Publications-2 | Richard D. Berlin Center for Cell Analysis & Modeling

2026

Katelyn M. Cooper, Carly A. Busch, Alice Accorsi, Derek A. Applewhite, Parth B. Bhanderi, Bruno da Rocha-Azevedo, Abhijit Deb Roy, Joseph P. Campanale, Fred Chang, Jerry E. Chipuk, Lee A. Ligon, G. W. Gant Luxton, Austin J. Graham, Camila Hochman-Mendez, Imge Ozugergin, Zachory M. Park, Claire M. Thomas, Alex M. Valm, C. Jynx Weaver, Hongxian Zhu, Rebecca S. Alvania. (2026) LGBTQ+ Realities in the Biological Sciences. eScholarship (California Digital Library) https://doi.org/10.1187/cbe.25-05-0098

Paul J. Michalski, Leslie M. Loew, Dan Vasilescu, Ezequiel Valencia, James C. Schaff, Joseph Masison, Ion I. Moraru. (2026) SpringSaLaD. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.22104788

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Logan Drescher, Ezequiel Valencia, Anuradha Lakshminarayana, Michael L. Blinov, Ann E. Cowan, Ion I. Moraru. (2026) Virtual Cell (VCell). Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21995407

Mark Alber, Marc R. Birtwistle, Stacey D. Finley, Pedro Mendes. (2026) Systems biology during 20 years of PLoS Computational Biology. PLoS Computational Biology, 22(7): e1014465-e1014465 https://doi.org/10.1371/journal.pcbi.1014465

James C. Schaff, Alexander Patrie, Logan Drescher, Ion I. Moraru. (2026) pyVCell. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21127438

James C. Schaff, Alexander Patrie, Harrison Burr, Eran Agmon, Ion I. Moraru. (2026) BioSimulations platform. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21127423

Ezequiel Valencia, James C. Schaff, Eran Agmon, Ion I. Moraru. (2026) compose-api. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21127422

Connor McShaffrey, Eran Agmon, Randall D. Beer. (2026) Matters of life and death in computational cell biology. npj Systems Biology and Applications, 12(1) https://doi.org/10.1038/s41540-026-00718-y

Zhenzhen Zhao, Karla Díaz-Rodríguez, Andrea A.E. Mendez, Lisandro M. Sommer, Pedro Mendes, Fernando C. Soncini, Susana K. Checa, Teresita Padilla‐Benavides, JOSÉ M. ARGÜELLO. (2026) CuiT is a Cu importer required for metal homeostasis in Salmonella enterica. Biochemistry and Biophysics Reports, 46: 102581-102581 https://doi.org/10.1016/j.bbrep.2026.102581

Herbert M. Sauro, Eran Agmon, Michael L. Blinov, John H. Gennari, Joseph L. Hellerstein, Adel Heydarabadipour, Bartholomew Jardine, Elebeoba E. May, David Phillip Nickerson, Lucian P. Smith, Gary D. Bader, Frank T. Bergmann, Patrick M. Boyle, Andreas Dräger, James R. Faeder, Song Lin Feng, Juliana Freire, Fabian Fröhlich, James A. Glazier, Thomas E. Gorochowski, Tomáš Helikar, Henning Hermjakob, Stefan Hoops, Peter J. Hunter, Princess I. Imoukhuede, Sarah Keating, Matthias König, Reinhard Laubenbacher, Leslie M. Loew, Carlos Fernandez Lopez, William W. Lytton, Rahuman S. Malik-Sheriff, Andrew D. McCulloch, Pedro Mendes, Lealem Mulugeta, Chris J. Myers, Jerry G. Myers, Anna Niarakis, David D. van Niekerk, Brett G. Olivier, Alexander A. Patrie, Ellen M. Quardokus, Nicole Erika Radde, Johann M. Rohwer, Sven Sahle, James C. Schaff, Falk Schreiber, T. J. Sego, Janis Shin, Jacky L. Snoep, Rajanikanth Vadigepalli, H. Steven Wiley, Dagmar Waltemath, Ion I. Moraru. (2026) From FAIR to CURE: guidelines for computational models of biological systems. npj Systems Biology and Applications, 12(1) https://doi.org/10.1038/s41540-026-00651-0

Reesha J. Patel, Michael L. Blinov. (2026) Rules railroad: Syntax-inspired diagrams for visualizing and understanding rule-based model specifications. PLoS Computational Biology, 22(3): e1014121-e1014121 https://doi.org/10.1371/journal.pcbi.1014121

Abhijit Deb Roy, Cristian Saez Gonzalez, Stanislauskas Milda, Farid Shahid, Eesha Yadav, Jalil Rezek, Takanari Inoue. (2026) OptoTAT reveals microtubule acetylation as a rapid trigger for GEF-H1–mediated cell migration. The Journal of Cell Biology, 225(5) https://doi.org/10.1083/jcb.202508095

Bilal Shaikh, Jonathan R. Karr, Alexander Patrie, James C. Schaff, Michael L. Blinov, Eran Agmon, Ion I. Moraru. (2026) BioSimulations. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21070398

Rudradeep Mukherjee, Michael J. Guertin. (2026) Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate. Nucleic Acids Research, 54(4) https://doi.org/10.1093/nar/gkag128

Jinhong Dong, Michael J. Guertin. (2026) Molecular Mechanisms of Transcription Factors with Dual Activator and Repressor Functions. Molecular and Cellular Biology, 46(6): 632-640 https://doi.org/10.1080/10985549.2026.2619741

Hasan Balcı, Adrien Rougny, Rupert W. Overall, Irina Balaur, Michael L. Blinov, Hanna Borlinghaus, Emek Demir, Andreas Dräger, Robin Haw, Alexander Mazein, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Vasundra Touré, Alice Villéger, Tobias Czauderna, Uğur Doğrusöz, Augustin Luna. (2026) Systems biology graphical notation: process description language level 1 version 2.1. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics https://doi.org/10.1515/jib-2025-0018

Abhijit Deb Roy, Elmer Rho, Takanari Inoue. (2026) Guiding Cells with Light and Chemicals: A Toolbox for Dynamic Studies of Cell Migration. Cold Spring Harbor Perspectives in Biology, 18(7): a041754-a041754 https://doi.org/10.1101/cshperspect.a041754

2025

Eran Agmon, Ryan K Spangler. (2025) Process Bigraphs and the Architecture of Compositional Systems Biology. arXiv (Cornell University) N/A

Jeffrey C. Hoch, Katherine A. Henzler‐Wildman, Arthur S. Edison, Chad M. Rienstra, Christopher Bontempi, Jonathan R. Wedell, Gerard Weatherby, Harrison Burr, Yulia E. Pustovalova, Seenat Thongdee, Michael Robert Gryk, Alexandra Pozhidaeva, Bernd Simon, Qi Cheng, Michael P. Wilson, Ion I. Moraru, Laura Morris, John Glushka, Mario Uchimiya, Alexander Eletsky, Archer Moore, John H. Grimes, Alexander L. Paterson, Songlin Wang, Paulo Pinheiro, Boden H. Vanderloop, Mark W. Maciejewski. (2025) Scalable cyberinfrastructure for experimental NMR data. Scientific Data, 13(1): 131-131 https://doi.org/10.1038/s41597-025-06446-y

Lucian P. Smith, Rahuman S. Malik‐Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R. Karr, Bilal Shaikh, Logan Drescher, Ion I. Moraru, James C. Schaff, Eran Agmon, Alexander A. Patrie, Michael L. Blinov, Joseph L. Hellerstein, Elebeoba E. May, David Phillip Nickerson, John H. Gennari, Herbert M. Sauro. (2025) Verification and reproducible curation of the BioModels repository. PLoS Computational Biology, 21(12): e1013239-e1013239 https://doi.org/10.1371/journal.pcbi.1013239

Xihua Qiu, Yamin Liu, Paola Vera‐Licona, Eran Agmon, Kshitiz Gupta, Yasir Suhail. (2025) Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers. npj Systems Biology and Applications, 11(1): 136-136 https://doi.org/10.1038/s41540-025-00612-z

Dan Dragos Vasilescu, James C. Schaff, Ion I. Moraru, Michael L. Blinov. (2025) Visualizing mechanistic models by integrating site-specific molecular details into reaction networks. Frontiers in Molecular Biosciences, 12: 1681081-1681081 https://doi.org/10.3389/fmolb.2025.1681081

Francesco Giardini, Camilla Olianti, Gerard A. Marchal, Fernando Otaviano Campos, Valentina Romanelli, Joshua Steyer, Josef Madl, Roberto Piersanti, Giulia Arecchi, Induja Perumal Vanaja, Valentina Biasci, Eva A. Rog‐Zielinska, Gabriella Nesi, Leslie M. Loew, Elisabetta Cerbai, Stephen P. Chelko, Francesco Regazzoni, Axel Loewe, Martin J. Bishop, Marco Mongillo, Peter Karl Kohl, Tania Zaglia, Callum Michael Zgierski-Johnston, Leonardo Sacconi. (2025) Correlative imaging integrates electrophysiology with three-dimensional murine heart reconstruction to reveal electrical coupling between cell types. Nature Cardiovascular Research, 4(11): 1466-1486 https://doi.org/10.1038/s44161-025-00728-9

James C. Schaff, Lucian P. Smith, Ion I. Moraru. (2025) biosim-client. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21127428

Stephen Curry, Eunice Mercado-Lara, Virginia Arechavala‐Gomeza, C. Glenn Begley, Christophe Sébastien Bernard, René Bernard, Stefano Bertuzzi, Needhi Bhalla, Dawn Bowers, Samuel Brod, Chris Chambers, Michael R. P. Dougherty, Yensi Flores Bueso, Stefânia Forner, Alexandra L. J. Freeman, Magali Haas, Darla P. Henderson, Kanika Khanna, Rebecca N Lawrence, Kifayathullah Liakath‐Ali, Christine M. Liu, Neil A. Malhotra, José G. Merino, Edward A. Miguel, Rachel Miles, Mary Munson, Shinichi Nakagawa, Robert Nobles, Joy Owango, Michel Tuan Pham, Gina R. Poe, Alexandra N. Ramirez, Sarvenaz Sarabipour, Jill L. Silverman, Laura N. Smith, P. Sriramarao, Paul W. Sternberg, Geeta Krishna Swamy, Malu Gámez Tansey, Gonzalo E. Torres, Erick H. Turner, Lauren von Klinggraeff, Frances Weis‐Garcia. (2025) Ending publication bias: A values-based approach to surface null and negative results. PLoS Biology, 23(9): e3003368-e3003368 https://doi.org/10.1371/journal.pbio.3003368

Anna Niarakis, Gary C. An, Luiz Carlos Maia Ladeira, Noriko F. Hiroi, Athina Papadopoulou, Francis P. Crawley, Niloofar Nikaein, Laurence Calzone, Eirini Tsirvouli, Hasan Balcı, Marina Esteban‐Medina, Lorenzo Veschini, Ozan Özışık, Francesco Messina, Malvina Marku, Van Du T. Tran, Arnau Montagud, Nikola Schlosserova, Yashwanth Subbannayya, Martina Kutmon, Michael L. Blinov, Rahuman S. Malik‐Sheriff, Robert D. Phair, Peter John Hunter, Kristin Reiche, Jasmin Fisher, Liesbet Geris, Yaron Ilan, James A. Glazier, Philippe E. Moingeon, Reinhard Laubenbacher. (2025) Building immune digital twins: An international and transdisciplinary community effort. ImmunoInformatics, 20: 100060-100060 https://doi.org/10.1016/j.immuno.2025.100060

Shermeen Khan, James Wicander, George Korza, Rebecca Caldbeck, Ann E. Cowan, Graham R. CHRISTIE, Peter Setlow. (2025) Resistance and germination of spores of Bacillus species lacking members of a spore integral inner membrane protein family and locations of these proteins in spores. Journal of Bacteriology, 207(10): e0021725-e0021725 https://doi.org/10.1128/jb.00217-25

Junaid M. Afzal, Yasir Suhail, Wenqiang Du, Yamin Liu, Ramalakshmi Ramasamy, Zukai Liu, Ruchi Goyal, Ashkan Novin, Sameera Suhail, Jamie D. Maziarz, Khadija H. Wali, Paul Robson, Günter P. Wagner, Kshitiz Gupta. (2025) Evidence for coopetition at the maternal–fetal interface shaping placental invasion. Proceedings of the National Academy of Sciences, 122(36): e2323038122-e2323038122 https://doi.org/10.1073/pnas.2323038122

Yasir Suhail, Wenqiang Du, Junaid M. Afzal, Günter P. Wagner, Kshitiz Gupta. (2025) Identifying genes underlying parallel evolution of stromal resistance to placental and cancer invasion. npj Systems Biology and Applications, 11(1): 95-95 https://doi.org/10.1038/s41540-025-00577-z

Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovács‐Kása, Brian Herb Annex, Victoria L. Bautch, Feilim Mac Gabhann. (2025) Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells. PLoS Computational Biology, 21(7): e1013254-e1013254 https://doi.org/10.1371/journal.pcbi.1013254

Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovács‐Kása, Brian Herb Annex, Victoria L. Bautch, Feilim Mac Gabhann. (2025) Abstract 1785 Mechanisms of VEGF Receptor Trafficking Dynamics and Regulation. Journal of Biological Chemistry, 301(5): 108975-108975 https://doi.org/10.1016/j.jbc.2025.108975

Sarvenaz Sarabipour. (2025) Abstract 1375 Improving Academic Mentorship. Journal of Biological Chemistry, 301(5): 108579-108579 https://doi.org/10.1016/j.jbc.2025.108579

Rudradeep Mukherjee, Michael J. Guertin. (2025) Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2025.03.27.645809

Srdjan D. Antic, Ping Yan, Corey D. Acker, Olivia T. Spagnola, Zehra Yagmur Erol, Ozge Baser, Leslie M. Loew. (2025) ElectroFluor Voltage‐Sensitive Dyes: Comprehensive Analysis of Wavelength‐Dependent Sensitivity and Cross‐Channel Bleed‐Through. Journal of Biophotonics, 18(8): e70008-e70008 https://doi.org/10.1002/jbio.70008

Joseph Masison, Pedro Mendes. (2025) Mathematical modeling reveals ferritin as the strongest cellular driver of dietary iron transfer block in enterocytes. PLoS Computational Biology, 21(3): e1012374-e1012374 https://doi.org/10.1371/journal.pcbi.1012374

Thomas G. Scott, Michael J. Guertin. (2025) Rapid protein degradation systems to determine gene function in vivo. Lab Animal, 54(3): 66-67 https://doi.org/10.1038/s41684-025-01519-2

M.K. Jayanthi Kannan, Gabrielle Bridgewater, Ming Zhang, Michael L. Blinov. (2025) Leveraging public AI tools to explore systems biology resources in mathematical modeling. npj Systems Biology and Applications, 11(1): 15-15 https://doi.org/10.1038/s41540-025-00496-z

James C. Schaff, Lucian P. Smith, Ion I. Moraru. (2025) BioSimulations runutils. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21127429

Lucian P. Smith, Rahuman S. Malik‐Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R. Karr, Bilal Shaikh, Logan Drescher, Ion I. Moraru, James C. Schaff, Eran Agmon, Alexander A. Patrie, Michael L. Blinov, Joseph L. Hellerstein, Elebeoba E. May, David Phillip Nickerson, John H. Gennari, Herbert M. Sauro. (2025) Verification and reproducible curation of the BioModels repository. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2025.01.16.633337

Mei Liang, Lee Ringham, Changning Ye, Yan Xu, Nathan Schaumburger, Mikolaj Cieslak, Michael L. Blinov, Przemysław Prusinkiewicz, Yao‐Wu Yuan. (2025) From spots to stripes: Evolution of pigmentation patterns in monkeyflowers via modulation of a reaction-diffusion system and its prepatterns. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2025.01.10.632501

Yasir Suhail, Yamin Liu, Junaid M. Afzal, Wenqiang Du, Paul Robson, Ashkan Novin, Rama Ramasamy, Kshitiz Gupta. (2025) Extravillous trophoblasts reverse the decidualization induced increase in matrix production by secreting TGFβ antagonists Emilin-1 and Gremlin-1. Cells and Development, 181: 203994-203994 https://doi.org/10.1016/j.cdev.2025.203994

2024

Mikhail D. Magnitov, Michela Maresca, Noemí Alonso Saiz, Hans Teunissen, Jinhong Dong, Kizhakke Mattada Sathyan, Luca Braccioli, Michael J. Guertin, Elzo de Wit. (2024) ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF. Molecular Cell, 85(1): 24-41.e11 https://doi.org/10.1016/j.molcel.2024.11.031

Abhijit Deb Roy, Cristian Saez Gonzalez, Farid Shahid, Eesha Yadav, Takanari Inoue. (2024) Optogenetically Induced Microtubule Acetylation Unveils the Molecular Dynamics of Actin-Microtubule Crosstalk in Directed Cell Migration. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2024.12.01.626286

Bilal Shaikh, Jonathan R. Karr, Alexander Patrie, James C. Schaff, Michael L. Blinov, Eran Agmon, Ion I. Moraru. (2024) BioSimulations. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21070330

Anna Niarakis, Reinhard Laubenbacher, Gary C. An, Yaron Ilan, Jasmin Fisher, Åsmund Flobak, Kristin Reiche, María Rodríguez Martínez, Liesbet Geris, Luiz Carlos Maia Ladeira, Lorenzo Veschini, Michael L. Blinov, Francesco Messina, Luís L. Fonseca, Sandra Saraiva Ferreira, Arnau Montagud, Vincent Noël, Malvina Marku, Eirini Tsirvouli, Marcella M. Torres, Leonard A. Harris, T. J. Sego, Robert Chase Cockrell, Amanda E. Shick, Hasan Balcı, Albin Salazar, Kinza Rian, Ahmed Abdelmonem Hemedan, Marina Esteban‐Medina, Bernard Staumont, Esteban Abelardo Hernandez-Vargas, Shiny Martis B, Alejandro Madrid-Valiente, Panagiotis Karampelesis, Luis Sordo Vieira, Pradyumna Vinod Harlapur, Alexander Jan Kulesza, Niloofar Nikaein, Winston Garira, Rahuman S. Malik‐Sheriff, Juilee Thakar, Van Du T. Tran, José Carbonell‐Caballero, Soroush Safaei, Alfonso Valencia, Andrei Y. Zinovyev, James A. Glazier. (2024) Immune digital twins for complex human pathologies: applications, limitations, and challenges. npj Systems Biology and Applications, 10(1): 141-141 https://doi.org/10.1038/s41540-024-00450-5

Lindsay Barnum, Mohamadmahdi Samandari, Yasir Suhail, Steven Toro, Ashkan Novin, Pejman Ghelich, Jacob P. Quint, Farnooosh Saeedinejad, Manu Komma, Kshitiz Gupta, Ali Tamayol. (2024) Biodegradable Oxygen‐Generating Microneedle Patches for Regenerative Medicine Applications. Advanced NanoBiomed Research, 5(1): 2400093-2400093 https://doi.org/10.1002/anbr.202400093

Eran Agmon. (2024) Foundations of a Compositional Systems Biology.. PubMed N/A

Jinhong Dong, Kizhakke Mattada Sathyan, Thomas G. Scott, Rudradeep Mukherjee, Michael J. Guertin. (2024) ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes. Nucleic Acids Research, 53(2) https://doi.org/10.1093/nar/gkae1182

Jonathan R. Karr, Lucian P. Smith, Alexander Patrie, Logan Drescher, James C. Schaff, Ion I. Moraru. (2024) BioSimulators utils. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21126775

Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn M. Quigley, Anita Kovács‐Kása, Brian Herb Annex, Victoria L. Bautch, Feilim Mac Gabhann. (2024) Impact of ligand binding on VEGFR1, VEGFR2, and NRP1 localization in human endothelial cells. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2024.09.29.615728

Wenqiang Du, Ashkan Novin, Yamin Liu, Junaid M. Afzal, Yasir Suhail, Shaofei Liu, Nicole R Gavin, Jennifer R. Jorgensen, Christopher Michael Morosky, Reinaldo Figueroa, Tannin A. Schmidt, Melinda E. Sanders, MOLLY A. BREWER, Kshitiz Gupta. (2024) Scar matrix drives Piezo1 mediated stromal inflammation leading to placenta accreta spectrum. Nature Communications, 15(1): 8379-8379 https://doi.org/10.1038/s41467-024-52351-0

Jonathan R. Karr, Logan Drescher, Lucian P. Smith, Alexander Patrie, Eran Agmon, Ion I. Moraru. (2024) BioSimulators test suite. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21126771

Blair M. Lyons, Saurabh S. Mogre, Karthik Vegesna, Jessica S. Yu, Mark H Hansen, Aadarsh Raghunathan, Graham T. Johnson, Eran Agmon, Matthew Akamatsu. (2024) Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist. PubMed, 2025 https://doi.org/10.17912/micropub.biology.001347

Yasir Suhail, Yamin Liu, Wenqiang Du, Junaid M. Afzal, Xihua Qiu, Amina Atiq, Paola Vera‐Licona, Eran Agmon, Kshitiz Gupta. (2024) Oscillatory hypoxia induced gene expression predicts low survival in human breast cancer patients. Molecular Carcinogenesis, 63(12): 2305-2315 https://doi.org/10.1002/mc.23810

Michael L. Blinov, Susan D. Mertins. (2024) Editorial: Network-based mathematical modeling in cell and developmental biology. Frontiers in Cell and Developmental Biology, 12: 1475005-1475005 https://doi.org/10.3389/fcell.2024.1475005

Aniruddha Chattaraj, Zeynep Baltaci, Steve S. Chung, Bruce J. Mayer, Leslie M. Loew, Jonathon A. Ditlev. (2024) Measurement of solubility product reveals the interplay of oligomerization and self-association for defining condensate formation. Molecular Biology of the Cell, 35(9): ar122-ar122 https://doi.org/10.1091/mbc.e24-01-0030

Sarvenaz Sarabipour, Paul Macklin, Natalie M. Niemi. (2024) Improving academic mentorship practices. Nature Human Behaviour, 8(7): 1228-1231 https://doi.org/10.1038/s41562-024-01910-y

Noah Liguori-Bills, Michael L. Blinov. (2024) bnglViz: online visualization of rule-based models. Bioinformatics, 40(6) https://doi.org/10.1093/bioinformatics/btae351

Jinhong Dong, Thomas G. Scott, Rudradeep Mukherjee, Michael J. Guertin. (2024) ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2024.05.13.594008

John W. Hickey, Eran Agmon, Nina B. Horowitz, Tze-Kai Tan, Matthew Lamore, John B. Sunwoo, Markus W. Covert, Garry P. Nolan. (2024) Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy. Cell Systems, 15(4): 322-338.e5 https://doi.org/10.1016/j.cels.2024.03.004

Thomas G. Scott, Kizhakke Mattada Sathyan, Daniel G. Gioeli, Michael J. Guertin. (2024) TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells. PLoS Genetics, 20(2): e1011159-e1011159 https://doi.org/10.1371/journal.pgen.1011159

Sharif M. Ridwan, Autumn Twillie, Samaneh Poursaeid, Emma Kristine Beard, Muhammed Burak Bener, Matthew Antel, Ann E. Cowan, Shinya Matsuda, Mayu Inaba. (2024) Diffusible fraction of niche BMP ligand safeguards stem-cell differentiation. Nature Communications, 15(1): 1166-1166 https://doi.org/10.1038/s41467-024-45408-7

Karthik Vegesna, Saurabh S. Mogre, Jessica Yu, Blair M. Lyons, Aadarsh Raghunathan, Eran Agmon, Matthew Akamatsu, Graham T. Johnson. (2024) Comparing spatial biophysical simulations across scales and methods. Biophysical Journal, 123(3): 130a-131a https://doi.org/10.1016/j.bpj.2023.11.907

Jonathon A. Ditlev, Zeynep Baltaci, Aniruddha Chattaraj, Bruce J. Mayer, Leslie M. Loew. (2024) Exploring the solubility product concept for describing the formation of biomolecular condensates by comparing in vitro and in silico systems. Biophysical Journal, 123(3): 445a-445a https://doi.org/10.1016/j.bpj.2023.11.2721

Aniruddha Chattaraj, Zeynep Baltaci, Bruce J. Mayer, Leslie M. Loew, Jonathon A. Ditlev. (2024) Measurement of solubility product in a model condensate reveals the interplay of small oligomerization and self-association. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2024.01.23.576869

Yasir Suhail, Yamin Liu, Wenqiang Du, Junaid M. Afzal, Xihua Qiu, Amina Atiq, Paola Vera‐Licona, Eran Agmon, Kshitiz Gupta. (2024) Oscillatory Hypoxia Induced Unfolded Protein Folding Response Gene Expression Predicts Low Survival in Human Breast Cancer Patients. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2024.01.25.577274

2023

John W. Hickey, Maximillian Haist, Nina B. Horowitz, Chiara Caraccio, Yuqi Tan, Andrew J. Rech, Marc‐Andrea Baertsch, Xavier Rovira Clavé, Bokai Zhu, Gustavo Vazquez, Graham L. Barlow, Eran Agmon, Yury Goltsev, John B. Sunwoo, Markus W. Covert, Garry P. Nolan. (2023) T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. Cell Reports, 42(12): 113494-113494 https://doi.org/10.1016/j.celrep.2023.113494

Sylwia Hasterok, Thomas G. Scott, Devin G. Roller, Adam Spencer, Arun Brendan Dutta, Kizhakke Mattada Sathyan, Daniel E. Frigo, Michael J. Guertin, Daniel G. Gioeli. (2023) SAT634 The Androgen Receptor Does Not Directly Regulate The Transcription Of DNA Damage Response Genes. Journal of the Endocrine Society, 7(Supplement_1) https://doi.org/10.1210/jendso/bvad114.2204

Sylwia Hasterok, Thomas G. Scott, Devin G. Roller, Adam Spencer, Arun Brendan Dutta, Kizhakke Mattada Sathyan, Daniel E. Frigo, Michael J. Guertin, Daniel G. Gioeli. (2023) The Androgen Receptor Does Not Directly Regulate the Transcription of DNA Damage Response Genes. Molecular Cancer Research, 21(12): 1329-1341 https://doi.org/10.1158/1541-7786.mcr-23-0358

Jonathan R. Karr, Logan Drescher, Lucian P. Smith, Alexander Patrie, Eran Agmon, Ion I. Moraru. (2023) BioSimulators test suite. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21126770

Thomas G. Scott, Kizhakke Mattada Sathyan, Daniel G. Gioeli, Michael J. Guertin. (2023) TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2023.07.03.547524

Ann E. Cowan, Leslie M. Loew. (2023) Beyond analytic solution: Analysis of FRAP experiments by spatial simulation of the forward problem. Biophysical Journal, 122(18): 3722-3737 https://doi.org/10.1016/j.bpj.2023.06.013

Christopher J. Skalnik, Sean Cheah, Mica Y. Yang, Mattheus Wolff, Ryan K. Spangler, Lee Talman, Jerry H. Morrison, Shayn M. Peirce, Eran Agmon, Markus W. Covert. (2023) Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses. PLoS Computational Biology, 19(6): e1011232-e1011232 https://doi.org/10.1371/journal.pcbi.1011232

Pedro Mendes. (2023) Reproducibility and FAIR principles: the case of a segment polarity network model. Frontiers in Cell and Developmental Biology, 11: 1201673-1201673 https://doi.org/10.3389/fcell.2023.1201673

Aniruddha Chattaraj, Indivar Nalagandla, Leslie M. Loew, Michael L. Blinov. (2023) MolClustPy: a Python package to characterize multivalent biomolecular clusters. Bioinformatics, 39(6) https://doi.org/10.1093/bioinformatics/btad385

Zhen Wang, Hongkui Li, Yuhan Li, Zhuanli Wu, Hui Ai, Ming Zhang, Libin Rong, Michael L. Blinov, Qi Tong, Litao Liu, Honglei Sun, Juan Pu, Wenhai Feng, Jinhua Liu, Yipeng Sun. (2023) Mixed selling of different poultry species facilitates emergence of public-health-threating avian influenza viruses. Emerging Microbes & Infections, 12(1): 2214255-2214255 https://doi.org/10.1080/22221751.2023.2214255

Sylwia Hasterok, Thomas G. Scott, Devin G. Roller, Adam Spencer, Arun Brendan Dutta, Kizhakke Mattada Sathyan, Daniel E. Frigo, Michael J. Guertin, Daniel G. Gioeli. (2023) The androgen receptor does not directly regulate the transcription of DNA damage response genes. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2023.05.13.540653

Nathan Schaumburger, Joel Pally, Ion I. Moraru, Jatupol Kositsawat, George A. Kuchel, Michael L. Blinov. (2023) Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology, 3: 1079070-1079070 https://doi.org/10.3389/fnetp.2023.1079070

Graham T. Johnson, Eran Agmon, Matthew Akamatsu, Emma K. Lundberg, Blair M. Lyons, Wei Ouyang, Omar A. Quintero, Megan M. Riel-Mehan, Susanne M. Rafelski, Rick Horwitz. (2023) Building the next generation of virtual cells to understand cellular biology. Biophysical Journal, 122(18): 3560-3569 https://doi.org/10.1016/j.bpj.2023.04.006

Pedro Mendes. (2023) Dataset for “Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model”. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.7772570

Linda S. Archambault, Sherli Koshy-Chenthittayil, Angela Knight Thompson, Anna I. Dongari‐Bagtzoglou, Reinhard Laubenbacher, Pedro Mendes. (2023) Corrected and Republished from: “Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling”. mSphere, 8(2): e0065622-e0065622 https://doi.org/10.1128/msphere.00656-22

Aniruddha Chattaraj, Indivar Nalagandla, Leslie M. Loew, Michael L. Blinov. (2023) MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2023.03.14.532640

Ann E. Cowan, Leslie M. Loew. (2023) Beyond analytic solution: analysis of FRAP experiments by spatial simulation of the forward problem. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2023.03.05.531160

Piotr Przanowski, Róża K. Przanowska, Michael J. Guertin. (2023) ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation. Communications Biology, 6(1): 231-231 https://doi.org/10.1038/s42003-023-04611-w

James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith. (2023) SBML level 3 package: spatial processes, version 1, release 1. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 20(1) https://doi.org/10.1515/jib-2022-0054

George Korza, Sarah DePratti, Daniel Fairchild, James Wicander, Julia Kanaan, Hannah Shames, Frank C. Nichols, Ann E. Cowan, Stanley Brul, Peter Setlow. (2023) Expression of the 2Duf protein in wild-typeBacillus subtilisspores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide. Journal of Applied Microbiology, 134(3) https://doi.org/10.1093/jambio/lxad040

Arun Brendan Dutta, Daniel S. Lank, Róża K. Przanowska, Piotr Przanowski, Lixin Wang, Bao Han Nguyen, Ninad M. Walavalkar, Fabiana M. Duarte, Michael J. Guertin. (2023) Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis. Genome Research, 33(3): 314-331 https://doi.org/10.1101/gr.277559.122

Joseph Masison, Pedro Mendes. (2023) Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics. PLoS ONE, 18(2): e0281401-e0281401 https://doi.org/10.1371/journal.pone.0281401

Michael L. Blinov, Nathan Schaumburger, Yao‐Wu Yuan. (2023) Monkeying around with monkeyflowers: Modeling pigmentation patterning mechanisms in Mimulus. Biophysical Journal, 122(3): 413a-413a https://doi.org/10.1016/j.bpj.2022.11.2244

Michael L. Blinov, Ion I. Moraru, James C. Schaff, Leslie M. Loew. (2023) Virtual cell modeling and simulation software. Biophysical Journal, 122(3): 414a-414a https://doi.org/10.1016/j.bpj.2022.11.2249

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2023) Virtual Cell 7.4.0.113. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21122838

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2023) Virtual Cell 7.4.0.111. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121845

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2023) Virtual Cell 7.4.0.112. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121846

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2023) Virtual Cell 7.4.0.110. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121839

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2023) Virtual Cell 7.4.0.109. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121838

2022

Thomas G. Scott, ANDRÉ LUIS MARTINS, Michael J. Guertin. (2022) Processing and evaluating the quality of genome-wide nascent transcription profiling libraries. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2022.12.14.520463

Jacob B. Wolpe, ANDRÉ LUIS MARTINS, Michael J. Guertin. (2022) Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2022.12.08.519600

Yuting Liu, Elizabeth M. Bafaro, Ann E. Cowan, Robert E. Dempski. (2022) The transmembrane domains mediate oligomerization of the human ZIP4 transporter in vivo. Scientific Reports, 12(1): 21083-21083 https://doi.org/10.1038/s41598-022-24782-6

Joseph Masison, Pedro Mendes. (2022) Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2022.11.03.515078

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2022) Virtual Cell 7.4.0.80. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121578

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2022) Virtual Cell 7.4.0.66. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121452

Shengen Shawn Hu, Lin Liu, Qi Li, Wenjing Ma, Michael J. Guertin, Clifford A. Meyer, Ke Deng, Tingting Zhang, Chongzhi Zang. (2022) Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA. Nature Communications, 13(1): 5533-5533 https://doi.org/10.1038/s41467-022-33194-z

Sharif M. Ridwan, Autumn Twillie, Samaneh Poursaeid, Emma Kristine Beard, Muhammed Burak Bener, Matthew Antel, Ann E. Cowan, Shinya Matsuda, Mayu Inaba. (2022) Diffusible fraction of niche BMP ligand safeguards stem-cell differentiation. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2022.09.13.507868

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2022) Virtual Cell 7.4.0.51. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121335

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2022) Virtual Cell 7.4.0.48. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21121309

Jacob B. Wolpe, ANDRÉ LUIS MARTINS, Michael J. Guertin. (2022) Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling. NAR Genomics and Bioinformatics, 5(2): lqad054-lqad054 https://doi.org/10.1093/nargab/lqad054

Jacob O. Brunkard, Caren Chang, Bruce J. Mayer, Christian Meyer, Jen Sheen. (2022) ConducTORs of a Signaling Symphony: Metabolic and Hormone Responses Converge on TOR and EIN2 in plants.. Faculty Reviews, 11(12): 12-12 https://doi.org/10.12703/r-01-000008

Jacob B. Wolpe, Michael J. Guertin. (2022) Regional and Single Nucleotide Correction of Sequence Bias in Chromatin Accessibility Data. The FASEB Journal, 36(S1) https://doi.org/10.1096/fasebj.2022.36.s1.l7579

Michael J. Guertin, Bao N. Nguyen, Ninad M. Walavalkar, Fabiana M. Duarte, Arun Brendan Dutta. (2022) Kinetic networks identify key regulatory nodes and transcription factor functions in early adipogenesis. The FASEB Journal, 36(S1) https://doi.org/10.1096/fasebj.2022.36.s1.r3047

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua M. Cooper, John Detloff, Brian Drawert, Michel J. Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Rahuman S Malik Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J Myers, Aurélien Naldi, Tung V. N. Nguyen, David Phillip Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda Petzold, Ankita Priya, Anand Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C Schaff, Michael L Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr. (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research, 50(W1): W108-W114 https://doi.org/10.1093/nar/gkac331

Jonathan R. Karr, Logan Drescher, Eran Agmon, Ion I. Moraru. (2022) BioSimulators. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21127432

Róża K. Przanowska, Chase A. Weidmann, Shekhar Saha, Magdalena A. Cichewicz, Kate N. Jensen, Piotr Przanowski, Patrick S. Irving, Kevin A. Janes, Michael J. Guertin, Kevin M. Weeks, Anindya Dutta. (2022) Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. Cell Reports, 38(7): 110361-110361 https://doi.org/10.1016/j.celrep.2022.110361

Aniruddha Chattaraj, Ming Hao Wang, Michael L. Blinov, Leslie M. Loew. (2022) Statistical methods for analyzing clustering and phase transitions of multivalent biomolecules. Biophysical Journal, 121(3): 308a-308a https://doi.org/10.1016/j.bpj.2021.11.1220

Bilal Shaikh, Lucian P. Smith, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr. (2022) Integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualizations enable facile model reuse with biosimulations. Biophysical Journal, 121(3): 127a-127a https://doi.org/10.1016/j.bpj.2021.11.2118

2021

Linda S. Archambault, Sherli Koshy-Chenthittayil, Angela Knight Thompson, Anna I. Dongari‐Bagtzoglou, Reinhard Laubenbacher, Pedro Mendes. (2021) Understanding Lactobacillus paracasei and Streptococcus oralis Biofilm Interactions through Agent-Based Modeling. mSphere, 6(6): e0087521-e0087521 https://doi.org/10.1128/msphere.00875-21

Arun Brendan Dutta, Daniel S. Lank, Róża K. Przanowska, Piotr Przanowski, Lixin Wang, Bao Han Nguyen, Ninad M. Walavalkar, Fabiana M. Duarte, Michael J. Guertin. (2021) Kinetic networks identify Twist2 as a key regulatory node in adipogenesis. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.11.17.469040

ManSai Acón, Carsten Geiß, Jorge Torres-Calvo, Diana M. Bravo‐Estupiñan, Guillermo Ruben Oviedo, Jorge L. Arias-Arias, Luis A. Rojas-Matey, Edwin Baéz, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, Jose Andres Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Anne Régnier‐Vigouroux, Pedro Mendes, Rodrigo Mora-Rodríguez. (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. iScience, 24(12): 103407-103407 https://doi.org/10.1016/j.isci.2021.103407

Piotr Przanowski, Róża K. Przanowska, Michael J. Guertin. (2021) ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.10.27.466184

Shengen Shawn Hu, Lin L. Liu, Qi Li, Wenjing Ma, Michael J. Guertin, Clifford A. Meyer, Ke Deng, Tingting Zhang, Chongzhi Zang. (2021) Accurate estimation of intrinsic biases for improved analysis of bulk and single-cell chromatin accessibility sequencing data using SELMA. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.10.22.465530

Abhishekh Gupta, Pedro Mendes. (2021) ShinyCOPASI: a web-based exploratory interface for COPASI models. arXiv (Cornell University) https://doi.org/10.48550/arxiv.2110.03796

Aniruddha Chattaraj, Michael L. Blinov, Leslie M. Loew. (2021) The solubility product extends the buffering concept to heterotypic biomolecular condensates. eLife, 10 https://doi.org/10.7554/elife.67176

Jasia King, Kerbaï Saïd Eroumé, Roman K. Truckenmüller, Stefan Giselbrecht, Ann E. Cowan, Leslie M. Loew, Aurélie Carlier. (2021) Teaching Mathematical Modeling of Cellular Systems with the VCell MathModel. The Biophysicist, 3(1): 1-12 https://doi.org/10.35459/tbp.2021.000198

Róża K. Przanowska, Chase A. Weidmann, Shekhar Saha, Magdalena A. Cichewicz, Kate N. Jensen, Piotr Przanowski, Patrick S. Irving, Michael J. Guertin, Kevin M. Weeks, Anindya Dutta. (2021) Distinct MUNC lncRNA structural domains regulate transcription of different promyogenic factors. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.06.22.449443

Michael L. Blinov, John H. Gennari, Jonathan R. Karr, Ion I. Moraru, David Phillip Nickerson, Herbert M. Sauro. (2021) Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology. Current Opinion in Systems Biology, 27: 100350-100350 https://doi.org/10.1016/j.coisb.2021.06.001

Jasia King, Kerbaï Saïd Eroumé, Roman K. Truckenmüller, Stefan Giselbrecht, Ann E. Cowan, Leslie M. Loew, Aurélie Carlier. (2021) Ten steps to investigate a cellular system with mathematical modeling. PLoS Computational Biology, 17(5): e1008921-e1008921 https://doi.org/10.1371/journal.pcbi.1008921

Aniruddha Chattaraj, Michael L. Blinov, Leslie M. Loew. (2021) Author response: The solubility product extends the buffering concept to heterotypic biomolecular condensates. N/A https://doi.org/10.7554/elife.67176.sa2

Bilal Shaikh, Gnaneswara Marupilla, Michael Wilson, Michael L. Blinov, Ion I. Moraru, Jonathan R. Karr. (2021) RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. Nucleic Acids Research, 49(W1): W597-W602 https://doi.org/10.1093/nar/gkab411

Linda S. Archambault, Sherli Koshy-Chenthittayil, Angela Knight Thompson, Anna I. Dongari‐Bagtzoglou, Reinhard Laubenbacher, Pedro Mendes. (2021) Understanding Lactobacillus paracasei and Streptococcus oralis biofilm interactions through agent-based modeling. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.04.29.441960

ManSai Acón, Carsten Geiß, Jorge Torres-Calvo, Diana M. Bravo‐Estupiñan, Guillermo Ruben Oviedo, Jorge L. Arias-Arias, Luis A. Rojas-Matey, Edwin Baéz, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, Jose Andres Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Anne Régnier‐Vigouroux, Pedro Mendes, Rodrígo Mora. (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.04.20.440572

Bilal Shaikh, Gnaneswara Marupilla, Michael Wilson, Michael L. Blinov, Ion I. Moraru, Jonathan R. Karr. (2021) runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2021.03.05.433787

Sherli Koshy-Chenthittayil, Linda S. Archambault, Dhananjai Senthilkumar, Reinhard Laubenbacher, Pedro Mendes, Anna I. Dongari‐Bagtzoglou. (2021) Agent Based Models of Polymicrobial Biofilms and the Microbiome—A Review. Microorganisms, 9(2): 417-417 https://doi.org/10.3390/microorganisms9020417

Adrien Rougny, Vasundra Touré, John S. Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein. (2021) SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Briefings in Bioinformatics, 22(5) https://doi.org/10.1093/bib/bbab049

Aniruddha Chattaraj, Michael L. Blinov, Leslie M. Loew. (2021) Modeling Multivalent Protein Phase Separations with Network-Free Rule-Based Modeling. Biophysical Journal, 120(3): 23a-23a https://doi.org/10.1016/j.bpj.2020.11.403

Aniruddha Chattaraj, Michael L. Blinov, Leslie M. Loew. (2021) Solubility Product Constant Governs Multivalent Protein Phase Separations. Biophysical Journal, 120(3): 208a-208a https://doi.org/10.1016/j.bpj.2020.11.1412

Anton V. Burakov, Ivan A. Vorobjev, Irina V. Semenova, Ann E. Cowan, John H. Carson, Yi Wu, Vladimir Rodionov. (2021) Persistent growth of microtubules at low density. Molecular Biology of the Cell, 32(5): 435-445 https://doi.org/10.1091/mbc.e20-08-0546

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2021) Virtual Cell 7.3.0.08. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21120911

ManSai Acón, Carsten Geiß, Jorge Torres-Calvo, Guillermo Ruben Oviedo, Jorge L. Arias-Arias, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, Jose Andres Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Anne Régnier‐Vigouroux, Pedro Mendes, Rodrigo Mora-Rodríguez. (2021) MYC Dosage Compensation is Mediated by miRNA-Transcription Factor Interactions in Aneuploid Cancer. SSRN Electronic Journal https://doi.org/10.2139/ssrn.3844728

2020

Aniruddha Chattaraj, Michael L. Blinov, Leslie M. Loew. (2020) Solubility product constant directs the formation of biomolecular condensates. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2020.12.26.424446

Sophia Ladyzhets, Matthew Antel, Taylor Simao, Nathan S. Gasek, Ann E. Cowan, Mayu Inaba. (2020) Self-limiting stem-cell niche signaling through degradation of a stem-cell receptor. PLoS Biology, 18(12): e3001003-e3001003 https://doi.org/10.1371/journal.pbio.3001003

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2020) Virtual Cell 7.3.0.01. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21120853

James C. Schaff, Dan Vasilescu, Frank Morgan, Fei Gao, Gerard Weatherby, Li Ye, Anuradha Lakshminarayana, Gnaneswara Marupilla, Michael L. Blinov, Ann E. Cowan, Michael Wilson, Jonathan R. Karr, Curtis Rueden, Bilal Shaikh, Ion I. Moraru. (2020) Virtual Cell 7.3.0.0. Zenodo (CERN European Organization for Nuclear Research) https://doi.org/10.5281/zenodo.21120846

Margaret E. Johnson, Athena Chen, James R. Faeder, Philipp Henning, Ion I. Moraru, Martin Meier-Schellersheim, Robert F. Murphy, Thorsten Prüstel, Julie A. Theriot, Adelinde M. Uhrmacher. (2020) Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry. Molecular Biology of the Cell, 32(2): 186-210 https://doi.org/10.1091/mbc.e20-08-0530

Adrien Rougny, Vasundra Touré, John S. Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein. (2020) SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2020.11.16.369330

Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, ROBERT FINN, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah Franziska Löchel, Maria Jesus Martin, Roman Martin, Julian Matschinske, Alice Carolyn McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Aine Niamh O’Toole, Nancy Ontiveros‐Palacios, Anton I. Petrov, Guillermo Andrés Rangel Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz. (2020) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22(2): 642-663 https://doi.org/10.1093/bib/bbaa232

Sarah Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank Bergmann, Andrew Finney, Colin S. Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S. Malik‐Sheriff, Stuart Moodie, Ion I. Moraru, Chris J. Myers, Aurélien Naldi, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Maciej J. Swat, Denis Thieffry, Leandro H. Watanabe, Darren J. Wilkinson, Michael L. Blinov, Kimberly Begley, James R. Faeder, Harold Gómez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson Lister, Daniel Lucio, Eric Mjolsness, Carole J. Proctor, Karthik Raman, Nicolás Rodríguez, Clifford A. Shaffer, Bruce E. Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Richard Wagner, Martin Meier‐Schellersheim, Herbert M. Sauro, Bernhard Ørn Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, Michael Hucka, SBML Level 3 Community members, Richard R. Adams, Nicholas A. Allen, Bastian R. Angermann, Marco Antoniotti, Gary D. Bader, Jan Červený, Mélanie Courtot, Chris D. Cox, Piero Dalle Pezze, Emek Demir, William S. Denney, Harish K. Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T. Evelo, Christoph Flamm, Ronan M. T. Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A. Harris, Ben Heavner, Ron Henkel, William S. Hlavacek, Bin Hu, Daniel R. Hyduke, Hidde de Jong, Nick Juty, Peter D. Karp, Jonathan R Karr, Douglas Bruce Kell, Roland Keller, Ilya N. Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon. (2020) SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16(8): e9110-e9110 https://doi.org/10.15252/msb.20199110

Margaret E. Johnson, Athena Chen, James R. Faeder, Philipp Henning, Ion I. Moraru, Martin Meier-Schellersheim, Robert F. Murphy, Thorsten Prüstel, Julie A. Theriot, Adelinde M. Uhrmacher. (2020) The Roles of Space and Stochasticity in Computational Simulations of Cellular Biochemistry: Quantitative Analysis and Qualitative Insights. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2020.07.02.185595

Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah Keating, Matthias König, Olga Krebs, Rahuman S. Malik‐Sheriff, David Phillip Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers. (2020) The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 17(2-3) https://doi.org/10.1515/jib-2020-0005

Frank Bergmann, Tobias Czauderna, Uğur Doğrusöz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, Augustin Luna. (2020) Systems biology graphical notation markup language (SBGNML) version 0.3. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 17(2-3) https://doi.org/10.1515/jib-2020-0016

Fengkai Zhang, Lucian P. Smith, Michael L. Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia, Sarah Keating, Nicolás Rodríguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier‐Schellersheim. (2020) Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 17(2-3) https://doi.org/10.1515/jib-2020-0015

Baoqing Ding, Erin L. Patterson, Srinidhi V. Holalu, Jingjian Li, Grace A. Johnson, Lauren E. Stanley, Anna B. Greenlee, Foen Peng, H. D. Bradshaw, Michael L. Blinov, Benjamin K. Blackman, Yao‐Wu Yuan. (2020) Two MYB Proteins in a Self-Organizing Activator-Inhibitor System Produce Spotted Pigmentation Patterns. Current Biology, 30(5): 802-814.e8 https://doi.org/10.1016/j.cub.2019.12.067

ManSai Acón, Guillermo Ruben Oviedo, Edwin Baéz, Gloriana Vásquez-Vargas, Jose Andres Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Pedro Mendes, Rodrígo Mora. (2020) Complex networks of miRNA-transcription factors mediate gene dosage compensation in aneuploid cancer. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2020.01.31.928507

Pedro Mendes, Enrico Girardi, Giulio Superti‐Furga, Douglas Bruce Kell. (2020) Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2020.01.16.909507

2019

Adam T. Lafontaine, Bruce J. Mayer, Kazuya Machida. (2019) Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data. Bioinformatics, 36(5): 1632-1633 https://doi.org/10.1093/bioinformatics/btz766

Ann E. Cowan, Pedro Mendes, Michael L. Blinov. (2019) ModelBricks—modules for reproducible modeling improving model annotation and provenance. npj Systems Biology and Applications, 5(1): 37-37 https://doi.org/10.1038/s41540-019-0114-3

Helena Firczuk, James Teahan, Pedro Mendes, John E.G. McCarthy. (2019) Multisite rate control analysis identifies ribosomal scanning as the sole high‐capacity/low‐flux‐control step in mRNA translation. FEBS Journal, 287(5): 925-940 https://doi.org/10.1111/febs.15059

Kizhakke Mattada Sathyan, Brian D. McKenna, Warren D. Anderson, Fabiana M. Duarte, Leighton J. Core, Michael J. Guertin. (2019) An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. Genes & Development, 33(19-20): 1441-1455 https://doi.org/10.1101/gad.328237.119

Kshitiz, Junaid M. Afzal, Yasir Suhail, Hao Chang, Chi V. Dang, Andre Levchenko. (2019) Abstract 4359: Oscillatory HIF-1α induction promotes proliferation of hypoxic cells through a lactate dependent quorum autophagy response. Molecular and Cellular Biology / Genetics, : 4359-4359 https://doi.org/10.1158/1538-7445.sabcs18-4359

Michael Hucka, Frank Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik‐Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang. (2019) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 16(2): 266-266 https://doi.org/10.1515/jib-2019-0021

Adrien Rougny, Vasundra Touré, Stuart Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Uğur Doğrusöz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly Sorokin, Falk Schreiber, Augustin Luna. (2019) Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 16(2) https://doi.org/10.1515/jib-2019-0022

Kizhakke Mattada Sathyan, Brian D. McKenna, Warren D. Anderson, Fabiana M. Duarte, Leighton J. Core, Michael J. Guertin. (2019) An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/585927

Meghan E. Ahern, Elizabeth M. Bafaro, Ann E. Cowan, Robert E. Dempski. (2019) Quantifying the Oligomeric State of hZIP4 on the Surface of Cells. Biochemistry, 58(13): 1705-1708 https://doi.org/10.1021/acs.biochem.9b00131

Jignesh H. Parmar, Pedro Mendes. (2019) A computational model to understand mouse iron physiology and disease. PLoS Computational Biology, 15(1): e1006680-e1006680 https://doi.org/10.1371/journal.pcbi.1006680

Natalie Stanford, Martin Scharm, Paul D. Dobson, Martin Golebiewski, Michael Hucka, Varun B. Kothamachu, David Phillip Nickerson, Stuart Owen, Jürgen Pahle, Ulrike Wittig, Dagmar Waltemath, Carole Goble, Pedro Mendes, Jacky L. Snoep. (2019) Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods in molecular biology, 2049: 285-314 https://doi.org/10.1007/978-1-4939-9736-7_17

2018

Dan Dragos Vasilescu, James B. Greene, James C. Schaff, Ion I. Moraru, Michael L. Blinov. (2018) Molecular Process Diagram: a precise, scalable and compact visualization of rule-based models. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/503359

A. G. Appu Rao, Gerardo Zavala, Abhijit Deb Roy, Richard E. Mains, Betty A. Eipper. (2018) A pH‐sensitive luminal His‐cluster promotes interaction of PAM with V‐ATPase along the secretory and endocytic pathways of peptidergic cells. Journal of Cellular Physiology, 234(6): 8683-8697 https://doi.org/10.1002/jcp.27528

Pedro Mendes. (2018) Reproducible Research Using Biomodels. Bulletin of Mathematical Biology, 80(12): 3081-3087 https://doi.org/10.1007/s11538-018-0498-z

Dagmar Waltemath, Frank Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Phillip Nickerson, Brett G. Olivier, Nicolás Rodríguez, Falk Schreiber, Lucian P. Smith, Fengkai Zhang, Éric Bonnet. (2018) Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences, 13(1): 17-17 https://doi.org/10.1186/s40793-018-0320-4

Jignesh H. Parmar, Julia Quintana, David Ramírez, Reinhard Laubenbacher, JOSÉ M. ARGÜELLO, Pedro Mendes. (2018) An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology, 110(3): 357-369 https://doi.org/10.1111/mmi.14086

Bruce J. Mayer, Ji Hoon Yu. (2018) Protein Clusters in Phosphotyrosine Signal Transduction. Journal of Molecular Biology, 430(22): 4547-4556 https://doi.org/10.1016/j.jmb.2018.05.040

Evan C Hadley, George A. Kuchel, Anne B. Newman, Heather G Allore, Jenna M. Bartley, Cindy S. Bergeman, Michael L. Blinov, Cathleen S Colon-Emeric, Firdaus S Dabhar, Laura L. Dugan, Chhanda Dutta, Basil A. Eldadah, Luigi Ferrucci, James L. Kirkland, Stephen B. Kritchevsky, Lewis Arnold Lipsitz, Neelesh K. Nadkarni, May J. Reed, Kenneth E. Schmader, Felipe Sierra, Stephanie A. Studenski, Ravi Varadhan, Jeremy D Walston, Heather Elizabeth Whitson, Raymond L. Yung. (2018) Corrigendum to: Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging. The Journals of Gerontology Series A, 73(7): 995-995 https://doi.org/10.1093/gerona/glx172

Jignesh H. Parmar, Pedro Mendes. (2018) A computational model to understand mouse iron physiology and diseases. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/323899

Michael Hucka, Frank Bergmann, Andreas Dräger, Stefan Hoops, Sarah Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson. (2018) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 15(1) https://doi.org/10.1515/jib-2017-0080

Jignesh H. Parmar, Julia Quintana, David Ramírez, Reinhard Laubenbacher, JOSÉ M. ARGÜELLO, Pedro Mendes. (2018) An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/301002

Michael Hucka, Frank Bergmann, Andreas Dräger, Stefan Hoops, Sarah Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson. (2018) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 15(1) https://doi.org/10.1515/jib-2017-0081

Judy E. Bloom, Carissa L. Sirois, Michael L. Blinov, Stormy J. Chamberlain, Leslie M. Loew. (2018) Examining UBE3A’s Possible Role in Dendritic Spine Morphogenesis. Biophysical Journal, 114(3): 666a-666a https://doi.org/10.1016/j.bpj.2017.11.3591

Abhishekh Gupta, Pedro Mendes. (2018) An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems. Computation, 6(1): 9-9 https://doi.org/10.3390/computation6010009

Dipika Gupta, Bo Lin, Ann E. Cowan, Christopher D. Heinen. (2018) ATR-Chk1 activation mitigates replication stress caused by mismatch repair-dependent processing of DNA damage. Proceedings of the National Academy of Sciences, 115(7): 1523-1528 https://doi.org/10.1073/pnas.1720355115

2017

Joshua A. Jadwin, Timothy G. Curran, Adam T. Lafontaine, Forest M. White, Bruce J. Mayer. (2017) Src homology 2 domains enhance tyrosine phosphorylation in vivo by protecting binding sites in their target proteins from dephosphorylation. Journal of Biological Chemistry, 293(2): 623-637 https://doi.org/10.1074/jbc.m117.794412

Michael L. Blinov, James C. Schaff, Dan Dragos Vasilescu, Ion I. Moraru, Judy E. Bloom, Leslie M. Loew. (2017) Compartmental and Spatial Rule-Based Modeling with Virtual Cell. Biophysical Journal, 113(7): 1365-1372 https://doi.org/10.1016/j.bpj.2017.08.022

Paul D. Dobson, Pedro Mendes, Douglas Bruce Kell, Neil Swainston. (2017) A Metabolic Reaction Balancing Web Service for Computational Systems Biology. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/187328

Neil Swainston, Riza Batista-Navarro, Pablo Carbonell, Paul D. Dobson, Mark S. Dunstan, Adrian J. Jervis, María Vinaixa, Alan R Williams, Sophia Ananiadou, Jean‐Loup Faulon, Pedro Mendes, Douglas Bruce Kell, Nigel Shaun Scrutton, Rainer Breitling. (2017) biochem4j: Integrated and extensible biochemical knowledge through graph databases. PLoS ONE, 12(7): e0179130-e0179130 https://doi.org/10.1371/journal.pone.0179130

Frank Bergmann, Stefan Hoops, Brian Klahn, Ursula Kummer, Pedro Mendes, Jürgen Pahle, Sven Sahle. (2017) COPASI and its applications in biotechnology. Journal of Biotechnology, 261: 215-220 https://doi.org/10.1016/j.jbiotec.2017.06.1200

Abhijit Deb Roy, Taofei Yin, Shilpa Choudhary, Vladimir Rodionov, Carol Coke Pilbeam, Yi Wu. (2017) Optogenetic activation of Plexin-B1 reveals contact repulsion between osteoclasts and osteoblasts. Nature Communications, 8(1): 15831-15831 https://doi.org/10.1038/ncomms15831

Mikhail Blinov, James C. Schaff, Dan Dragos Vasilescu, Ion I. Moraru, Judy E. Bloom, Leslie M. Loew. (2017) Compartmental and spatial rule-based modeling with Virtual Cell (VCell). bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/146225

Jignesh H. Parmar, Grey Davis, Hope Shevchuk, Pedro Mendes. (2017) Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. BMC Systems Biology, 11(1): 57-57 https://doi.org/10.1186/s12918-017-0431-3

Estelle Dacheux, Naglis Malys, Xiang Meng, Vinoy K. Ramachandran, Pedro Mendes, John E.G. McCarthy. (2017) Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Research, 45(11): 6981-6992 https://doi.org/10.1093/nar/gkx430

Evan C Hadley, George A. Kuchel, Anne B. Newman, Heather G Allore, Jenna M. Bartley, Cindy S. Bergeman, Michael L. Blinov, Cathleen S Colon-Emeric, Firdaus S Dabhar, Laura L. Dugan, Chhanda Dutta, Basil A. Eldadah, Luigi Ferrucci, James L. Kirkland, Stephen B. Kritchevsky, Lewis Arnold Lipsitz, Neelesh K. Nadkarni, May J. Reed, Kenneth E. Schmader, Felipe Sierra, Stephanie A. Studenski, Ravi Varadhan, Jeremy D Walston, Heather Elizabeth Whitson, Raymond L. Yung. (2017) Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging. The Journals of Gerontology Series A, 72(7): 980-990 https://doi.org/10.1093/gerona/glx015

Irina V. Semenova, Dipika Gupta, Takeo Usui, Ichiro Hayakawa, Ann E. Cowan, Vladimir Rodionov. (2017) Stimulation of microtubule-based transport by nucleation of microtubules on pigment granules. Molecular Biology of the Cell, 28(11): 1418-1425 https://doi.org/10.1091/mbc.e16-08-0571

Mark W. Maciejewski, Adam D. Schuyler, Michael Robert Gryk, Ion I. Moraru, Pedro R Romero, Eldon L. Ulrich, Hamid R. Eghbalnia, Miron Livny, Frank Delaglio, Jeffrey C. Hoch. (2017) NMRbox: A Resource for Biomolecular NMR Computation. Biophysical Journal, 112(8): 1529-1534 https://doi.org/10.1016/j.bpj.2017.03.011

Cibele Vieira Falkenberg, John H. Carson, Michael L. Blinov. (2017) Multivalent Molecules as Modulators of RNA Granule Size and Composition. Biophysical Journal, 113(2): 235-245 https://doi.org/10.1016/j.bpj.2017.01.031

Pierre Millard, Kieran Smallbone, Pedro Mendes. (2017) Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Computational Biology, 13(2): e1005396-e1005396 https://doi.org/10.1371/journal.pcbi.1005396

Madeleine Youngstrom, Aniruddha Chattaraj, Paul J. Michalski, James C. Schaff, Michael L. Blinov, Leslie M. Loew. (2017) Multivalent Signaling Clusters have Unique Sizes Determined by Membrane Localization and Excluded Volume: the Nephrin/Nck/N-WASP System. Biophysical Journal, 112(3): 281a-281a https://doi.org/10.1016/j.bpj.2016.11.1524

James C. Schaff, Dan Dragos Vasilescu, Ion I. Moraru, Leslie M. Loew, Michael L. Blinov. (2017) Extending Rule-Based Modeling to the Spatial Domain with Virtual Cell (VCELL). Biophysical Journal, 112(3): 451a-451a https://doi.org/10.1016/j.bpj.2016.11.2417

Cibele Vieira Falkenberg, John H. Carson, Michael L. Blinov. (2017) Modeling Analysis of RNA Granule Formation and Selectivity Mediated by Multivalent Interactions. Biophysical Journal, 112(3): 281a-281a https://doi.org/10.1016/j.bpj.2016.11.1521

Bruce J. Mayer. (2017) What Have We Learned from SH2 Domains?. Methods in molecular biology, 1555: 37-43 https://doi.org/10.1007/978-1-4939-6762-9_2

2016

James C. Schaff, Fei Gao, Ye Li, Igor L. Novak, Boris M. Slepchenko. (2016) Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Computational Biology, 12(12): e1005236-e1005236 https://doi.org/10.1371/journal.pcbi.1005236

Xiang Meng, Helena Firczuk, Paola Pietroni, Richard Westbrook, Estelle Dacheux, Pedro Mendes, John E.G. McCarthy. (2016) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Research, 45(2): 1015-1025 https://doi.org/10.1093/nar/gkw1194

Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer. (2016) COMODI: an ontology to characterise differences in versions of computational models in biology. Journal of Biomedical Semantics, 7(1): 46-46 https://doi.org/10.1186/s13326-016-0080-2

Jignesh H. Parmar, Grey Davis, Hope Shevchuk, Pedro Mendes. (2016) Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/062901

Dagmar Waltemath, Jonathan R. Karr, Frank Bergmann, Vijayalakshmi Chelliah, Michael Hucka, Marcus Krantz, Wolfram Liebermeister, Pedro Mendes, Chris J. Myers, Pınar Pir, Begum Alaybeyoglu, Naveen K. Aranganathan, Kambiz Baghalian, Arne T. Bittig, Paulo E. P. Burke, Matteo Cantarelli, Yin Hoon Chew, Rafael S. Costa, Joseph Cursons, Tobias Czauderna, Arthur P. Goldberg, Harold Gómez, Jens Hahn, Hameri Tuure, Daniel F. Hernandez Gardiol, Denis Kazakiewicz, Ilya N. Kiselev, Vincent R. Knight-Schrijver, Christian Knüpfer, Matthias König, Daewon Lee, Audald Lloret‐Villas, Nikita Mandrik, Kyle Medley, Bertrand Moreau, Hojjat Naderi‐Meshkin, Sucheendra K. Palaniappan, Daniel A. Priego-Espinosa, Martin Scharm, Mahesh Kumar Sharma, Kieran Smallbone, Natalie Stanford, Je-Hoon Song, Tom Theile, Milenko S. Tokić, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek Varusai, Leandro H. Watanabe, Florian Wendland, Markus Wolfien, James T. Yurkovich, Yan Zhu, Argyris Zardilis, Anna Zhukova, Falk Schreiber. (2016) Toward Community Standards and Software for Whole-Cell Modeling. IEEE Transactions on Biomedical Engineering, 63(10): 2007-2014 https://doi.org/10.1109/tbme.2016.2560762

James C. Schaff, Dan Dragos Vasilescu, Ion I. Moraru, Leslie M. Loew, Michael L. Blinov. (2016) Rule-based modeling with Virtual Cell. Bioinformatics, 32(18): 2880-2882 https://doi.org/10.1093/bioinformatics/btw353

Neil Swainston, Kieran Smallbone, Hooman Hefzi, Paul D. Dobson, Judy McKinley Brewer, Michael Hanscho, Daniel Craig Zielinski, Kok Siong Ang, Natalie J. Gardiner, Jahir M. Gutierrez, Sarantos Kyriakopoulos, Meiyappan Lakshmanan, Shangzhong Li, Joanne K. Liu, Verónica S. Martínez, Camila A. Orellana, Lake‐Ee Quek, Alex Thomas, Jürgen Zanghellini, Nicole Borth, Dong‐Yup Lee, Lars Keld Nielsen, Douglas Bruce Kell, Nathan E. Lewis, Pedro Mendes. (2016) Recon 2.2: from reconstruction to model of human metabolism. Metabolomics, 12(7): 109-109 https://doi.org/10.1007/s11306-016-1051-4

Joshua A. Jadwin, Dongmyung Oh, Timothy G. Curran, Mari Ogiue‐Ikeda, Lin Jia, Forest M. White, Kazuya Machida, Ji Hoon Yu, Bruce J. Mayer. (2016) Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases. eLife, 5: e11835-e11835 https://doi.org/10.7554/elife.11835

Martin Scharm, Dagmar Waltemath, Pedro Mendes, Olaf Wolkenhauer. (2016) COMODI: An ontology to characterise differences in versions of computational models in biology. N/A https://doi.org/10.7287/peerj.preprints.1857v1

Neil Swainston, Janna Hastings, Adriano Dekker, Venkatesh Muthukrishnan, John W. May, Christoph Steinbeck, Pedro Mendes. (2016) libChEBI: an API for accessing the ChEBI database. Journal of Cheminformatics, 8(1): 11-11 https://doi.org/10.1186/s13321-016-0123-9

Pedro Mendes, Stephen G. Oliver, Douglas Bruce Kell. (2016) Response to ‘The Need for Speed’, by Matsson et al .. Trends in Pharmacological Sciences, 37(4): 245-246 https://doi.org/10.1016/j.tips.2016.02.004

Joshua A. Jadwin, Dongmyung Oh, Timothy G. Curran, Mari Ogiue‐Ikeda, Lin Jia, Forest M. White, Kazuya Machida, Ji Hoon Yu, Bruce J. Mayer. (2016) Author response: Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases. N/A https://doi.org/10.7554/elife.11835.028

Karim Rezaul, Dipika Gupta, Irina V. Semenova, Kazuho Ikeda, Pavel Kraikivski, Ji Hoon Yu, Ann E. Cowan, Ilya Zaliapin, Vladimir Rodionov. (2016) Engineered Tug‐of‐War Between Kinesin and Dynein Controls Direction of Microtubule Based Transport In Vivo. Traffic, 17(5): 475-486 https://doi.org/10.1111/tra.12385

Michael L. Blinov, Dan Dragos Vasilescu, Ion I. Moraru, Leslie M. Loew, James C. Schaff. (2016) Rule-Based Modeling and Simulation for Beginners: Intuitive Graphical Interface within Virtual Cell. Biophysical Journal, 110(3): 494a-494a https://doi.org/10.1016/j.bpj.2015.11.2644

Judy E. Bloom, Michael L. Blinov, Leslie M. Loew. (2016) Rule-Based Modeling with Virtual Cell: Effect of UBE3A on Dendritic Spine Morphogenesis. Biophysical Journal, 110(3): 477a-477a https://doi.org/10.1016/j.bpj.2015.11.2553

Marc Rigatti, Paul J. Michalski, Kimberly L. Dodge‐Kafka, Ion I. Moraru. (2016) Langevin Dynamics Simulation of AKAP-PKA Complex: Re-Envisioning the Local Concentration Mechanism for Directing PKA Phosphorylation. Biophysical Journal, 110(3): 425a-425a https://doi.org/10.1016/j.bpj.2015.11.2297