2025
Thomas G. Scott, Michael J. Guertin. (2025) Rapid protein degradation systems to determine gene function in vivo. Lab Animal 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) https://doi.org/10.1038/s41540-025-00496-z
Blair Lyons, Saurabh S. Mogre, Karthik Vegesna, Jessica S. Yu, Mark Hansen, Aadarsh Raghunathan, Graham T. Johnson, Eran Agmon, Matthew Akamatsu. (2025) Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist.. PubMed, 2025 https://doi.org/10.17912/micropub.biology.001347
2024
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 https://doi.org/10.1016/j.molcel.2024.11.031
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) 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 https://doi.org/10.1093/nar/gkae1182
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 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) https://doi.org/10.1091/mbc.e24-01-0030
Sarvenaz Sarabipour, Paul Macklin, Natalie M. Niemi. (2024) Improving academic mentorship practices. Nature Human Behaviour 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
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
Marina Scardigli, Michal Pásek, Lorenzo Santini, Chiara Palandri, Emilia Conti, Claudia Crocini, Marina Campione, Leslie M. Loew, Antoine A.F. de Vries, Daniël A. Pijnappels, Francesco S. Pavone, Corrado Poggesi, Elisabetta Cerbai, Raffaele Coppini, Peter Köhl, Cecilia Ferrantini, Leonardo Sacconi. (2024) Optogenetic confirmation of transverse‐tubular membrane excitability in intact cardiac myocytes. The Journal of Physiology, 602(5): 791-808 https://doi.org/10.1113/jp285202
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) https://doi.org/10.1038/s41467-024-45408-7
Kelvin J. Peterson, Leslie M. Loew. (2024) Using SpringSaLaD mesoscale simulations with COPASI ODE parameter optimization to model membrane-associated kinetics based on measured volumetric rate constants. Biophysical Journal, 123(3): 22a-22a https://doi.org/10.1016/j.bpj.2023.11.241
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
Francesco Giardini, Camilla Olianti, Giulia Arecchi, Fernando O. Campos, Tania Zaglia, Marco Mongillo, Stephen P. Chelko, Leslie M. Loew, Elisabetta Cerbai, Callum M. Zgierski‐Johnston, Peter Köhl, Martin J. Bishop, Leonardo Sacconi. (2024) Dissecting the role of structural remodeling on trans-scar conduction in arrhythmogenic mouse hearts by advanced optical methods. Biophysical Journal, 123(3): 435a-435a https://doi.org/10.1016/j.bpj.2023.11.2633
Ping Yan, Corey D. Acker, Srdjan D. Antic, Leslie M. Loew. (2024) Near infrared voltage sensitive dyes based on a novel chromophore. Biophysical Journal, 123(3): 416a-416a https://doi.org/10.1016/j.bpj.2023.11.2539
2023
Patricia J. Hare, Juliet R. Gonzalez, Ryan M. Quelle, Yi Wu, Wendy W. K. Mok. (2023) Metabolic and transcriptional activities underlie stationary-phase Pseudomonas aeruginosa sensitivity to Levofloxacin. Microbiology Spectrum, 12(1) https://doi.org/10.1128/spectrum.03567-23
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
Hanyu Zhang, Haley N. Patton, Garrett A. Wood, Ping Yan, Leslie M. Loew, Corey D. Acker, Gregory P. Walcott, Jack M. Rogers. (2023) Optical mapping of cardiac electromechanics in beating in vivo hearts. Biophysical Journal, 122(21): 4207-4219 https://doi.org/10.1016/j.bpj.2023.09.017
Gerard A. Marchal, Valentina Biasci, Ping Yan, Chiara Palandri, Marina Campione, Elisabetta Cerbai, Leslie M. Loew, Leonardo Sacconi. (2023) Recent advances and current limitations of available technology to optically manipulate and observe cardiac electrophysiology. Pflügers Archiv – European Journal of Physiology, 475(11): 1357-1366 https://doi.org/10.1007/s00424-023-02858-0
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
Ji Yu. (2023) Point-Supervised Single-Cell Segmentation via Collaborative Knowledge Sharing. IEEE Transactions on Medical Imaging, 42(12): 3884-3894 https://doi.org/10.1109/tmi.2023.3312988
Klaus M. Hahn, Michelle S. Itano, Leslie M. Loew, Eric A. Vitriol. (2023) Celebrating the creative scientific life of Ken Jacobson. Biophysical Journal, 122(18): E1-E4 https://doi.org/10.1016/j.bpj.2023.08.013
Ping Yan, Corey D. Acker, Valentina Biasci, Giuliana Judge, Alexa Monroe, Leonardo Sacconi, Leslie M. Loew. (2023) Near-infrared voltage-sensitive dyes based on chromene donor. Proceedings of the National Academy of Sciences, 120(34) https://doi.org/10.1073/pnas.2305093120
Daniel Enríquez-Vázquez, Jorge G. Quintanilla, Alba García-Escolano, Marinela Couselo‐Seijas, Ana Simón-Chica, Peter Lee, José Manuel Alfonso-Almazán, P Mahia, Andrés Redondo‐Rodríguez, Javier Modrego, Adriana Ortega‐Hernández, Pedro Marcos‐Alberca, Ricardo Magni, Enrique Calvo, Rubén Gómez-Gordo, Ping Yan, Giulio La Rosa, José Bustamante-Madrión, Carlos Nicolás Pérez‐García, Francisco Javier Martín‐Sánchez, David Calvo, Jesús M. de la Hera, María Jesús García-Torrent, Álvaro García‐Osuna, Jordi Ordóñez‐Llanos, Jesús Vázquez, Julián Pérez-Villacastı́n, Nicasio Pérez‐Castellano, Leslie M. Loew, Javier Sánchez‐González, Dulcenombre Gómez‐Garré, David Filgueiras‐Rama. (2023) Non-invasive electromechanical assessment during atrial fibrillation identifies underlying atrial myopathy alterations with early prognostic value. Nature Communications, 14(1) https://doi.org/10.1038/s41467-023-40196-y
Hanyu Zhang, Haley N. Patton, Garrett A. Wood, Ping Yan, Leslie M. Loew, Corey D. Acker, Gregory P. Walcott, Jack M. Rogers. (2023) Di-5-ANEQ(F)PTEA Offers Better Performance than Di-4-ANEQ(F)PTEA for In-Situ Cardiac Optical Mapping*. 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), : 1-4 https://doi.org/10.1109/embc40787.2023.10340445
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 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) https://doi.org/10.1080/22221751.2023.2214255
Gerard A. Marchal, Valentina Biasci, Leslie M. Loew, Annibale Biggeri, Marina Campione, Leonardo Sacconi. (2023) Optogenetic manipulation of cardiac repolarization gradients using sub-threshold illumination. Frontiers in Physiology, 14 https://doi.org/10.3389/fphys.2023.1167524
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 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
Aniruddha Chattaraj, Leslie M. Loew. (2023) The maximum solubility product marks the threshold for condensation of multivalent biomolecules. Biophysical Journal, 122(9): 1678-1690 https://doi.org/10.1016/j.bpj.2023.03.036
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) https://doi.org/10.1128/msphere.00656-22
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
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) 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
Aniruddha Chattaraj, Leslie M. Loew. (2023) The concentration threshold for condensation of multivalent molecules is set by by the maximum solubility product. Biophysical Journal, 122(3): 65a-65a https://doi.org/10.1016/j.bpj.2022.11.557
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
Ping Yan, Valentina Biasci, Giuliana Judge, Corey D. Acker, Alexa Monroe, Leonardo Sacconi, Leslie M. Loew. (2023) Near infrared voltage sensitive dyes based on chromene electron donors. Biophysical Journal, 122(3): 381a-381a https://doi.org/10.1016/j.bpj.2022.11.2092
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
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) https://doi.org/10.1038/s41598-022-24782-6
Peter Quicke, Yilin Sun, Mar Arias-García, Melina Beykou, Corey D. Acker, Mustafa B.A. Djamgoz, Chris Bakal, Amanda J. Foust. (2022) Voltage imaging reveals the dynamic electrical signatures of human breast cancer cells. Communications Biology, 5(1) https://doi.org/10.1038/s42003-022-04077-2
Shengen 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) https://doi.org/10.1038/s41467-022-33194-z
Lauren Marazzi, Milan Shah, Shreedula Balakrishnan, Ananya Patil, Paola Vera‐Licona. (2022) NETISCE: a network-based tool for cell fate reprogramming. npj Systems Biology and Applications, 8(1) https://doi.org/10.1038/s41540-022-00231-y
Valentina Biasci, Lorenzo Santini, Sayedeh Hussaini, Cecilia Ferrantini, Raffaele Coppini, Leslie M. Loew, Stefan Luther, Marina Campione, Corrado Poggesi, FS Pavone, Elisabetta Cerbai, Gil Bub, Leonardo Sacconi. (2022) Optogenetic manipulation of cardiac electrical dynamics using sub-threshold illumination: dissecting the role of cardiac alternans in terminating rapid rhythms. Cardiovascular Research, 118(Supplement_1) https://doi.org/10.1093/cvr/cvac066.161
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) 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) https://doi.org/10.12703/r-01-000008
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
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
Valentina Biasci, Lorenzo Santini, Gerard A. Marchal, Sayedeh Hussaini, Cecilia Ferrantini, Raffaele Coppini, Leslie M. Loew, Stefan Luther, Marina Campione, Corrado Poggesi, Francesco S. Pavone, Elisabetta Cerbai, Gil Bub, Leonardo Sacconi. (2022) Optogenetic manipulation of cardiac electrical dynamics using sub-threshold illumination: dissecting the role of cardiac alternans in terminating rapid rhythms. Basic Research in Cardiology, 117(1) https://doi.org/10.1007/s00395-022-00933-8
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz Emanuel Beber, Frank Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, Bard Ermentrout, James R. Faeder, Andrew 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, Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V N Nguyen, David 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 K. 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
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
Aniruddha Chattaraj, Sujay Champati, Leslie M. Loew. (2022) Noise regulation by heterotypic biomolecular condensates. Biophysical Journal, 121(3): 358a-358a https://doi.org/10.1016/j.bpj.2021.11.977
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 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) https://doi.org/10.1128/msphere.00875-21
Masoud Nickaeen, Julien Berro, Thomas D. Pollard, Boris M. Slepchenko. (2021) A model of actin-driven endocytosis explains differences of endocytic motility in budding and fission yeast. Molecular Biology of the Cell, 33(3) https://doi.org/10.1091/mbc.e21-07-0362
Marie Caroline Müllenbroich, Allen Kelly, Corey D. Acker, Gil Bub, Tobias Bruegmann, Anna Di Bona, Emilia Entcheva, Cecilia Ferrantini, Peter Köhl, Stephan E. Lehnart, Marco Mongillo, Camilla Parmeggiani, Claudia Richter, Philipp Sasse, Tania Zaglia, Leonardo Sacconi, Godfrey L. Smith. (2021) Novel Optics-Based Approaches for Cardiac Electrophysiology: A Review. Frontiers in Physiology, 12 https://doi.org/10.3389/fphys.2021.769586
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
Aaron D. Rosenbloom, Elizabeth W. Kovar, David R. Kovar, Leslie M. Loew, Thomas D. Pollard. (2021) Mechanism of actin filament nucleation. Biophysical Journal, 120(20): 4399-4417 https://doi.org/10.1016/j.bpj.2021.09.006
Caterina Credi, Valentina Balducci, Uday Munagala, C. Cianca, S. Bigiarini, Antoine A.F. de Vries, Leslie M. Loew, Francesco S. Pavone, Elisabetta Cerbai, Laura Sartiani, Leonardo Sacconi. (2021) Fast Optical Investigation of Cardiac Electrophysiology by Parallel Detection in Multiwell Plates. Frontiers in Physiology, 12 https://doi.org/10.3389/fphys.2021.692496
Corey D. Acker, Ping Yan, Anthony M. Pettinato, Travis Hinson, Leslie M. Loew. (2021) Voltage imaging of single contracting human iPSC-CMs using ratiometric voltage-sensitive dyes. Journal of Pharmacological and Toxicological Methods, 111: 107038-107038 https://doi.org/10.1016/j.vascn.2021.107038
Manuel Marina‐Breysse, Alba García-Escolano, Joaquín Vila García, Gabriel Reale-Nosei, José Manuel Alfonso-Almazán, Ping Yan, Jorge G. Quintanilla, Leslie M. Loew, Peter Lee, David Filgueiras‐Rama. (2021) A Complete and Low-Cost Cardiac Optical Mapping System in Translational Animal Models. Frontiers in Physiology, 12 https://doi.org/10.3389/fphys.2021.696270
James J. Fink, Jeremy D. Schreiner, Judy E. Bloom, Jadin James, Dylan Baker, Tiwanna M. Robinson, Richard Lieberman, Leslie M. Loew, Stormy J. Chamberlain, Eric S. Levine. (2021) Hyperexcitable Phenotypes in Induced Pluripotent Stem Cell–Derived Neurons From Patients With 15q11-q13 Duplication Syndrome, a Genetic Form of Autism. Biological Psychiatry, 90(11): 756-765 https://doi.org/10.1016/j.biopsych.2021.07.018
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
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
Sarah J. Benjamin, Kelly L. Hawley, Paola Vera‐Licona, Carson J. La Vake, Jorge Cervantes, Yijun Ruan, Justin D. Radolf, Juan C. Salazar. (2021) Macrophage mediated recognition and clearance of Borrelia burgdorferi elicits MyD88-dependent and -independent phagosomal signals that contribute to phagocytosis and inflammation. BMC Immunology, 22(1) https://doi.org/10.1186/s12865-021-00418-8
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
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
Justin Sardi, Muhammed Burak Bener, Taylor Simao, Abigail E. Descoteaux, Boris M. Slepchenko, Mayu Inaba. (2021) Mad dephosphorylation at the nuclear pore is essential for asymmetric stem cell division. Proceedings of the National Academy of Sciences, 118(13) https://doi.org/10.1073/pnas.2006786118
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
Corey D. Acker, Ping Yan, Anthony M. Pettinato, Travis Hinson, Leslie M. Loew. (2021) Optimization and Validation of Fast Ratiometric Voltage-Sensitive Dye Imaging in Neuronal and Cardiac Tissues and Cultures. Biophysical Journal, 120(3): 331a-331a https://doi.org/10.1016/j.bpj.2020.11.2082
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, 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
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) https://doi.org/10.30707/lib8.1.1647878866.083342
2020
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
Xudong Wang, Ping Yan, Peter Kerns, Steven L. Suib, Leslie M. Loew, Jing Zhao. (2020) Voltage-Dependent Photoluminescence of Carbon Dots. Journal of The Electrochemical Society, 167(14): 147515-147515 https://doi.org/10.1149/1945-7111/abc7e5
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 Martin, 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/10.1093/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 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) https://doi.org/10.15252/msb.20199110
Lauren Marazzi, Andrew Gainer-Dewar, Paola Vera‐Licona. (2020) OCSANA+: optimal control and simulation of signaling networks from network analysis. Bioinformatics, 36(19): 4960-4962 https://doi.org/10.1093/bioinformatics/btaa625
Frank Bergmann, Tobias Czauderna, Uḡur Doḡrusöz, 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
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 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
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
Basak B. Ural, Stephen T. Yeung, Payal Damani‐Yokota, Joseph C. Devlin, Maren de Vries, Paola Vera‐Licona, Tasleem Samji, Catherine M. Sawai, Geunhyo Jang, Oriana A. Perez, Quynh Pham, Leigh Maher, P’ng Loke, Meike Dittmann, Boris Reizis, Kamal M. Khanna. (2020) Identification of a nerve-associated, lung-resident interstitial macrophage subset with distinct localization and immunoregulatory properties. Science Immunology, 5(45) https://doi.org/10.1126/sciimmunol.aax8756
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
Jeeun Kang, Shilpa D. Kadam, Joshua S. Elmore, Brennan J. Sullivan, Heather Valentine, Adarsha P. Malla, Maged M. Harraz, Arman Rahmim, Jin U. Kang, Leslie M. Loew, Michael H. Baumann, Anthony A. Grace, Albert Gjedde, Emad M. Boctor, Dean F. Wong. (2020) Transcranial photoacoustic imaging of NMDA-evoked focal circuit dynamics in the rat hippocampus. Journal of Neural Engineering, 17(2): 025001-025001 https://doi.org/10.1088/1741-2552/ab78ca