Aviv Regev

According to our database, Aviv Regev authored at least 30 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design.

Chenyu Wang, Masatoshi Uehara, Yichun He, Amy Wang, Tommaso Biancalani, Avantika Lal, Tommi S. Jaakkola, Sergey Levine, Hanchen Wang, Aviv Regev

CoRR, 2024

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.

Charlotte Bunne, Yusuf H. Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B. Burkhardt, Andrea Califano, Jonah Cool, Abby F. Dernburg, Kirsty Ewing, Emily B. Fox, Matthias Haury, Amy E. Herr, Eric Horvitz, Patrick D. Hsu, Viren Jain, Gregory R. Johnson, Thomas Kalil, David R. Kelley, Shana O. Kelley, Anna Kreshuk, Tim Mitchison, Stephani Otte, Jay Shendure, Nicolas J. Sofroniew, Fabian J. Theis, Christina V. Theodoris, Srigokul Upadhyayula, Marc Valer, Bo Wang, Eric Xing, Serena Yeung-Levy, Marinka Zitnik, Theofanis Karaletsos, Aviv Regev, Emma Lundberg, Jure Leskovec, Stephen R. Quake

CoRR, 2024

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding.

Xiner Li, Yulai Zhao, Chenyu Wang, Gabriele Scalia, Gökcen Eraslan, Surag Nair, Tommaso Biancalani, Aviv Regev, Sergey Levine, Masatoshi Uehara

CoRR, 2024

Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors.

Kexin Huang, Romain Lopez, Jan-Christian Hütter, Takamasa Kudo, Antonio Rios, Aviv Regev

Proceedings of the Research in Computational Molecular Biology, 2024

Toward the Identifiability of Comparative Deep Generative Models.

Romain Lopez, Jan-Christian Hütter, Ehsan Hajiramezanali, Jonathan K. Pritchard, Aviv Regev

Proceedings of the Causal Learning and Reasoning, 2024

2023

A Supervised Contrastive Framework for Learning Disentangled Representations of Cellular Perturbation Data.

Xinming Tu, Jan-Christian Hütter, Zitong Jerry Wang, Takamasa Kudo, Aviv Regev, Romain Lopez

Proceedings of the Machine Learning in Computational Biology, November 30, 2023

Learning Causal Representations of Single Cells via Sparse Mechanism Shift Modeling.

Romain Lopez, Natasa Tagasovska, Stephen Ra, Kyunghyun Cho, Jonathan K. Pritchard, Aviv Regev

Proceedings of the Conference on Causal Learning and Reasoning, 2023

2022

Large-Scale Differentiable Causal Discovery of Factor Graphs.

Romain Lopez, Jan-Christian Hütter, Jonathan K. Pritchard, Aviv Regev

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Disentangling shared and group-specific variations in single-cell transcriptomics data with multiGroupVI.

Ethan Weinberger, Romain Lopez, Jan-Christian Hütter, Aviv Regev

Proceedings of the Machine Learning in Computational Biology, 21-22 November 2022, Online, 2022

2021

Inference of cell dynamics on perturbation data using adjoint sensitivity.

Weiqi Ji, Bo Yuan, Ciyue Shen, Aviv Regev, Chris Sander, Sili Deng

CoRR, 2021

Inherent Limitations of Parameter Estimation of a Tempo-Spatial Field Using an Array of Heterogeneous Sensors.

Aviv Regev, Jonatan Ostrometzky, Hagit Messer

Proceedings of the 29th European Signal Processing Conference, 2021

2019

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson

Nat., 2019

Decoding human fetal liver haematopoiesis.

Dorin-Mirel Popescu, Rachel A. Botting, Emily Stephenson, Kile Green, Simone Webb, Laura Jardine, Emily F. Calderbank, Krzysztof Polanski, Issac Goh, Mirjana Efremova, Meghan Acres, Daniel Maunder, Peter Vegh, Yorick Gitton, Jong-Eun Park, Roser Vento-Tormo, Zhichao Miao, David Dixon, Rachel Rowell, David McDonald, James Fletcher, Elizabeth Poyner, Gary Reynolds, Michael Mather, Corina Moldovan, Lira Mamanova, Frankie Greig, Matthew D. Young, Kerstin B. Meyer, Steven Lisgo, Jaume Bacardit, Andrew Fuller, Ben Millar, Barbara Innes, Susan Lindsay, Michael J. T. Stubbington, Monika S. Kowalczyk, Bo Li, Orr Ashenberg, Marcin Tabaka, Danielle Dionne, Timothy L. Tickle, Michal Slyper, Orit Rozenblatt-Rosen, Andrew Filby, Peter Carey, Alexandra-Chloé Villani, Anindita Roy, Aviv Regev, Alain Chédotal, Irene Roberts, Berthold Göttgens, Sam Behjati, Elisa Laurenti, Sarah A. Teichmann, Muzlifah Haniffa

Nat., 2019

Resolving medulloblastoma cellular architecture by single-cell genomics.

Volker Hovestadt, Kyle S. Smith, Laure Bihannic, Mariella G. Filbin, McKenzie L. Shaw, Alicia Baumgartner, John C. DeWitt, Andrew Groves, Lisa Mayr, Hannah R. Weisman, Alyssa R. Richman, Marni E. Shore, Liliana Goumnerova, Celeste Rosencrance, Robert A. Carter, Timothy N. Phoenix, Jennifer L. Hadley, Yiai Tong, Jim Houston, Richard A. Ashmun, Michael DeCuypere, Tanvi Sharma, Diane Flasch, Antonina Silkov, Keith L. Ligon, Scott L. Pomeroy, Miguel N. Rivera, Orit Rozenblatt-Rosen, Jessica M. Rusert, Robert J. Wechsler-Reya, Xiao-Nan Li, Andreas Peyrl, Johannes Gojo, Dominik Kirchhofer, Daniela Lötsch, Thomas Czech, Christian Dorfer, Christine Haberler, Rene Geyeregger, Angela Halfmann, Charles Gawad, John Easton, Stefan M. Pfister, Aviv Regev, Amar Gajjar, Brent A. Orr, Irene Slavc, Giles W. Robinson, Bradley E. Bernstein, Mario L. Suvà, Paul A. Northcott

Nat., 2019

2018

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes.

Daniel T. Montoro, Adam L. Haber, Moshe Biton, Vladimir Vinarsky, Brian Lin, Susan E. Birket, Feng Yuan, Sijia Chen, Hui Min Leung, Jorge Villoria, Noga Rogel, Grace Burgin, Alexander M. Tsankov, Avinash Waghray, Michal Slyper, Julia Waldman, Lan Nguyen, Danielle Dionne, Orit Rozenblatt-Rosen, Purushothama Rao Tata, Hongmei Mou, Manjunatha Shivaraju, Hermann Bihler, Martin Mense, Guillermo J. Tearney, Steven M. Rowe, John F. Engelhardt, Aviv Regev, Jayaraj Rajagopal

Nat., 2018

Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data.

Miriam Shiffman, William T. Stephenson, Geoffrey Schiebinger, Jonathan H. Huggins, Trevor Campbell, Aviv Regev, Tamara Broderick

CoRR, 2018

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.

Carl G. de Boer, Aviv Regev

BMC Bioinform., 2018

2017

A single-cell survey of the small intestinal epithelium.

Adam L. Haber, Moshe Biton, Noga Rogel, Rebecca H. Herbst, Karthik Shekhar, Christopher Smillie, Grace Burgin, Toni M. Delorey, Michael R. Howitt, Yarden Katz, Itay Tirosh, Semir Beyaz, Danielle Dionne, Mei Zhang, Raktima Raychowdhury, Wendy S. Garrett, Orit Rozenblatt-Rosen, Hai Ning Shi, Omer Yilmaz, Ramnik J. Xavier, Aviv Regev

Nat., 2017

2011

Physical Module Networks: an integrative approach for reconstructing transcription regulation.

Noa Novershtern, Aviv Regev, Nir Friedman

Bioinform., 2011

Metabolic Network Analysis Demystified.

Leonid Chindelevitch, Aviv Regev, Bonnie Berger

Proceedings of the Research in Computational Molecular Biology, 2011

2009

BRNI: Modular analysis of transcriptional regulatory programs.

Iftach Nachman, Aviv Regev

BMC Bioinform., 2009

2007

Automatic genome-wide reconstruction of phylogenetic gene trees.

Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

MinReg: A Scalable Algorithm for Learning Parsimonious Regulatory Networks in Yeast and Mammals.

Dana Pe'er, Amos Tanay, Aviv Regev

J. Mach. Learn. Res., 2006

2005

Learning Module Networks.

Eran Segal, Dana Pe'er, Aviv Regev, Daphne Koller, Nir Friedman

J. Mach. Learn. Res., 2005

2004

BioAmbients: an abstraction for biological compartments.

Aviv Regev, Ekaterina M. Panina, William Silverman, Luca Cardelli, Ehud Shapiro

Theor. Comput. Sci., 2004

Inferring quantitative models of regulatory networks from expression data.

Iftach Nachman, Aviv Regev, Nir Friedman

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2002

Minreg: Inferring an active regulator set.

Dana Pe'er, Aviv Regev, Amos Tanay

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001

Application of a stochastic name-passing calculus to representation and simulation of molecular processes.

Corrado Priami, Aviv Regev, Ehud Shapiro, William Silverman

Inf. Process. Lett., 2001

Representation and Simulation of Biochemical Processes Using the pi-Calculus Process Algebra.

Aviv Regev, William Silverman, Ehud Shapiro

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

Inferring subnetworks from perturbed expression profiles.

Dana Pe'er, Aviv Regev, Gal Elidan, Nir Friedman

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001