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2020 – today
- 2024
[c3]Yuxin Yang
, Zixu Wang, Pegah Ahadian, Abby Jerger, Jeremy Zucker, Song Feng, Feixiong Cheng, Qiang Guan:
A Deep Multimodal Representation Learning Framework for Accurate Molecular Properties Prediction. ACM Great Lakes Symposium on VLSI 2024: 760-765- 2023
- [j8]Sara Mohammad Taheri, Vartika Tewari, Rohan Kapre, Ehsan Rahiminasab, Karen Sachs, Charles Tapley Hoyt, Jeremy Zucker, Olga Vitek:
Optimal adjustment sets for causal query estimation in partially observed biomolecular networks. Bioinform. 39(Supplement-1): 494-503 (2023) - 2021
- [j7]Jeremy Zucker, Kaushal Paneri, Sara Mohammad Taheri, Somya Bhargava, Pallavi Kolambkar, Craig Bakker, Jeremy Teuton, Charles Tapley Hoyt, Kristie L. Oxford, Robert Osazuwa Ness, Olga Vitek:
Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis. IEEE Trans. Big Data 7(1): 25-37 (2021) - [c2]Sumit Purohit, Patrick Mackey, Jeremy D. Zucker, Ankur Bohra, Rahul D. Deshmukh, George Chin:
QLiG: Query Like a Graph For Subgraph Matching. AIKE 2021: 121-128 - [i3]Jeremy Zucker, Kaushal Paneri, Sara Mohammad Taheri, Somya Bhargava, Pallavi Kolambkar, Craig Bakker, Jeremy Teuton, Charles Tapley Hoyt, Kristie L. Oxford, Robert Osazuwa Ness, Olga Vitek:
Leveraging Structured Biological Knowledge for Counterfactual Inference: a Case Study of Viral Pathogenesis. CoRR abs/2101.05136 (2021) - [i2]Sara Mohammad Taheri, Robert Osazuwa Ness, Jeremy Zucker, Olga Vitek:
Do-calculus enables causal reasoning with latent variable models. CoRR abs/2102.06626 (2021)
2010 – 2019
- 2017
- [i1]Richard Allen White III, Joseph Brown, Sean Colby, Christopher C. Overall, Joon-Yong Lee, Jeremy Zucker, Kurt R. Glaesemann, Christer Jansson, Janet K. Jansson:
ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data. PeerJ Prepr. 5: e2843 (2017) - 2015
- [j6]Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer:
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. PLoS Comput. Biol. 11(5) (2015) - 2013
- [j5]James E. Galagan, Kyle J. Minch, Matthew Peterson, Anna Lyubetskaya, Elham Azizi, Linsday Sweet, Antonio Gomes, Tige R. Rustad, Gregory Dolganov, Irina Glotova, Thomas Abeel, Chris Mahwinney, Adam D. Kennedy, René Allard, William Brabant, Andrew Krueger, Suma Jaini, Brent Honda, Wen-Han Yu, Mark J. Hickey, Jeremy Zucker, Christopher Garay, Brian Weiner, Peter Sisk, Christian Stolte, Jessica K. Winkler, Yves Van de Peer, Paul Iazzetti, Diogo Camacho, Jonathan M. Dreyfuss, Yang Liu, Anca Dorhoi, Hans-Joachim Mollenkopf, Paul Drogaris, Julie Lamontagne, Yiyong Zhou, Julie Piquenot, Sang Tae Park, Sahadevan Raman, Stefan H. E. Kaufmann, Robert P. Mohney, Daniel Chelsky, D. Branch Moody, David R. Sherman, Gary K. Schoolnik:
The Mycobacterium tuberculosis regulatory network and hypoxia. Nat. 499(7457): 178-183 (2013) - [j4]Jonathan M. Dreyfuss, Jeremy D. Zucker, Heather M. Hood, Linda R. Ocasio, Matthew S. Sachs, James E. Galagan:
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM. PLoS Comput. Biol. 9(7) (2013) - 2012
- [j3]Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara A. Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Dautova Mitreva, Curtis Huttenhower:
Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome. PLoS Comput. Biol. 8(6) (2012)
2000 – 2009
- 2009
- [j2]Gavin H. Thomas, Jeremy Zucker, Sandy J. Macdonald, Anatoly A. Sorokin, Igor Goryanin, Angela E. Douglas:
A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. BMC Syst. Biol. 3: 24 (2009) - [j1]Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan:
Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production. PLoS Comput. Biol. 5(8) (2009) - 2006
- [c1]Alan Ruttenberg, Jonathan Rees, Jeremy Zucker:
What BioPAX Communicates and how to extend OWL to help it. OWLED 2006
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