Rahuman S. Malik-Sheriff

According to our database, Rahuman S. Malik-Sheriff authored at least 15 papers between 2015 and 2025.

Collaborative distances:

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

2025

Talk2Biomodels: AI agent-based open-source LLM initiative for kinetic biological models.

Lilija Wehling, Gurdeep Singh, Ahmad Wisnu Mulyadi, Rakesh Hadne Sreenath, Henning Hermjakob, Tung V. N. Nguyen, Thomas Rückle, Mohammed H. Mosa, Henrik Cordes, Tommaso Andreani, Thomas Klabunde, Rahuman S. Malik-Sheriff, Douglas McCloskey

BMC Bioinform., December, 2025

Verification and reproducible curation of the BioModels repository.

Lucian P. Smith, Rahuman S. Malik-Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan R. Karr, Bilal Shaikh, Logan Drescher, Ion I. Moraru, James C. Schaff, Eran Agmon, Alexander A. Patrie, Michael L. Blinov, Joseph L. Hellerstein, Elebeoba E. May, David P. Nickerson, John H. Gennari, Herbert M. Sauro

PLoS Comput. Biol., 2025

SBMLtoOdin and Menelmacar: interactive visualisation of systems biology models for expert and non-expert audiences.

Leonie J. Lorenz, Antoine Andréoletti, Tung V. N. Nguyen, Henning Hermjakob, Richard G. FitzJohn, Rahuman S. Malik-Sheriff, John A. Lees

Bioinform., 2025

2024

Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems.

Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik-Sheriff, Hernán E. Grecco

Bioinform., 2024

2022

Building digital twins of the human immune system: toward a roadmap.

Reinhard C. Laubenbacher, Anna Niarakis, Tomás Helikar, Gary An, Bruce Shapiro, Rahuman S. Malik-Sheriff, T. J. Sego, Adam C. Knapp, Paul Macklin, James A. Glazier

npj Digit. Medicine, 2022

BioSimulators: a central registry of simulation engines and services for recommending specific tools.

Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. 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 D. 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

Nucleic Acids Res., 2022

The European Bioinformatics Institute (EMBL-EBI) in 2021.

Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton I. Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna R. McEntyre

Nucleic Acids Res., 2022

KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study.

Barbara Füzi, Rahuman S. Malik-Sheriff, Emma J. Manners, Henning Hermjakob, Gerhard F. Ecker

J. Cheminformatics, 2022

2021

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.

Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone

Briefings Bioinform., 2021

2020

BioModels - 15 years of sharing computational models in life science.

Rahuman S. Malik-Sheriff, Mihai Glont, Tung V. N. Nguyen, Krishan K. Tiwari, Matthew G. Roberts, Ashley Xavier, Manh T. Vu, Jinghao Men, Matthieu Maire, Sarubini Kananathan, Emma L. Fairbanks, Johannes P. Meyer, Chinmay Arankalle, Thawfeek M. Varusai, Vincent Knight-Schrijver, Lu Li, Corina Dueñas-Roca, Gaurhari Dass, Sarah M. Keating, Young Mi Park, Nicola Buso, Nicolas Rodriguez, Michael Hucka, Henning Hermjakob

Nucleic Acids Res., 2020

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).

Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers

J. Integr. Bioinform., 2020

BioModels Parameters: a treasure trove of parameter values from published systems biology models.

Mihai Glont, Chinmay Arankalle, Krishan K. Tiwari, Tung V. N. Nguyen, Henning Hermjakob, Rahuman S. Malik-Sheriff

Bioinform., 2020

2019

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang

J. Integr. Bioinform., 2019

2018

BioModels: expanding horizons to include more modelling approaches and formats.

Mihai Glont, Tung V. N. Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M. Wimalaratne, Varun B. Kothamachu, Nicolas Rodriguez, Maciej J. Swat, Jurgen Eils, Roland Eils, Camille Laibe, Rahuman S. Malik-Sheriff, Vijayalakshmi Chelliah, Nicolas Le Novère, Henning Hermjakob

Nucleic Acids Res., 2018

2015

Uncovering distinct protein-network topologies in heterogeneous cell populations.

Jakob Wieczorek, Rahuman S. Malik-Sheriff, Yessica Fermin, Hernán E. Grecco, Eli Zamir, Katja Ickstadt

BMC Syst. Biol., 2015