Ernest Fraenkel

39 papers A* 2A 1B 3Misc 6Journal 25Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
Biologically Disentangled Multi-Omic Modeling Reveals Mechanistic Insights into Pan-Cancer Immunotherapy Resistance.
CoRR
Ifrah Tariq, Ernest Fraenkel
2025 J jnl
CHAMMI-75: pre-training multi-channel models with heterogeneous microscopy images.
CoRR
Vidit Agrawal, John Peters, Tyler N. Thompson, Mohammad V. Sanian, Chau Pham, Nikita Moshkov, Arshad Kazi, Aditya Pillai, Jack Freeman, Byunguk Kang, Samouil L. Farhi, Ernest Fraenkel, Ron Stewart, Lassi Paavolainen, Bryan A. Plummer, Juan C. Caicedo
2025 J jnl
Clinical assessment and interpretation of dysarthria in ALS using attention based deep learning AI models.
npj Digit. Medicine
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
2024 — conf
Harnessing Remote Speech Tasks for Early ALS Biomarker Identification.
ICDH
Carla Agurto, Michele Merler, Esteban Roitberg, Alan Taitz, Marcos A. Trevisan, Diego E. Shalom, Julian Peller, Lyle W. Ostrow, Indu Navar, Ernest Fraenkel, James D. Berry, Guillermo A. Cecchi, Raquel Norel
2023 A* conf
Efficiently predicting high resolution mass spectra with graph neural networks.
ICML
Michael Murphy, Stefanie Jegelka, Ernest Fraenkel, Tobias Kind, David Healey, Thomas Butler
2023 J jnl
Efficiently predicting high resolution mass spectra with graph neural networks.
CoRR
Michael Murphy, Stefanie Jegelka, Ernest Fraenkel, Tobias Kind, David Healey, Thomas Butler
2023 — conf
Remote Inference of Cognitive Scores in ALS Patients Using a Picture Description.
ICDH
Carla Agurto, Guillermo A. Cecchi, Bo Wen, Ernest Fraenkel, James D. Berry, Indu Navar, Raquel Norel
2023 J jnl
Remote Inference of Cognitive Scores in ALS Patients Using a Picture Description.
CoRR
Carla Agurto, Guillermo A. Cecchi, Bo Wen, Ernest Fraenkel, James D. Berry, Indu Navar, Raquel Norel
2023 A* conf
SubseasonalClimateUSA: A Dataset for Subseasonal Forecasting and Benchmarking.
NeurIPS
Soukayna Mouatadid, Paulo Orenstein, Genevieve Flaspohler, Miruna Oprescu, Judah Cohen, Franklyn Wang, Sean Knight, Maria Geogdzhayeva, Sam Levang, Ernest Fraenkel, Lester Mackey
2022 Misc conf
ALS community pressing issues: lessons from a survey.
AMIA
Aria Anvar, James D. Berry, Ernest Fraenkel, Indu Navar, Guillermo A. Cecchi, Raquel Norel
2022 J jnl
Adaptive Bias Correction for Improved Subseasonal Forecasting.
CoRR
Soukayna Mouatadid, Paulo Orenstein, Genevieve Flaspohler, Judah Cohen, Miruna Oprescu, Ernest Fraenkel, Lester Mackey
2022 J jnl
Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data.
Nat. Comput. Sci.
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, John W. Krakauer, Jonathan Li, Aneesh Donde, Nhan Huynh, Miriam Adam, Brook T. Wassie, Alexander LeNail, Natasha Leanna Patel-Murray, Yogindra Raghav, Velina Kozareva, Stanislav Tsitkov, Tobias Ehrenberger, Julia A. Kaye, Leandro Lima, Stacia K. Wyman, Edward Vertudes, Naufa Amirani, Krishna Raja, Reuben Thomas, Ryan G. Lim, Ricardo Miramontes, Jie Wu, Vineet Vaibhav, Andrea Matlock, Vidya Venkatraman, Ronald Holewenski, Niveda Sundararaman, Rakhi Pandey, Danica-Mae Manalo, Aaron Frank, Loren Ornelas, Lindsey Panther, Emilda Gomez, Erick Galvez, Daniel Pérez, Imara Meepe, Susan Lei, Louis Pinedo, Chunyan Liu, Ruby Moran, Dhruv Sareen, Barry Landin, Carla Agurto, Guillermo A. Cecchi, Raquel Norel, Sara Thrower, Sarah Luppino, Alanna Farrar, Lindsay Pothier, Hong Yu, Ervin Sinani, Prasha Vigneswaran, Alexander V. Sherman, S. Michelle Farr, Berhan Mandefro, Hannah Trost, Maria G. Banuelos, Veronica Garcia, Michael Workman, Richie Ho, Robert Baloh, Jennifer Roggenbuck, Matthew B. Harms, Carolyn Prina, Sarah Heintzman, Stephen Kolb, Jennifer Stocksdale, Keona Wang, Todd Morgan, Daragh Heitzman, Arish Jamil, Jennifer Jockel-Balsarotti, Elizabeth Karanja, Jesse Markway, Molly McCallum, Tim Miller, Ben Joslin, Deniz Alibazoglu, Senda Ajroud-Driss, Jay C. Beavers, Mary Bellard, Elizabeth Bruce, Nicholas J. Maragakis, Merit E. Cudkowicz, James D. Berry, Terri Thompson, Steven Finkbeiner, Leslie M. Thompson, Jennifer E. Van Eyk, Clive N. Svendsen, Jeffrey D. Rothstein, Jonathan D. Glass, Christina N. Fournier, Alexander Sherman, Christian Lunetta, David Walk, Ghazala Hayat, James Wymer, Kelly Gwathmey, Nicholas Olney, Terry Heiman-Patterson, Ximena Arcila-Londono, Kenneth Faulconer, Ervin Sanani, Alex Berger, Julia Mirochnick, Todd M. Herrington, Kenney Ng, Ernest Fraenkel
2022 J jnl
Self-supervised learning of cell type specificity from immunohistochemical images.
Bioinform.
Michael Murphy, Stefanie Jegelka, Ernest Fraenkel
2021 A conf
Investigating the Utility of Multimodal Conversational Technology and Audiovisual Analytic Measures for the Assessment and Monitoring of Amyotrophic Lateral Sclerosis at Scale.
Interspeech
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, James D. Berry, Gary L. Pattee, Jun Wang, Jordan R. Green, Vikram Ramanarayanan
2021 J jnl
Investigating the Utility of Multimodal Conversational Technology and Audiovisual Analytic Measures for the Assessment and Monitoring of Amyotrophic Lateral Sclerosis at Scale.
CoRR
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, James D. Berry, Gary L. Pattee, Jun Wang, Jordan R. Green, Vikram Ramanarayanan
2021 J jnl
Learned Benchmarks for Subseasonal Forecasting.
CoRR
Soukayna Mouatadid, Paulo Orenstein, Genevieve Flaspohler, Miruna Oprescu, Judah Cohen, Franklyn Wang, Sean Knight, Maria Geogdzhayeva, Sam Levang, Ernest Fraenkel, Lester Mackey
2020 Misc conf
Evaluating the utility of a picture description task for monitoring progression of ALS at home.
AMIA
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
2019 Misc conf
Shallow Sparsely-Connected Autoencoders for Gene Set Projection.
PSB
Maxwell P. Gold, Alexander LeNail, Ernest Fraenkel
2017 B conf
A Fast Prize-Collecting Steiner Forest Algorithm for Functional Analyses in Biological Networks.
CPAIOR
Murodzhon Akhmedov, Alexander LeNail, Francesco Bertoni, Ivo Kwee, Ernest Fraenkel, Roberto Montemanni
2017 J jnl
Graph-Sparse Logistic Regression.
CoRR
Alexander LeNail, Ludwig Schmidt, Johnathan Li, Tobias Ehrenberger, Karen Sachs, Stefanie Jegelka, Ernest Fraenkel
2017 J jnl
PCSF: An R-package for network-based interpretation of high-throughput data.
PLoS Comput. Biol.
Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee
2016 J jnl
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.
PLoS Comput. Biol.
Nurcan Tuncbag, Sara J. C. Gosline, Amanda J. Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel
2016 J jnl
Unsupervised learning of transcriptional regulatory networks via latent tree graphical models.
CoRR
Anthony Gitter, Furong Huang, Ragupathyraj Valluvan, Ernest Fraenkel, Animashree Anandkumar
2015 J jnl
SAMNetWeb: identifying condition-specific networks linking signaling and transcription.
Bioinform.
Sara J. C. Gosline, Coyin Oh, Ernest Fraenkel
2014 Misc conf
Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases.
Pacific Symposium on Biocomputing
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer T. Chayes, Riccardo Zecchina, Ernest Fraenkel
2013 J jnl
Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling.
PLoS Comput. Biol.
Shao-Shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
2013 J jnl
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem.
J. Comput. Biol.
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
2012 B conf
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem.
RECOMB
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
2012 J jnl
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways.
Nucleic Acids Res.
Nurcan Tuncbag, Scott McCallum, Shao-Shan Carol Huang, Ernest Fraenkel
2011 J jnl
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data.
Nucleic Acids Res.
Alex Lan, Ilan Y. Smoly, Guy Rapaport, Susan Lindquist, Ernest Fraenkel, Esti Yeger Lotem
2010 J jnl
A Quantitative Model of Transcriptional Regulation Reveals the Influence of Binding Location on Expression.
PLoS Comput. Biol.
Kenzie D. MacIsaac, Kinyui A. Lo, William Gordon, Shmulik Motola, Tali Mazor, Ernest Fraenkel
2008 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund
2007 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo
2007 J jnl
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.
Nucleic Acids Res.
Katherine A. Romer, Guy-Richard Kayombya, Ernest Fraenkel
2006 J jnl
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.
Bioinform.
Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel
2006 J jnl
An improved map of conserved regulatory sites for
BMC Bioinform.
Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel
2006 J jnl
Practical Strategies for Discovering Regulatory DNA Sequence Motifs.
PLoS Comput. Biol.
Kenzie D. MacIsaac, Ernest Fraenkel
2005 J jnl
TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs.
Bioinform.
D. Benjamin Gordon, Lena Nekludova, Scott McCallum, Ernest Fraenkel
2005 B conf
Yeast Cells as a Discovery Platform for Neurodegenerative Disease.
RECOMB
Susan Lindquist, Ernest Fraenkel, Tiago Outeiro, Aaron Gitler, Julie Su, Anil Cashikar, Smitha Jagadish