James R. Faeder - Publications, H-index & Citations

James R. Faeder

university of pittsburgh

46H指数

184论文数

7.5K被引数

收录论文 35

发表时间

Mathematical modeling of processive Ras activation by SOS reveals a general mechanism for digital signaling 过程性SOS介导的Ras激活的数学建模揭示了一种数字信号传导的通用机制

npj Systems Biology and Applications

IF3.5

2026-10-14

OAAI

Katherine A. Yonosh; James R. Faeder

From FAIR to CURE: guidelines for computational models of biological systems 从FAIR到CURE：生物系统计算模型的指南

npj Systems Biology and Applications

IF3.5

2026-03-27

OAAI

Herbert M. Sauro; Eran Agmon; Michael L. Blinov; John H. Gennari; Joseph L. Hellerstein; Adel Heydarabadipour; Bartholomew E. Jardine; Elebeoba May; David P. Nickerson; Lucian P. Smith; Gary D. Bader; Frank T. Bergmann; Patrick M. Boyle; Andreas Dräger; James R. Faeder; Song Feng; Juliana Freire; Fabian Fröhlich; James A. Glazier; Thomas E. Gorochowski; Tomas Helikar; Henning Hermjakob; Stefan Hoops; Peter Hunter; Princess I. Imoukhuede; Sarah M. Keating; Matthias König; Reinhard Laubenbacher; Leslie M. Loew; Carlos F. Lopez; William W. Lytton; Rahuman S. Malik-Sheriff; Andrew McCulloch; Pedro Mendes; Lealem Mulugeta; Chris J. Myers; Jerry G. Myers Jr; Anna Niarakis; David D. van Niekerk; Brett G. Olivier; Alexander A. Patrie; Ellen M. Quardokus; Nicole Radde; Johann M. Rohwer; Sven Sahle; James C. Schaff; Falk Schreiber; T. J. Sego; Janis Shin; Jacky L. Snoep; Rajanikanth Vadigepalli; H. Steven Wiley; Dagmar Waltemath; Ion I. Moraru

STAT3 S727 phosphorylation drives pathogenic Th17 differentiation and neuroinflammation in autoimmune disease STAT3 S727磷酸化驱动自身免疫病中致病性Th17分化及神经炎症。

Journal of Neuroinflammation

IF10.1

2025-10-30

OAAI

Douglas S. Prado; Achyudhan R. Kutuva; Richard T. Cattley; Andreza Buzolin Sonego; Parth Sutariya; Elena Im; Shuxian Wu; Mijoon Lee; Rachel L. Cumberland; Isha Mehta; Greg M. Delgoffe; William C. Boggess; James R. Faeder; Mark J. Shlomchik; William F. Hawse

Predicting gene-level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework

CELL SYSTEMS

IF7.7

2024-01-01

OAAI

Cheemalavagu, Neha; Shoger, Karsen E.; Cao, Yuqi M.; Michalides, Brandon A.; Botta, Samuel A.; Faeder, James R.; Gottschalk, Rachel A.

BioSimulators: a central registry of simulation engines and services for recommending specific tools BioSimulators: 用于推荐特定工具的模拟引擎和服务的中央注册表

NUCLEIC ACIDS RESEARCH

IF13.1

2022-05-07

OAAI

Shaikh, Bilal; Smith, Lucian P.; Vasilescu, Dan; Marupilla, Gnaneswara; Wilson, Michael; Agmon, Eran; Agnew, Henry; Andrews, Steven S.; Anwar, Azraf; Beber, Moritz E.; Bergmann, Frank T.; Brooks, David; Brusch, Lutz; Calzone, Laurence; Choi, Kiri; Cooper, Joshua; Detloff, John; Drawert, Brian; Dumontier, Michel; Ermentrout, G. Bard; Faeder, James R.; Freiburger, Andrew P.; Frohlich, Fabian; Funahashi, Akira; Garny, Alan; Gennari, John H.; Gleeson, Padraig; Goelzer, Anne; Haiman, Zachary; Hasenauer, Jan; Hellerstein, Joseph L.; Hermjakob, Henning; Hoops, Stefan; Ison, Jon C.; Jahn, Diego; Jakubowski, Henry, V; Jordan, Ryann; Kalas, Matus; Koenig, Matthias; Liebermeister, Wolfram; Sheriff, Rahuman S. Malik; Mandal, Synchon; McDougal, Robert; Medley, J. Kyle; Mendes, Pedro; Mueller, Robert; Myers, Chris J.; Naldi, Aurelien; Nguyen, Tung V. N.; Nickerson, David P.; Olivier, Brett G.; Patoliya, Drashti; Pauleve, Loic; Petzold, Linda R.; Priya, Ankita; Rampadarath, Anand K.; Rohwer, Johann M.; Saglam, Ali S.; Singh, Dilawar; Sinha, Ankur; Snoep, Jacky; Sorby, Hugh; Spangler, Ryan; Starruss, Joern; Thomas, Payton J.; van Niekerk, David; Weindl, Daniel; Zhang, Fengkai; Zhukova, Anna; Goldberg, Arthur P.; Schaff, James C.; Blinov, Michael L.; Sauro, Herbert M.; Moraru, Ion I.; Karr, Jonathan R.

Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry

MOLECULAR BIOLOGY OF THE CELL

IF2.7

2021-01-15

OAAI

Johnson, M. E.; Chen, A.; Faeder, J. R.; Henning, P.; Moraru, I. I.; Meier-Schellersheim, M.; Murphy, R. F.; Prustel, T.; Theriot, J. A.; Uhrmacher, A. M.

SBML Level 3: an extensible format for the exchange and reuse of biological models

MOLECULAR SYSTEMS BIOLOGY

IF7.7

2020-08-26

170

OAAI

Keating, Sarah M.; Waltemath, Dagmar; Koenig, Matthias; Zhang, Fengkai; Draeger, Andreas; Chaouiya, Claudine; Bergmann, Frank T.; Finney, Andrew; Gillespie, Colin S.; Helikar, Tomas; Hoops, Stefan; Malik-Sheriff, Rahuman S.; Moodie, Stuart L.; Moraru, Ion I.; Myers, Chris J.; Naldi, Aurelien; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Swat, Maciej J.; Thieffry, Denis; Watanabe, Leandro; Wilkinson, Darren J.; Blinov, Michael L.; Begley, Kimberly; Faeder, James R.; Gomez, Harold F.; Hamm, Thomas M.; Inagaki, Yuichiro; Liebermeister, Wolfram; Lister, Allyson L.; Lucio, Daniel; Mjolsness, Eric; Proctor, Carole J.; Raman, Karthik; Rodriguez, Nicolas; Shaffer, Clifford A.; Shapiro, Bruce E.; Stelling, Joerg; Swainston, Neil; Tanimura, Naoki; Wagner, John; Meier-Schellersheim, Martin; Sauro, Herbert M.; Palsson, Bernhard; Bolouri, Hamid; Kitano, Hiroaki; Funahashi, Akira; Hermjakob, Henning; Doyle, John C.; Hucka, Michael

Shift from stochastic to spatially-ordered expression of serine-glycine synthesis enzymes in 3D microtumors

SCIENTIFIC REPORTS

IF3.9

2018-06-20

OAAI

Singh, Manjulata; Warita, Katsuhiko; Warita, Tomoko; Faeder, James R.; Lee, Robin E. C.; Sant, Shilpa; Oltvai, Zoltan N.

NF-κB Dynamics Discriminate between TNF Doses in Single Cells

CELL SYSTEMS

IF7.7

2017-12-01

OAAI

Zhang, Qiuhong; Gupta, Sanjana; Schipper, David L.; Kowalczyk, Gabriel J.; Mancini, Allison E.; Faeder, James R.; Lee, Robin E. C.