Reproducibility in systems biology modelling by Tiwari, Krishna, Kananathan, Sarubini, Roberts, Matthew G, Meyer, Johannes P, Sharif Shohan, Mohammad Umer, Xavier, Ashley, Maire, Matthieu, Zyoud, Ahmad, Men, Jinghao, Ng, Szeyi, Nguyen, Tung V N, Glont, Mihai, Hermjakob, Henning, Malik‐Sheriff, Rahuman S

Get full text

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

Request full text

The European Bioinformatics Institute (EMBL-EBI) in 2021 by Cantelli, Gaia, Bateman, Alex, Brooksbank, Cath, Petrov, Anton I, Malik-Sheriff, Rahuman S, Ide-Smith, Michele, Hermjakob, Henning, Flicek, Paul, Apweiler, Rolf, Birney, Ewan, McEntyre, Johanna

Get full text

Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network by Cucurull‐Sanchez, Lourdes, Chappell, Michael J., Chelliah, Vijayalakshmi, Amy Cheung, S. Y., Derks, Gianne, Penney, Mark, Phipps, Alex, Malik‐Sheriff, Rahuman S., Timmis, Jon, Tindall, Marcus J., Graaf, Piet H., Vicini, Paolo, Yates, James W. T.

Get full text

BioModels Parameters: a treasure trove of parameter values from published systems biology models by Glont, Mihai, Arankalle, Chinmay, Tiwari, Krishna, Nguyen, Tung V N, Hermjakob, Henning, Malik-Sheriff, Rahuman S

Get full text

BioSimulators: a central registry of simulation engines and services for recommending specific tools by 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, Fröhlich, 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, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, 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, Jörn, 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

Get full text

KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study by Füzi, Barbara, Malik-Sheriff, Rahuman S., Manners, Emma J., Hermjakob, Henning, Ecker, Gerhard F.

Get full text

Highly Multiplexed Imaging Uncovers Changes in Compositional Noise within Assembling Focal Adhesions by Harizanova, Jana, Fermin, Yessica, Malik-Sheriff, Rahuman S, Wieczorek, Jakob, Ickstadt, Katja, Grecco, Hernán E, Zamir, Eli

Get full text

BioModels’ Model of the Year 2023 by Malik Sheriff, Rahuman S., Asari, Hiroki, Hermjakob, Henning, Huber, Wolfgang, Quail, Thomas, Santos, Silvia D. M., Smith, Amber M., Uhlmann, Virginie

Get full text

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) by Waltemath, Dagmar, Golebiewski, Martin, Blinov, Michael L, Gleeson, Padraig, Hermjakob, Henning, Hucka, Michael, Inau, Esther Thea, Keating, Sarah M, König, Matthias, Krebs, Olga, Malik-Sheriff, Rahuman S, Nickerson, David, Oberortner, Ernst, Sauro, Herbert M, Schreiber, Falk, Smith, Lucian, Stefan, Melanie I, Wittig, Ulrike, Myers, Chris J

Get full text

BioModels—15 years of sharing computational models in life science by Malik-Sheriff, Rahuman S, Glont, Mihai, Nguyen, Tung V N, Tiwari, Krishna, Roberts, Matthew G, Xavier, Ashley, Vu, Manh T, Men, Jinghao, Maire, Matthieu, Kananathan, Sarubini, Fairbanks, Emma L, Meyer, Johannes P, Arankalle, Chinmay, Varusai, Thawfeek M, Knight-Schrijver, Vincent, Li, Lu, Dueñas-Roca, Corina, Dass, Gaurhari, Keating, Sarah M, Park, Young M, Buso, Nicola, Rodriguez, Nicolas, Hucka, Michael, Hermjakob, Henning

Get full text

Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems by Silberberg, Mauro, Hermjakob, Henning, Malik-Sheriff, Rahuman S, Grecco, Hernán E

Get full text

Systems Biology in ELIXIR: modelling in the spotlight [version 1; peer review: 1 approved, 2 approved with reservations] by Martins dos Santos, Vitor, Anton, Mihail, Szomolay, Barbara, Ostaszewski, Marek, Arts, Ilja, Benfeitas, Rui, Dominguez Del Angel, Victoria, Ferk, Polonca, Fey, Dirk, Goble, Carole, Golebiewski, Martin, Gruden, Kristina, Heil, Katharina F., Hermjakob, Henning, Kahlem, Pascal, Klapa, Maria I., Koehorst, Jasper, Kolodkin, Alexey, Kutmon, Martina, Leskošek, Brane, Moretti, Sébastien, Müller, Wolfgang, Pagni, Marco, Rezen, Tadeja, Rocha, Miguel, Rozman, Damjana, Šafránek, David, Sheriff, Rahuman S. Malik, Suarez Diez, Maria, Van Steen, Kristel, Westerhoff, Hans V, Wittig, Ulrike, Wolstencroft, Katherine, Zupanic, Anze, Evelo, Chris T., Hancock, John M.

Get full text

Systems Biology in ELIXIR: modelling in the spotlight [version 2; peer review: 2 approved, 1 approved with reservations] by Martins dos Santos, Vitor, Anton, Mihail, Szomolay, Barbara, Ostaszewski, Marek, Arts, Ilja, Benfeitas, Rui, Dominguez Del Angel, Victoria, Domínguez-Romero, Elena, Ferk, Polonca, Fey, Dirk, Goble, Carole, Golebiewski, Martin, Gruden, Kristina, Heil, Katharina F., Hermjakob, Henning, Kahlem, Pascal, Klapa, Maria I., Koehorst, Jasper, Kolodkin, Alexey, Kutmon, Martina, Leskošek, Brane, Moretti, Sébastien, Müller, Wolfgang, Pagni, Marco, Rezen, Tadeja, Rocha, Miguel, Rozman, Damjana, Šafránek, David, T. Scott, William, Sheriff, Rahuman S. Malik, Suarez Diez, Maria, Van Steen, Kristel, Westerhoff, Hans V, Wittig, Ulrike, Wolstencroft, Katherine, Zupanic, Anze, Evelo, Chris T., Hancock, John M.

Get full text

BioModels: expanding horizons to include more modelling approaches and formats by Glont, Mihai, Nguyen, Tung V N, Graesslin, Martin, Hälke, Robert, Ali, Raza, Schramm, Jochen, Wimalaratne, Sarala M, Kothamachu, Varun B, Rodriguez, Nicolas, Swat, Maciej J, Eils, Jurgen, Eils, Roland, Laibe, Camille, Malik-Sheriff, Rahuman S, Chelliah, Vijayalakshmi, Le Novère, Nicolas, Hermjakob, Henning

Get full text

Diverse patterns of molecular changes in the mechano-responsiveness of focal adhesions by Malik-Sheriff, Rahuman S., Imtiaz, Sarah, Grecco, Hernán E., Zamir, Eli

Get full text

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing by Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars Keld, Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard O., Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Sheriff, Rahuman S. Malik, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng

Get full text

Immune digital twins for complex human pathologies: applications, limitations, and challenges by Niarakis, Anna, Laubenbacher, Reinhard, An, Gary, Ilan, Yaron, Fisher, Jasmin, Flobak, Åsmund, Reiche, Kristin, Rodríguez Martínez, María, Geris, Liesbet, Ladeira, Luiz, Veschini, Lorenzo, Blinov, Michael L., Messina, Francesco, Fonseca, Luis L., Ferreira, Sandra, Montagud, Arnau, Noël, Vincent, Marku, Malvina, Tsirvouli, Eirini, Torres, Marcella M., Harris, Leonard A., Sego, T. J., Cockrell, Chase, Shick, Amanda E., Balci, Hasan, Salazar, Albin, Rian, Kinza, Hemedan, Ahmed Abdelmonem, Esteban-Medina, Marina, Staumont, Bernard, Hernandez-Vargas, Esteban, Martis B, Shiny, Madrid-Valiente, Alejandro, Karampelesis, Panagiotis, Sordo Vieira, Luis, Harlapur, Pradyumna, Kulesza, Alexander, Nikaein, Niloofar, Garira, Winston, Malik Sheriff, Rahuman S., Thakar, Juilee, Tran, Van Du T., Carbonell-Caballero, Jose, Safaei, Soroush, Valencia, Alfonso, Zinovyev, Andrei, Glazier, James A.

Get full text

Uncovering distinct protein-network topologies in heterogeneous cell populations by Wieczorek, Jakob, Malik-Sheriff, Rahuman S, Fermin, Yessica, Grecco, Hernán E, Zamir, Eli, Ickstadt, Katja

Get full text

Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility by Karr, Jonathan, Malik-Sheriff, Rahuman S, Osborne, James, Gonzalez-Parra, Gilberto, Forgoston, Eric, Bowness, Ruth, Liu, Yaling, Thompson, Robin, Garira, Winston, Barhak, Jacob, Rice, John, Torres, Marcella, Dobrovolny, Hana M, Tang, Tingting, Waites, William, Glazier, James A, Faeder, James R, Kulesza, Alexander

Get full text