Low dimensionality of phenotypic space as an emergent property of coordinated teams in biological regulatory networks by Kishore Hari, Pradyumna Harlapur, Aashna Saxena, Kushal Haldar, Aishwarya Girish, Tanisha Malpani, Herbert Levine, Mohit Kumar Jolly

Subjects: “…Systems biology…”
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Potential Antidepressant Effects of Omeprazole Introduced Through Network Analysis and Systems Biology Should Be Interpreted with Caution in the Clinical Environment by Seyed-Ali Mostafavi

Subjects: “…Systems Biology…”
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Questions from the fourth son: A clinician reflects on immunomonitoring, surrogate markers and systems biology by Charles Wiseman, M.D.

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Ontologies in bioinformatics and systems biology by N. L. Podkolodnyy, O. A. Podkolodnaya

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Online resources on gene networks containing human and animal data by E. V. Ignatieva, D. A. Afonnikov, N. A.  Kolchanov

Subjects: “…systems biology…”
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Protocol for predicting the single-cell network-based gene activity landscape during human B cell development by Xin Huang, Xuetong Hou, Yizhen Li, Jun J. Yang, Jiyang Yu

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Protocol to study the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation by Ana Laura Cano-Argüelles, Alejandra Wu-Chuang, Lourdes Mateos-Hernandez, Lianet Abuin-Denis, Apolline Maitre, Janet Avellanet, Arlem García, Dasha Fuentes, Alejandro Cabezas-Cruz

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Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink by Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros

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Protocol to denoise spatially resolved transcriptomics data utilizing optimal transport-based gene filtering algorithm by Lin Du, Jingmin Kang, Jie Li, Hua Qin, Yong Hou, Hai-Xi Sun

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Causal models and prediction in cell line perturbation experiments by James P. Long, Yumeng Yang, Shohei Shimizu, Thong Pham, Kim-Anh Do

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Protocol for cell image-based spatiotemporal proteomics in budding yeast by Athanasios Litsios, Myra Paz David Masinas, Helena Friesen, Charles Boone, Brenda J. Andrews

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Protocol to generate dual-target compounds using a transformer chemical language model by Sanjana Srinivasan, Jürgen Bajorath

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State of the interactomes: an evaluation of molecular networks for generating biological insights by Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker

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Diversity in Notch ligand-receptor signaling interactions by Rachael Kuintzle, Leah A Santat, Michael B Elowitz

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Analyzing sorbitol biosynthesis using a metabolic network flux model of a lichenized strain of the green microalga Diplosphaera chodatii by Hadi Nazem-Bokaee, Erik F. Y. Hom, Sarah Mathews, Cécile Gueidan

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Liver transcriptomics-metabolomics integration reveals biological pathways associated with fetal programming in beef cattle by Guilherme Henrique Gebim Polizel, Simara Larissa Fanalli, Wellison J. S. Diniz, Aline Silva Mello Cesar, Nara Regina Brandão Cônsolo, Heidge Fukumasu, Angela Cánovas, Arícia Christofaro Fernandes, Barbara Carolina Teixeira Prati, Édison Furlan, Gabriela do Vale Pombo, Miguel Henrique de Almeida Santana

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The systemic evolutionary theory of the origin of cancer (SETOC): an update by Antonio Mazzocca, Giovanni Ferraro, Giovanni Misciagna

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The relative biologic effectiveness versus linear energy transfercurve as an output-input relation for linear cellular systems by Quoc T. Luu, Paul DuChateau

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A multi-omics strategy to understand PASC through the RECOVER cohorts: a paradigm for a systems biology approach to the study of chronic conditions by Jun Sun, Masanori Aikawa, Hassan Ashktorab, Noam D. Beckmann, Noam D. Beckmann, Michael L. Enger, Joaquin M. Espinosa, Xiaowu Gai, Xiaowu Gai, Benjamin D. Horne, Benjamin D. Horne, Paul Keim, Paul Keim, Paul Keim, Jessica Lasky-Su, Rebecca Letts, Cheryl L. Maier, Meisha Mandal, Lauren Nichols, Nadia R. Roan, Nadia R. Roan, Mark W. Russell, Jacqueline Rutter, George R. Saade, George R. Saade, Kumar Sharma, Kumar Sharma, Stephanie Shiau, Stephen N. Thibodeau, Samuel Yang, Lucio Miele, NIH Researching COVID to Enhance Recovery (RECOVER) Consortium

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The TB27 Transcriptomic Model for Predicting Mycobacterium tuberculosis Culture Conversion by Maja Reimann, Korkut Avsar, Andrew DiNardo, Torsten Goldmann, Gunar Günther, Michael Hoelscher, Elmira Ibraim, Barbara Kalsdorf, Stefan Kaufmann, Niklas Köhler, Anna Mandalakas, Florian Maurer, Marius Müller, Dörte Nitschkowski, Ioana Olaru, Cristina Popa, Andrea Rachow, Thierry Rolling, Helmut Salzer, Patricia Sanchez-Carballo, Maren Schuhmann, Dagmar Schaub, Victor Spinu, Elena Terhalle, Markus Unnewehr, Nika Zielinski, Jan Heyckendorf, Christoph Lange

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