2025
Anna Niarakis, Gary An, Luiz Carlos Maia Ladeira, Noriko 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 Hunter, Kristin Reiche, Jasmin Fisher, Liesbet Geris, Yaron Ilan, James A. Glazier, Philippe 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
Yasir Suhail, Wenqiang Du, Junaid 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
Yasir Suhail, Yamin Liu, Junaid 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
Srdjan D. Antic, Ping Yan, Corey D. Acker, Olivia T. Spagnola, Zehra Y. 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
Francesco Giardini, Camilla Olianti, Gerard A. Marchal, Fernando O. 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 Köhl, Tania Zaglia, Callum M. 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
Sk Ashif Akram, Aniruddha Chattaraj, Terry Salava, Jonathon A. Ditlev, Leslie M. Loew, Jeremy D. Schmit, Sk Ashif Akram, Aniruddha Chattaraj, Terry Salava, Jonathon A. Ditlev, Leslie M. Loew, Jeremy D. Schmit. (2025) Biomolecular Phase Boundaries are Described by a Solubility Product That Accounts for Variable Stoichiometry and Soluble Oligomers. Journal of the American Chemical Society https://doi.org/10.1021/jacs.5c16034
Dan 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 https://doi.org/10.3389/fmolb.2025.1681081
Stephen Curry, Eunice Mercado-Lara, Virginia Arechavala‐Gomeza, C. Glenn Begley, C. Bernard, René Bernard, Stefano Bertuzzi, Needhi Bhalla, Dawn Bowers, Samuel Brod, Chris Chambers, Michael R. Dougherty, Yensi Flores Bueso, Stefânia Forner, Alexandra L. J. Freeman, Magali Haas, Darla P. Henderson, Kanika Khanna, Rebecca Lawrence, Kifayathullah Liakath‐Ali, Christine Liu, Neil Malhotra, José G. Merino, Edward Miguel, Rachel Miles, Mary Munson, Shinichi Nakagawa, Robert Nobles, Joy Owango, Michel Tuan Pham, Gina R. Poe, Ana María Ramírez, Sarvenaz Sarabipour, Jill L. Silverman, Laura N. Smith, P. Sriramarao, Paul W. Sternberg, Geeta K. Swamy, Malú G. 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
Sehroon Khan, James Wicander, George Korza, Rebecca Caldbeck, Ann E. Cowan, Graham 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
Sarvenaz Sarabipour, Karina Kinghorn, Kaitlyn Quigley, Anita Kovács‐Kása, Brian H. 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
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
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
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, Hongxian Zhu, Rebecca Alvania. (2025) LGBTQ+ realities in the biological sciences. bioRxiv (Cold Spring Harbor Laboratory) https://doi.org/10.1101/2025.01.24.634486
Lucian 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 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
2024
Lindsay Barnum, Mohamadmahdi Samandari, Yasir Suhail, Steven Toro, Ashkan Novin, Pejman Ghelich, Jacob 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
Wenqiang Du, Ashkan Novin, Yamin Liu, Junaid Afzal, Yasir Suhail, Shaofei Liu, Nicole R Gavin, Jennifer R. Jorgensen, Christopher M. Morosky, Reinaldo Figueroa, Tannin A. Schmidt, Melinda E. Sanders, Molly 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
Mikhail 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
Anna Niarakis, Reinhard Laubenbacher, Gary 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 S. Ferreira, Arnau Montagud, Vincent Noël, Malvina Marku, Eirini Tsirvouli, Marcella Torres, Leonard A. Harris, T. J. Sego, R. Chase Cockrell, Amanda E. Shick, Hasan Balcı, Albin Salazar, Kinza Rian, Ahmed Abdelmonem Hemedan, Marina Esteban‐Medina, Bernard Staumont, Esteban A. Hernández-Vargas, Shiny Martis B, Alejandro Madrid-Valiente, Panagiotis Karampelesis, Luis Sordo Vieira, Pradyumna Harlapur, Alexander Kulesza, Niloofar Nikaein, Winston Garira, Rahuman S. Malik‐Sheriff, Juilee Thakar, Van Du T. Tran, José Carbonell‐Caballero, Soroush Safaei, Alfonso Valencia, Andreï 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
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
Blair Lyons, Saurabh S. Mogre, Karthik Vegesna, Jessica S. Yu, Mark 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 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 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 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
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
Karthik Vegesna, Saurabh S. Mogre, Jessica Yu, Blair 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
Yasir Suhail, Yamin Liu, Wenqiang Du, Junaid 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
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
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 B. Dutta, Kizhakke Mattada Sathyan, Daniel E. Frigo, Michael J. Guertin, Daniel 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 B. Dutta, Kizhakke Mattada Sathyan, Daniel E. Frigo, Michael J. Guertin, Daniel 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
Thomas G. Scott, Kizhakke Mattada Sathyan, Daniel 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 B. Dutta, Kizhakke Mattada Sathyan, Daniel E. Frigo, Michael J. Guertin, Daniel 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 Lundberg, Blair Lyons, Wei Ouyang, Omar A. Quintero, Megan 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.7772569
Pedro Mendes. (2023) Dataset for “Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model”. Zenodo (CERN European Organization for Nuclear Research) N/A
Linda Archambault, Sherli Koshy-Chenthittayil, Angela Thompson, Anna 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
James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian 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
Piotr Przanowski, Roza 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
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 B. Dutta, Daniel Lank, Roza Przanowska, Piotr Przanowski, Lixin Wang, Bao 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
2022
Thomas G. Scott, André L. 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 L. 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
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
Jacob B. Wolpe, André L. 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 B. 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
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 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
Roza Przanowska, Chase A. Weidmann, Shekhar Saha, Magdalena A. Cichewicz, Kate 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
2021
Linda Archambault, Sherli Koshy-Chenthittayil, Angela Thompson, Anna 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 B. Dutta, Daniel Lank, Roza Przanowska, Piotr Przanowski, Lixin Wang, Bao 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 Oviedo, Jorge L. Arias-Arias, Luis A. Rojas-Matey, Edwin Baéz, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, José 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, Roza 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 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 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
Roza Przanowska, Chase A. Weidmann, Shekhar Saha, Magdalena A. Cichewicz, Kate 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 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 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 Archambault, Sherli Koshy-Chenthittayil, Angela Thompson, Anna Dongari‐Bagtzoglou, Reinhard Laubenbacher, Pedro Mendes. (2021) UnderstandingLactobacillus paracaseiandStreptococcus oralisbiofilm 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 Oviedo, Jorge L. Arias-Arias, Luis A. Rojas-Matey, Edwin Baéz, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, José Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Anne Régnier‐Vigouroux, Pedro Mendes, Rodrígo Mora. (2021) MYCdosage 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 Archambault, Dhananjai Senthilkumar, Reinhard Laubenbacher, Pedro Mendes, Anna 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) Solubility Product Constant Governs Multivalent Protein Phase Separations. Biophysical Journal, 120(3): 208a-208a https://doi.org/10.1016/j.bpj.2020.11.1412
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
Anton V. Burakov, Ivan A. Vorobjev, И. В. Семенова, 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
Bruce J. Mayer. (2021) Decision letter: Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. N/A https://doi.org/10.7554/elife.64251.sa1
ManSai Acón, Carsten Geiß, Jorge Torres-Calvo, Guillermo Oviedo, Jorge L. Arias-Arias, Gloriana Vásquez-Vargas, Yendry Oses-Vargas, José Guevara-Coto, Andrés Segura-Castillo, Francisco Siles-Canales, Steve Quirós-Barrantes, Anne Régnier‐Vigouroux, Pedro Mendes, Rodrigo Mora-Rodríguez. (2021) <i>MYC</i> Dosage Compensation is Mediated by miRNA-Transcription Factor Interactions in Aneuploid Cancer. SSRN Electronic Journal https://doi.org/10.2139/ssrn.3844728
Sherli Koshy-Chenthittayil, Pedro Mendes, Reinhard Laubenbacher. (2021) Optimization of Agent-Based Models Through Coarse-Graining. Letters in Biomathematics, 8(1): 167-178 https://doi.org/10.30707/lib8.1.1647878866.083342
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 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
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 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 F. Löchel, María Martín, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine O’Toole, Nancy Ontiveros‐Palacios, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David S. 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/10.3929/ethz-b-000464448
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 Smith, Maciej J. Swat, Denis Thieffry, Leandro 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 Wagner, Martin Meier‐Schellersheim, Herbert M. Sauro, Bernhard Ø. Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, Michael Hucka, Richard R. Adams, Nicholas 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 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, D. 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 B. Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe. (2020) SBMLLevel 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, 16(8): e9110-e9110 https://doi.org/10.3929/ethz-b-000438614
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
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 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
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 Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian 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
Baoqing Ding, Erin 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 Oviedo, Edwin Baéz, Gloriana Vásquez-Vargas, José 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 B. 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 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 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/10.2390/biecoll-jib-2015-266
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
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 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 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 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 Nickerson, Brett G. Olivier, Nicolás Rodríguez, Falk Schreiber, Lucian 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 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 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
Marianne Nygaard, George A. Kuchel, Anne B. Newman, Heather Allore, Jenna M. Bartley, C. S. Bergeman, Michael L. Blinov, Cathleen Colón‐Emeric, Firdaus S Dabhar, Laura L. Dugan, Chhanda Dutta, Basil A. Eldadah, Luigi Ferrucci, James L. Kirkland, Stephen B. Kritchevsky, Lewis A. Lipsitz, Neelesh K. Nadkarni, May J. Reed, Kenneth E. Schmader, Felipe Sierra, Stephanie A. Studenski, Ravi Varadhan, Jeremy Walston, Heather E. Whitson, Raymond 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 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 Argüello, Pedro Mendes. (2018) An important role for periplasmic storage inPseudomonas aeruginosacopper 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 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 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 B. 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
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 C. 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 Vasilescu, Ion I. Moraru, Judy E. Bloom, Leslie M. Loew. (2017) Compartmental and spatial rule-based modeling withVirtual 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
Marianne Nygaard, George A. Kuchel, Anne B. Newman, Heather Allore, Jenna M. Bartley, C. S. Bergeman, Michael L. Blinov, Cathleen Colón‐Emeric, Firdaus S Dabhar, Laura L. Dugan, Chhanda Dutta, Basil A. Eldadah, Luigi Ferrucci, James L. Kirkland, Stephen B. Kritchevsky, Lewis A. Lipsitz, Neelesh K. Nadkarni, May J. Reed, Kenneth E. Schmader, Felipe Sierra, Stephanie A. Studenski, Ravi Varadhan, Jeremy Walston, Heather E. Whitson, Raymond 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
И. В. Семенова, 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 R. Gryk, Ion I. Moraru, Pedro 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 V. 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
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 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 V. 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
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 Kiselev, Vincent 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 Tokic, Namrata Tomar, Vasundra Touré, Jannis Uhlendorf, Thawfeek Varusai, Leandro 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 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 C. 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 K. Nielsen, Douglas B. 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 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.1857
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 B. 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 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, И. В. Семенова, Kazuho Ikeda, Pavel Kraikivski, Ji 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
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
Michael L. Blinov, Dan 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
2015
Yueming Chang, Jeffrey S. Wasser, Adam Boruchov, Bruce J. Mayer, Kazuya Machida. (2015) BCR Signalosome-Oriented Phosphotyrosine Profiling of CLL. Blood, 126(23): 4128-4128 https://doi.org/10.1182/blood.v126.23.4128.4128
Sofya Borinskaya, Katrina Velle, Kenneth G. Campellone, Arthur M. Talman, Diego E. Álvarez, Hervé Agaisse, Yi Wu, Leslie M. Loew, Bruce J. Mayer. (2015) Integration of linear and dendritic actin nucleation in Nck-induced actin comets. Molecular Biology of the Cell, 27(2): 247-259 https://doi.org/10.1091/mbc.e14-11-1555
Pedro Mendes, Stephen G. Oliver, Douglas B. Kell. (2015) Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends in Pharmacological Sciences, 36(11): 710-723 https://doi.org/10.1016/j.tips.2015.07.006
Bruce J. Mayer. (2015) The discovery of modular binding domains: building blocks of cell signalling. Nature Reviews Molecular Cell Biology, 16(11): 691-698 https://doi.org/10.1038/nrm4068
Arpita Singh, Marc Rigatti, Andrew V. Le, Cathrine R. Carlson, Ion I. Moraru, Kimberly L. Dodge‐Kafka. (2015) Analysis of AKAP7γ Dimerization. Journal of Signal Transduction, 2015: 1-15 https://doi.org/10.1155/2015/371626
Anthony Santella, Raúl Catena, Ismar Kovacevic, Pavak K. Shah, Zidong Yu, Javier Marquina-Solis, Abhishek Kumar, Yicong Wu, James C. Schaff, Daniel A. Colón‐Ramos, Hari Shroff, William A. Mohler, Zhirong Bao. (2015) WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. BMC Bioinformatics, 16(1): 189-189 https://doi.org/10.1186/s12859-015-0627-8
Michael Hucka, Frank Bergmann, Stefan Hoops, Sarah Keating, Sven Sahle, James C. Schaff, Lucian Smith, Darren J. Wilkinson. (2015) 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, 12(2): 382-549 https://doi.org/10.1515/jib-2015-266
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 Smith, Dagmar Waltemath, Darren J. Wilkinson. (2015) Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 12(2): 731-901 https://doi.org/10.1515/jib-2015-271
Lucian Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion I. Moraru, Wolfram Liebermeister. (2015) SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3. Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics, 12(2): 603-659 https://doi.org/10.1515/jib-2015-268
Marc Rigatti, Andrew V. Le, Claire Gerber, Ion I. Moraru, Kimberly L. Dodge‐Kafka. (2015) Phosphorylation state-dependent interaction between AKAP7δ/γ and phospholamban increases phospholamban phosphorylation. Cellular Signalling, 27(9): 1807-1815 https://doi.org/10.1016/j.cellsig.2015.05.016
Ahmed Elmokadem, Ion I. Moraru, Ji Yu. (2015) Super‐resolution Imaging Shows Spatial Regulation of p130Cas Phosporylation within Focal Adhesions. The FASEB Journal, 29(S1) https://doi.org/10.1096/fasebj.29.1_supplement.lb30
Abhijit Deb Roy, Taofei Yin, Yi Wu. (2015) An Optogenetic Approach to Delineate Spatial Regulation of Plexin Signaling. The FASEB Journal, 29(S1) https://doi.org/10.1096/fasebj.29.1_supplement.728.37
Marc Rigatti, Paul J. Michalski, Ion I. Moraru, Kimberly L. Dodge‐Kafka. (2015) Length and Flexibility of the Disordered Tether Region of the PKA Regulatory Subunit Modulates Phosphorylation Kinetics of PKA within an AKAP Complex. The FASEB Journal, 29(S1) https://doi.org/10.1096/fasebj.29.1_supplement.881.10
Katharine Herrick‐Davis, Ellinor Grinde, Tara A. Lindsley, Milt Teitler, Filippo Mancia, Ann E. Cowan, Joseph E. Mazurkiewicz. (2015) Native Serotonin 5-HT2C Receptors Are Expressed as Homodimers on the Apical Surface of Choroid Plexus Epithelial Cells. Molecular Pharmacology, 87(4): 660-673 https://doi.org/10.1124/mol.114.096636
Michael L. Blinov, Dan Vasilescu, James C. Schaff, Ion I. Moraru, Leslie M. Loew. (2015) Using Rules & Pathway Databases to Create Quantitative Mechanistic Models in Virtual Cell. Biophysical Journal, 108(2): 473a-473a https://doi.org/10.1016/j.bpj.2014.11.2586
Joshua A. Jadwin, Bruce J. Mayer, Kazuya Machida. (2015) Detection and Quantification of Protein–Protein Interactions by Far-Western Blotting. Methods in molecular biology, 1312: 379-398 https://doi.org/10.1007/978-1-4939-2694-7_38