function for 29 Years. - Michael Bernhofer; Christian Dallago; Timothy Karl; Venkata P. Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; et al. (Nucleic Acids Res., 2021)

mebipred: identifying metal-binding potential in protein sequence. - Ariel A. Aptekmann; J. Buongiorno; D. Giovannelli; M. Glamoclija; Diego U. Ferreiro; Yana Bromberg (Bioinform., 2022)

Better AI For Understanding Life on Earth: Predict First, Design Later. - Yana Bromberg; Amarda Shehu (SDM, 2025)