Crop pests and predators exhibit inconsistent responses to surrounding landscape composition

by Karp, Daniel S., Meehan, Timothy D., Martin, Emily A., DeClerck, Fabrice, Grab, Heather, Gratton, Claudio, Larsen, Ashley E., Rusch, Adrien, Poveda, Katja, Jonsson, Mattias, Rosenheim, Jay A., Tscharntke, Teja, Wratten, Stephen D., Zhang, Wei, Iverson, Aaron L., Adler, Lynn S., Albrecht, Matthias, Alignier, Audrey, Angelella, Gina M., Bohnenblust, Eric W., Bommarco, Riccardo, Brewer, Michael J., Caballero-López, Berta, Carrière, Yves, Carvalheiro, Luísa G., Centrella, Mary, Henri, Dominic Charles, Chabert, Ariane, Costamagna, Alejandro C., De la Mora, Aldo, de Kraker, Joop, Desneux, Nicolas, Dormann, Carsten F., Eckberg, James O., Fiedler, Daniela, Franck, Pierre, van Veen, F. J. Frank, Frank, Thomas, Gagic, Vesna, Garratt, Michael P. D., Gonthier, David J., Graziosi, Ignazio, Hajian-Forooshani, Zachary, Heimpel, George E., Herrmann, John D., Huseth, Anders S., Inclán, Diego J., Iv, Phirun, Johnson, Gregg A., Kaiser, Marina, Keasar, Tamar, Kim, Tania N., Kishinevsky, Miriam, Landis, Douglas A., Lavandero, Blas, Lu, Yanhui, Lubin, Yael, Maas, Bea, Mace, Kevi, Madeira, Filipe, Cortesero, Anne Marie, Martinez, Eliana, Martinson, Holly M., Menozzi, Philippe, Miyashit, Tadashi, Molina, Gonzalo A. R., O’Neal, Matthew E., Opatovsky, Itai, Ortiz-Martinez, Sebaastian, Nash, Michael, Ouin, Annie, Pak, Damie, Paredes, Daniel, Parsa, Soroush, Parry, Hazel, Perović, David J., Peterson, Julie A., Petit, Sandrine, Philpott, Stacy M., Pluess, Therese, Pons, Xavier, Ragsdale, David W., Saulais, Julia, Schäckermann, Jessica, Schmidt, Nick P., Schneider, Gudrun, Schüepp, Christof, Smith, Henrik G., Whitney, Kaitlin Stack, Stutz, Sonja, Takada, Mayura B., Tamburini, Giovanni, Valantin-Morison, Muriel, Van Trinh, Mai, van der Werf, Wopke, Vierling, Kerri T., Wickens, Victoria J., Woodcock, Ben A., Wyckhuys, Kris, Yoshioka, Akira
Published in Proceedings of the National Academy of Sciences - PNAS

Predicting perturbation patterns from the topology of biological networks

by Santolini, Marc, Barabási, Albert-László
Published in Proceedings of the National Academy of Sciences - PNAS

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

by Keating, Sarah M, Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Chaouiya, Claudine, Finney, Andrew, Gillespie, Colin S, Helikar, Tomáš, Malik‐Sheriff, Rahuman S, Moraru, Ion I, Naldi, Aurélien, Sahle, Sven, Schaff, James C, Smith, Lucian P, Swat, Maciej J, Thieffry, Denis, Wilkinson, Darren J, Blinov, Michael L, Begley, Kimberly, Faeder, James R, Gómez, Harold F, Hamm, Thomas M, Inagaki, Yuichiro, Liebermeister, Wolfram, Lucio, Daniel, Proctor, Carole J, Raman, Karthik, Rodriguez, Nicolas, Shapiro, Bruce E, Tanimura, Naoki, Wagner, John, Sauro, Herbert M, Palsson, Bernhard, Bolouri, Hamid, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C, Hucka, Michael, Adams, Richard R, Allen, Nicholas A, Angermann, Bastian R, Antoniotti, Marco, Courtot, Mélanie, Cox, Chris D, Dalle Pezze, Piero, Demir, Emek, Denney, William S, Dharuri, Harish, Dorier, Julien, Drasdo, Dirk, Ebrahim, Ali, Eichner, Johannes, Elf, Johan, Flamm, Christoph, Fleming, Ronan MT, Fröhlich, Martina, Gonçalves, Emanuel, Golebiewski, Martin, Grabski, Hovakim, Heavner, Benjamin D, Hyduke, Daniel R, Jong, Hidde, Juty, Nick, Karp, Peter D, Kiselev, Ilya, Klipp, Edda, Knüpfer, Christian, Kolpakov, Fedor, Laibe, Camille, Lawless, Conor, Li, Lu, Machne, Rainer, Mendes, Pedro, Mittag, Florian, Monteiro, Pedro T, Natarajan, Kedar Nath, Nguyen, Tramy, Pfau, Thomas, Phair, Robert D, Radivoyevitch, Tomas, Rohwer, Johann M, Saez‐Rodriguez, Julio, Scharm, Martin, Schmidt, Henning, Schreiber, Falk, Schubert, Michael, Schulte, Roman, Sealfon, Stuart C, Soliman, Sylvain, Stefan, Melanie I, Sullivan, Devin P, Takahashi, Koichi, Teusink, Bas, Tolnay, David, Vazirabad, Ibrahim, Kamp, Axel, Wittig, Ulrike, Wrzodek, Clemens, Zucker, Jeremy
Published in Molecular systems biology

The bioprinting roadmap

by Sun, Wei, Starly, Binil, Daly, Andrew C, Burdick, Jason A, Groll, Jürgen, Skeldon, Gregor, Shu, Wenmiao, Sakai, Yasuyuki, Shinohara, Marie, Nishikawa, Masaki, Jang, Jinah, Cho, Dong-Woo, Nie, Minghao, Takeuchi, Shoji, Ostrovidov, Serge, Khademhosseini, Ali, Kamm, Roger D, Mironov, Vladimir, Moroni, Lorenzo, Ozbolat, Ibrahim T
Published in Biofabrication

Structural identifiability of systems biology models: a critical comparison of methods

by Chis, Oana-Teodora, Banga, Julio R, Balsa-Canto, Eva
Published in PloS one

Multi-endpoint toxicological assessment of polystyrene nano- and microparticles in different biological models in vitro

by Hesler, Michelle, Aengenheister, Leonie, Ellinger, Bernhard, Drexel, Roland, Straskraba, Susanne, Jost, Carsten, Wagner, Sylvia, Meier, Florian, von Briesen, Hagen, Büchel, Claudia, Wick, Peter, Buerki-Thurnherr, Tina, Kohl, Yvonne
Published in Toxicology in vitro

Systems biology informed deep learning for inferring parameters and hidden dynamics

by Yazdani, Alireza, Lu, Lu, Raissi, Maziar, Karniadakis, George Em
Published in PLoS computational biology

Topological data analysis of biological aggregation models

by Topaz, Chad M, Ziegelmeier, Lori, Halverson, Tom
Published in PloS one

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

by Oftadeh, Omid, Salvy, Pierre, Masid, Maria, Curvat, Maxime, Miskovic, Ljubisa, Hatzimanikatis, Vassily
Published in Nature communications

Multi-timescale systems and fast-slow analysis

by Bertram, Richard, Rubin, Jonathan E.
Published in Mathematical biosciences

New genetic loci link adipose and insulin biology to body fat distribution

by Ferreira, Teresa, Pers, Tune H, Justice, Anne E, Workalemahu, Tsegaselassie, Kutalik, Zoltán, Randall, Joshua C, Wood, Andrew R, Kahali, Bratati, Ehret, Georg B, Goel, Anuj, Van Vliet-Ostaptchouk, Jana V, Albrecht, Eva, Arscott, Gillian M, Bellis, Claire, Böttcher, Yvonne, Clarke, Robert, Eklund, Niina, Friedrich, Nele, Giedraitis, Vilmantas, Gigante, Bruna, Grallert, Harald, Grewal, Jagvir, Hallmans, Goran, Hayward, Caroline, Hillege, Hans L, Johansson, Ingegerd, Kalafati, Ioanna-Panagiota, Koenig, Wolfgang, Kratzer, Wolfgang, Lindström, Jaana, McArdle, Wendy L, Menni, Cristina, Merger, Sigrun, Mihailov, Evelin, Mühleisen, Thomas W, Mulas, Antonella, Seufferlein, Thomas, Sitlani, Colleen M, Stirrups, Kathleen, Stringham, Heather M, Syvänen, Ann-Christine, Tayo, Bamidele O, Wennauer, Roman, Wojczynski, Mary K, Brennan, Eoin P, Folkersen, Lasse, Franco-Cereceda, Anders, Hedman, Åsa K, Kanoni, Stavroula, Keildson, Sarah, Kiryluk, Krzysztof, Liang, Liming, Min, Josine L, Moffatt, Miriam F, Schadt, Eric E, Westra, Harm-Jan, Zondervan, Krina T, Franco, Oscar H, Gudnason, Vilmundur, Haiman, Christopher A, Heliövaara, Markku, Jarvelin, Marjo-Riitta, Johansen, Berit, Keinanen-Kiukaanniemi, Sirkka M, Kooner, Jaspal S, Kraja, Aldi T, Le Marchand, Loic, Möhlenkamp, Stefan, Nelis, Mari, Ohlsson, Claes, Peters, Annette, Ritchie, Marylyn D, Shuldiner, Alan R, Stolk, Ronald P, Vollenweider, Peter, Adair, Linda S, Boehm, Bernhard O, Grabe, Hans-Jörgen, Hveem, Kristian, Kivimaki, Mika, Njølstad, Inger, Oostra, Ben A, Palmer, Colin Na, Pérusse, Louis, Peters, Ulrike, Quertermous, Thomas, Sinisalo, Juha, Stumvoll, Michael, Uusitupa, Matti, Veronesi, Giovanni, Berndt, Sonja I, Borecki, Ingrid B, Hunter, David J, Thorsteinsdottir, Unnur, Willer, Cristen J, Hirschhorn, Joel N, Fox, Caroline S, Loos, Ruth Jf, Lindgren, Cecilia M, Mohlke, Karen L
Published in Nature (London)

Integrated cancer tissue engineering models for precision medicine

by Bregenzer, Michael E, Horst, Eric N, Mehta, Pooja, Novak, Caymen M, Raghavan, Shreya, Snyder, Catherine S, Mehta, Geeta
Published in PloS one

Composite Patankar-Euler methods for positive simulations of stochastic differential equation models for biological regulatory systems

by Chen, Aimin, Zhou, Tianshou, Burrage, Pamela, Tian, Tianhai, Burrage, Kevin
Published in The Journal of chemical physics

Universally sloppy parameter sensitivities in systems biology models

by Gutenkunst, Ryan N, Waterfall, Joshua J, Casey, Fergal P, Brown, Kevin S, Myers, Christopher R, Sethna, James P
Published in PLoS computational biology

Massive computational acceleration by using neural networks to emulate mechanism-based biological models

by Wang, Shangying, Fan, Kai, Luo, Nan, Cao, Yangxiaolu, Wu, Feilun, Zhang, Carolyn, Heller, Katherine A, You, Lingchong
Published in Nature communications

Methods of Model Reduction for Large-Scale Biological Systems: A Survey of Current Methods and Trends

by Snowden, Thomas J., van der Graaf, Piet H., Tindall, Marcus J.
Published in Bulletin of mathematical biology

Efficient rejection-based simulation of biochemical reactions with stochastic noise and delays

by Thanh, Vo Hong, Priami, Corrado, Zunino, Roberto
Published in The Journal of chemical physics

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems

by Gábor, Attila, Villaverde, Alejandro F, Banga, Julio R
Published in BMC systems biology

Sloppiness: Fundamental study, new formalism and its application in model assessment

by Jagadeesan, Prem, Raman, Karthik, Tangirala, Arun K
Published in PloS one

Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation

by Villaverde, Alejandro F, Banga, Julio R
Published in PLoS computational biology