Causal identification with Y0.

Jeremy Zucker Jeremy D. Zucker https://orcid.org/0000-0002-7276-9009 https://www.wikidata.org/entity/Q30513835

Charles Tapley Hoyt Craig Bakker Richard J. Callahan Joseph Cottam August George Benjamin M. Gyori Haley M. Hummel Nathaniel Merrill Sara Mohammad Taheri Pruthvi Prakash Navada Marc-Antoine Parent Adam Rupe Olga Vitek Jeremy Zucker Causal identification with Y0. 2025 August abs/2508.03167 CoRR https://doi.org/10.48550/arXiv.2508.03167 https://www.wikidata.org/entity/Q135651916 db/journals/corr/corr2508.html#abs-2508-03167 streams/journals/corr

Sara Mohammad Taheri Pruthvi Prakash Navada Charles Tapley Hoyt Jeremy Zucker Karen Sachs Benjamin M. Gyori Olga Vitek <tt>Eliater</tt>: a Python package for estimating outcomes of perturbations in biomolecular networks. 2024 40 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btae527 db/journals/bioinformatics/bioinformatics40.html#TaheriNHZSGV24

Yuxin Yang 0001 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. 760-765 2024 ACM Great Lakes Symposium on VLSI https://doi.org/10.1145/3649476.3660377 conf/glvlsi/2024 db/conf/glvlsi/glvlsi2024.html#YangWAJZFCG24

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. 494-503 2023 39 Bioinform. Supplement-1 https://doi.org/10.1093/bioinformatics/btad270 https://www.wikidata.org/entity/Q122028693 db/journals/bioinformatics/bioinformatics39.html#TaheriTKRSHZV23

Sara Mohammad Taheri Jeremy Zucker Charles Tapley Hoyt Karen Sachs Vartika Tewari Robert Osazuwa Ness Olga Vitek Do-calculus enables estimation of causal effects in partially observed biomolecular pathways. i350-i358 2022 38 Bioinform. Supplement_1 https://doi.org/10.1093/bioinformatics/btac251 https://www.wikidata.org/entity/Q114037635 db/journals/bioinformatics/bioinformatics38.html#TaheriZHSTNV22

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. 25-37 2021 7 IEEE Trans. Big Data 1 https://doi.org/10.1109/TBDATA.2021.3050680 https://www.wikidata.org/entity/Q114032921 db/journals/tbd/tbd7.html#ZuckerPTBKBTHON21

Sumit Purohit Patrick Mackey Jeremy D. Zucker Ankur Bohra Rahul D. Deshmukh George Chin QLiG: Query Like a Graph For Subgraph Matching. 121-128 2021 AIKE https://doi.org/10.1109/AIKE52691.2021.00025 conf/aike/2021 db/conf/aike/aike2021.html#PurohitMZBDC21

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. 2021 abs/2101.05136 CoRR https://arxiv.org/abs/2101.05136 db/journals/corr/corr2101.html#abs-2101-05136

Sara Mohammad Taheri Robert Osazuwa Ness Jeremy Zucker Olga Vitek Do-calculus enables causal reasoning with latent variable models. 2021 abs/2102.06626 CoRR https://arxiv.org/abs/2102.06626 db/journals/corr/corr2102.html#abs-2102-06626

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. e2843 2017 5 PeerJ Prepr. https://doi.org/10.7287/peerj.preprints.2843v1 https://www.wikidata.org/entity/Q61963326 db/journals/peerjpre/peerjpre5.html#WhiteBCOLZGJJ17

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 0001 Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models. 2015 11 PLoS Comput. Biol. 5 https://doi.org/10.1371/journal.pcbi.1004096 https://www.wikidata.org/entity/Q35644952 db/journals/ploscb/ploscb11.html#KarrWZRSTKWABHK15

James E. Galagan Kyle J. Minch Matthew Peterson Anna Lyubetskaya Elham Azizi Linsday Sweet Antonio Gomes 0002 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. 178-183 2013 499 Nat. 7457 https://doi.org/10.1038/nature12337 https://www.wikidata.org/entity/Q28655962 db/journals/nature/nature499.html#GalaganMPLASGRD13

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. 2013 9 PLoS Comput. Biol. 7 https://doi.org/10.1371/journal.pcbi.1003126 https://www.wikidata.org/entity/Q28535020 db/journals/ploscb/ploscb9.html#DreyfussZHOSG13

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. 2012 8 PLoS Comput. Biol. 6 https://doi.org/10.1371/journal.pcbi.1002358 https://www.wikidata.org/entity/Q21092513 db/journals/ploscb/ploscb8.html#AbubuckerSGSICRZTHWKMSGMH12

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. 24 2009 3 BMC Syst. Biol. https://doi.org/10.1186/1752-0509-3-24 https://www.wikidata.org/entity/Q33411076 db/journals/bmcsb/bmcsb3.html#ThomasZMSGD09

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. 2009 5 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000489 https://www.wikidata.org/entity/Q28475985 db/journals/ploscb/ploscb5.html#ColijnBZLWFCMMG09

Alan Ruttenberg Jonathan Rees Jeremy Zucker What BioPAX Communicates and how to extend OWL to help it. 2006 OWLED https://ceur-ws.org/Vol-216/submission_26.pdf conf/owled/2006 db/conf/owled/owled2006.html#RuttenbergRZ06 Thomas Abeel Sahar Abubucker Pegah Ahadian René Allard Brandon A. Allgood Elham Azizi Craig Bakker Somya Bhargava Ankur Bohra Brian M. Bot William Brabant Aaron Brandes Joseph Brown Richard J. Callahan Diogo Camacho Brandi L. Cantarel Daniel Chelsky Feixiong Cheng Tan-Yun Cheng George Chin Sean Colby Caroline Colijn Joseph Cottam Markus W. Covert Rahul D. Deshmukh Gregory Dolganov Anca Dorhoi Angela E. Douglas Jonathan M. Dreyfuss Paul Drogaris Maha R. Farhat Song Feng James E. Galagan Christopher Garay August George Dirk Gevers Kurt R. Glaesemann Irina Glotova Johannes Goll Antonio Gomes 0002 Igor Goryanin Qiang Guan Benjamin M. Gyori Bernard Henrissat Mark J. Hickey Bruce R. Hoff Brent Honda Heather M. Hood Charles Tapley Hoyt Haley M. Hummel Curtis Huttenhower Paul Iazzetti Jacques Izard Suma Jaini Christer Jansson Janet K. Jansson Abby Jerger Rohan Kapre Jonathan R. Karr Stefan H. E. Kaufmann Michael R. Kellen Scott T. Kelley Adam D. Kennedy Pallavi Kolambkar Clemens Kreutz Andrew Krueger Julie Lamontagne Joon-Yong Lee Yang Liu Desmond S. Lun Anna Lyubetskaya Sandy J. Macdonald Patrick Mackey Chris Mahwinney Nathaniel W. MerrillNathaniel Merrill Barbara A. Methé Pablo Meyer 0001 Kyle J. Minch Makedonka MitrevaMakedonka Dautova Mitreva Robert P. Mohney Hans-Joachim Mollenkopf D. Branch Moody Megan Murray Pruthvi Prakash Navada Robert Osazuwa Ness Linda R. Ocasio Christopher C. Overall Kristie L. Oxford Kaushal Paneri Marc-Antoine Parent Sang Tae Park Yves Van de Peer Matthew Peterson Julie Piquenot Sumit Purohit Ehsan Rahiminasab Sahadevan Raman Andreas Raue Jonathan Rees Beltran Rodriguez-Mueller Adam Rupe Tige R. Rustad Alan Ruttenberg Karen Sachs Matthew S. Sachs Patrick D. Schloss Gary K. Schoolnik Alyxandria M. Schubert Nicola Segata David R. Sherman Peter Sisk Anatoly A. Sorokin Bernhard Steiert Gustavo StolovitzkyGustavo A. Stolovitzky Christian Stolte Linsday Sweet Sara Mohammad Taheri Jeremy Teuton Vartika Tewari Mathangi Thiagarajan Gavin H. Thomas Jens Timmer Olga Vitek Zixu Wang Brian Weiner Owen White Richard Allen White III Simon Wilkinson Alex H. Williams Jessica K. Winkler Yuxin Yang 0001 Wen-Han Yu Yiyong Zhou