Computational Systems Biology by Xing-Ming Zhao, Weidong Tian, Rui Jiang, Jun Wan

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Integration of clinical, pathological, radiological, and transcriptomic data improves prediction for first-line immunotherapy outcome in metastatic non-small cell lung cancer by Nicolas Captier, Marvin Lerousseau, Fanny Orlhac, Narinée Hovhannisyan-Baghdasarian, Marie Luporsi, Erwin Woff, Sarah Lagha, Paulette Salamoun Feghali, Christine Lonjou, Clément Beaulaton, Andrei Zinovyev, Hélène Salmon, Thomas Walter, Irène Buvat, Nicolas Girard, Emmanuel Barillot

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Deep Learning Approaches for the Prediction of Protein Functional Sites by Borja Pitarch, Florencio Pazos

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Population models with quasi-constant-yield harvest rates by Kunquan Lan, Wei Lin

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Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure by Sophie Shen, Tessa Werner, Samuel W. Lukowski, Stacey Andersen, Yuliangzi Sun, Woo Jun Shim, Dalia Mizikovsky, Sakurako Kobayashi, Jennifer Outhwaite, Han Sheng Chiu, Xiaoli Chen, Gavin Chapman, Ella M. M. A. Martin, Di Xia, Duy Pham, Zezhuo Su, Daniel Kim, Pengyi Yang, Men Chee Tan, Enakshi Sinniah, Qiongyi Zhao, Sumedha Negi, Meredith A. Redd, Joseph E. Powell, Sally L. Dunwoodie, Patrick P. L. Tam, Mikael Bodén, Joshua W. K. Ho, Quan Nguyen, Nathan J. Palpant

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PharmRL: pharmacophore elucidation with deep geometric reinforcement learning by Rishal Aggarwal, David R. Koes

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Author Correction: A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain by Pere Gelabert, Victoria Oberreiter, Lawrence Guy Straus, Manuel Ramón González Morales, Susanna Sawyer, Ana B. Marín-Arroyo, Jeanne Marie Geiling, Florian Exler, Florian Brueck, Stefan Franz, Fernanda Tenorio Cano, Sophie Szedlacsek, Evelyn Zelger, Michelle Hämmerle, Brina Zagorc, Alejandro Llanos-Lizcano, Olivia Cheronet, José-Miguel Tejero, Thomas Rattei, Stephan M. Kraemer, Ron Pinhasi

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A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain by Pere Gelabert, Victoria Oberreiter, Lawrence Guy Straus, Manuel Ramón González Morales, Susanna Sawyer, Ana B. Marín-Arroyo, Jeanne Marie Geiling, Florian Exler, Florian Brueck, Stefan Franz, Fernanda Tenorio Cano, Sophie Szedlacsek, Evelyn Zelger, Michelle Hämmerle, Brina Zagorc, Alejandro Llanos-Lizcano, Olivia Cheronet, José-Miguel Tejero, Thomas Rattei, Stephan M. Kraemer, Ron Pinhasi

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Better understanding the phenotypic effects of drugs through shared targets in genetic disease networks by Elena Díaz-Santiago, Aurelio A. Moya-García, Jesús Pérez-García, Raquel Yahyaoui, Raquel Yahyaoui, Christine Orengo, Florencio Pazos, James R. Perkins, James R. Perkins, James R. Perkins, Juan A. G. Ranea, Juan A. G. Ranea, Juan A. G. Ranea, Juan A. G. Ranea

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Reconstruction and computational analysis of the microRNA regulation gene network in wheat drought response mechanisms by M. A. Kleshchev, A. V. Maltseva, E. A. Antropova, P. S. Demenkov, T. V. Ivanisenko, Y. L. Orlov, H. Chao, M. Chen, N. A. Kolchanov, V. A. Ivanisenko

“…Studying these mechanisms necessitates computational systems biology methods. This work aims to reconstruct and analyze the gene network associated with miRNA regulation of wheat adaptation to drought. …”
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Investigation of metabolic features of glioblastoma tissue and the peritumoral environment using targeted metabolomics screening by LC-MS/MS and gene network analysis by N. V. Basov, A. V. Adamovskaya, A. D. Rogachev, E. V. Gaisler, P. S. Demenkov, T. V. Ivanisenko, A. S. Venzel, S. V. Mishinov, V. V. Stupak, S. V. Cheresiz, O. S. Oleshko, E. A. Butikova, A. E. Osechkova, Yu. S. Sotnikova, Y. V. Patrushev, A. S. Pozdnyakov, I. N. Lavrik, V. A. Ivanisenko, A. G. Pokrovsky

“…Pathway analysis using the KEGG database, conducted with MetaboAnalyst 6.0, revealed a statistically sig­nificant overrepresentation of sphingolipid metabolism, suggesting a critical role of these lipid molecules in glio­blastoma pathogenesis. Using computational systems biology and artificial intelligence methods implemented in a cognitive platform, ANDSystem, molecular genetic regulatory pathways were reconstructed to describe potential mechanisms underlying the dysfunction of sphingolipid metabolism enzymes. …”
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