Yeast Cells as a Discovery Platform for Neurodegenerative Disease. - Susan Lindquist; Ernest Fraenkel; Tiago Outeiro; Aaron Gitler; Julie Su; Anil Cashikar; Smitha Jagadish (RECOMB, 2005)

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. - D. Benjamin Gordon; Lena Nekludova; Scott McCallum; Ernest Fraenkel (Bioinform., 2005)

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. - Kenzie D. MacIsaac; D. Benjamin Gordon; Lena Nekludova; Duncan T. Odom; Joerg Schreiber; David K. Gifford; Richard A. Young; Ernest Fraenkel (Bioinform., 2006)

An improved map of conserved regulatory sites for Saccharomyces cerevisiae. - Kenzie D. MacIsaac; Ting Wang; D. Benjamin Gordon; David K. Gifford; Gary D. Stormo; Ernest Fraenkel (BMC Bioinform., 2006)

Practical Strategies for Discovering Regulatory DNA Sequence Motifs. - Kenzie D. MacIsaac; Ernest Fraenkel (PLoS Comput. Biol., 2006)

Session Introduction. - Martha L. Bulyk; Alexander J. Hartemink; Ernest Fraenkel; Gary D. Stormo (Pacific Symposium on Biocomputing, 2007)

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches. - Katherine A. Romer; Guy-Richard Kayombya; Ernest Fraenkel (Nucleic Acids Res., 2007)

Session Introduction. - Martha L. Bulyk; Ernest Fraenkel; Alexander J. Hartemink; Yael Mandel-Gutfreund (Pacific Symposium on Biocomputing, 2008)

A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression. - Kenzie D. MacIsaac; Kinyui A. Lo; William Gordon; Shmulik Motola; Tali Mazor; Ernest Fraenkel (PLoS Comput. Biol., 2010)

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data. - Alex Lan; Ilan Y. Smoly; Guy Rapaport; Susan Lindquist; Ernest Fraenkel; Esti Yeger Lotem (Nucleic Acids Res., 2011)

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. - Nurcan Tuncbag; Scott McCallum; Shao-Shan Carol Huang; Ernest Fraenkel (Nucleic Acids Res., 2012)

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. - Nurcan Tuncbag; Alfredo Braunstein; Andrea Pagnani; Shao-Shan Carol Huang; Jennifer T. Chayes; Christian Borgs; Riccardo Zecchina; Ernest Fraenkel (J. Comput. Biol., 2013)

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling. - Shao-Shan Carol Huang; David C. Clarke; Sara J. C. Gosline; Adam Labadorf; Candace R. Chouinard; William Gordon; Douglas A. Lauffenburger; Ernest Fraenkel (PLoS Comput. Biol., 2013)

Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases. - Anthony Gitter; Alfredo Braunstein; Andrea Pagnani; Carlo Baldassi; Christian Borgs; Jennifer T. Chayes; Riccardo Zecchina; Ernest Fraenkel (Pacific Symposium on Biocomputing, 2014)

SAMNetWeb: identifying condition-specific networks linking signaling and transcription. - Sara J. C. Gosline; Coyin Oh; Ernest Fraenkel (Bioinform., 2015)

Unsupervised learning of transcriptional regulatory networks via latent tree graphical models. - Anthony Gitter; Furong Huang; Ragupathyraj Valluvan; Ernest Fraenkel; Animashree Anandkumar (CoRR, 2016)

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package. - Nurcan Tuncbag; Sara J. C. Gosline; Amanda J. Kedaigle; Anthony R. Soltis; Anthony Gitter; Ernest Fraenkel (PLoS Comput. Biol., 2016)

A Fast Prize-Collecting Steiner Forest Algorithm for Functional Analyses in Biological Networks. - Murodzhon Akhmedov; Alexander LeNail; Francesco Bertoni; Ivo Kwee; Ernest Fraenkel; Roberto Montemanni (CPAIOR, 2017)

Graph-Sparse Logistic Regression. - Alexander LeNail; Ludwig Schmidt; Johnathan Li; Tobias Ehrenberger; Karen Sachs; Stefanie Jegelka; Ernest Fraenkel (CoRR, 2017)

PCSF: An R-package for network-based interpretation of high-throughput data. - Murodzhon Akhmedov; Amanda J. Kedaigle; Renan Escalante Chong; Roberto Montemanni; Francesco Bertoni; Ernest Fraenkel; Ivo Kwee (PLoS Comput. Biol., 2017)

Shallow Sparsely-Connected Autoencoders for Gene Set Projection. - Maxwell P. Gold; Alexander LeNail; Ernest Fraenkel (PSB, 2019)

Evaluating the utility of a picture description task for monitoring progression of ALS at home. - Carla Agurto; Guillermo A. Cecchi; Mary Pietrowicz; Divya Ramamoorthy; Lorin Wilde; Elizabeth Mosmiller; Emily G. Baxi; Nicholas J. Maragakis; James D. Berry; Ernest Fraenkel; Jeffrey D. Rothstein; Raquel Norel (AMIA, 2020)

Investigating the Utility of Multimodal Conversational Technology and Audiovisual Analytic Measures for the Assessment and Monitoring of Amyotrophic Lateral Sclerosis at Scale. - Michael Neumann; Oliver Roesler; Jackson Liscombe; Hardik Kothare; David Suendermann-Oeft; David Pautler; Indu Navar; Aria Anvar; Jochen Kumm; Raquel Norel; Ernest Fraenkel; Alexander V. Sherman; et al. (Interspeech, 2021)

Learned Benchmarks for Subseasonal Forecasting. - Soukayna Mouatadid; Paulo Orenstein; Genevieve Flaspohler; Miruna Oprescu; Judah Cohen; Franklyn Wang; Sean Knight; Maria Geogdzhayeva; Sam Levang; Ernest Fraenkel; Lester Mackey (CoRR, 2021)

ALS community pressing issues: lessons from a survey. - Aria Anvar; James D. Berry; Ernest Fraenkel; Indu Navar; Guillermo A. Cecchi; Raquel Norel (AMIA, 2022)

Self-supervised learning of cell type specificity from immunohistochemical images. - Michael Murphy; Stefanie Jegelka; Ernest Fraenkel (Bioinform., 2022)

Adaptive Bias Correction for Improved Subseasonal Forecasting. - Soukayna Mouatadid; Paulo Orenstein; Genevieve Flaspohler; Judah Cohen; Miruna Oprescu; Ernest Fraenkel; Lester Mackey (CoRR, 2022)

Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data. - Divya Ramamoorthy; Kristen Severson; Soumya Ghosh; Karen Sachs; Emily G. Baxi; Alyssa N. Coyne; Elizabeth Mosmiller; Lindsey Hayes; Aianna Cerezo; Omar Ahmad; Promit Roy; Steven Zeiler; et al. (Nat. Comput. Sci., 2022)

Remote Inference of Cognitive Scores in ALS Patients Using a Picture Description. - Carla Agurto; Guillermo A. Cecchi; Bo Wen; Ernest Fraenkel; James D. Berry; Indu Navar; Raquel Norel (ICDH, 2023)

Efficiently predicting high resolution mass spectra with graph neural networks. - Michael Murphy; Stefanie Jegelka; Ernest Fraenkel; Tobias Kind; David Healey; Thomas Butler (ICML, 2023)

SubseasonalClimateUSA: A Dataset for Subseasonal Forecasting and Benchmarking. - Soukayna Mouatadid; Paulo Orenstein; Genevieve Flaspohler; Miruna Oprescu; Judah Cohen; Franklyn Wang; Sean Knight; Maria Geogdzhayeva; Sam Levang; Ernest Fraenkel; Lester Mackey (NeurIPS, 2023)

Clinical assessment and interpretation of dysarthria in ALS using attention based deep learning AI models. - Michele Merler; Carla Agurto; Julian Peller; Esteban Roitberg; Alan Taitz; Marcos A. Trevisan; Indu Navar; James D. Berry; Ernest Fraenkel; Lyle W. Ostrow; Guillermo A. Cecchi; Raquel Norel (npj Digit. Medicine, 2025)