Vaccination strategies for Ebola in the democratic republic of Congo: the who-Ebola modeling collaboration by Marco Ajelli, Jean-Jacques Muyembe, Alhassane Touré, Abdourahamane Diallo, Maria Litvinova, Stefano Merler, Sabué Mulangu, Aminata Bagayoko, Aissatou Bah, Ibrahima Bah, Aissatou Barry, Fatoumata Barry, Mohamed Chérif, Doussou Condé, Alpha A. Diallo, Fatoumata Diallo, Mory Diakité, Kassié Doré, Koundouno A. Mapan, Thérèse Koundouno, Patrice K. Onivogui, Fassou Lamah, Henry Maneno, Alphonse Nomou, Kourouma Sekouba, Ismaila Sani, Abdoulaye Soumah, Mamadou M. Sy, Pierre-Stéphane Gsell, M. Elizabeth Halloran, Ana Maria Henao-Restrepo, Ibrahima Socé Fall, Mike J. Ryan, Peter Salama, Alessandro Vespignani, Ira M. Longini, Jr.

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Retinoblastoma-binding Protein 9 Suppresses Intestinal Inflammation and Inflammation-induced Tumorigenesis in MiceSummary by Kensuke Hamada, Yuki Nakanishi, Yu Muta, Mayuki Omatsu, Kosuke Iwane, Munehiro Ikeda, Jiayu Chen, Yoko Masui, Naoki Aoyama, Nobukazu Agatsuma, Go Yamakawa, Takahiro Utsumi, Hiroki Kitamoto, Makoto Okabe, Yoshiro Itatani, Takumi Adachi, Koubun Yasuda, Shuji Yamamoto, Akihisa Fukuda, Etsushi Kuroda, Masaki Ohmuraya, Kazutaka Obama, Seiichi Hirota, Hiroki Ikeuchi, Kenji Nakanishi, Hiroshi Seno

“…Methods: Human samples of UC and CAC were examined by immunohistochemical and bioinformatics analyses. We established dextran sodium sulfate (DSS)-induced colitis, azoxymethane (AOM)/DSS-induced CAC model, and ApcMin/+ sporadic tumor model using wild-type and Rbbp9-/- mice. …”
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STAGER checklist: Standardized testing and assessment guidelines for evaluating generative artificial intelligence reliability by Jinghong Chen, Lingxuan Zhu, Weiming Mou, Anqi Lin, Dongqiang Zeng, Chang Qi, Zaoqu Liu, Aimin Jiang, Bufu Tang, Wenjie Shi, Ulf D. Kahlert, Jianguo Zhou, Shipeng Guo, Xiaofan Lu, Xu Sun, Trunghieu Ngo, Zhongji Pu, Baolei Jia, Che Ok Jeon, Yongbin He, Haiyang Wu, Shuqin Gu, Wisit Cheungpasitporn, Haojie Huang, Weipu Mao, Shixiang Wang, Xin Chen, Loïc Cabannes, Gerald Sng Gui Ren, Iain S. Whitaker, Stephen Ali, Quan Cheng, Kai Miao, Shuofeng Yuan, Peng Luo

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Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis by Wei-Min Xiang, Yu-Ting Jiang, Jie Zou, Yan Deng, Kai Jiang, Kai-Jian Zhang, Xin-Yu Zhou, Kai-Xi Quan, Zi-Wen Han, Wei-Chao Liu, Liang Tang, Yuan-Yuan Li, Simon T. Segar, Yuan-Ye Zhang, Xing-Hua Hu, Rong Wang, Xiao-Yong Chen

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Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression by Alena Laschtowitz, Eric L. Lindberg, Anna-Maria Liebhoff, Laura Anne Liebig, Christian Casar, Silja Steinmann, Adrien Guillot, Jun Xu, Dorothee Schwinge, Michael Trauner, Ansgar Wilhelm Lohse, Stefan Bonn, Norbert Hübner, Christoph Schramm

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Progression and mortality of patients with cystic fibrosis in China by Wangji Zhou, Yaqi Wang, Yanli Yang, Yanyan Sun, Chongsheng Cheng, Jinrong Dai, Shuzhen Meng, Keqi Chen, Yang Zhao, Xueqi Liu, Dingding Zhang, Song Liu, Weiguo Zhu, Yaping Liu, Kai-Feng Xu, Xinlun Tian

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Gut dysbiosis is associated with difficult-to-treat rheumatoid arthritis by Patricia Ruiz-Limón, Patricia Ruiz-Limón, Patricia Ruiz-Limón, Natalia Mena-Vázquez, Natalia Mena-Vázquez, Isabel Moreno-Indias, Isabel Moreno-Indias, Isabel Moreno-Indias, Jose Manuel Lisbona-Montañez, Jose Manuel Lisbona-Montañez, Jose Manuel Lisbona-Montañez, Arkaitz Mucientes, Arkaitz Mucientes, Sara Manrique-Arija, Sara Manrique-Arija, Sara Manrique-Arija, Rocío Redondo-Rodriguez, Rocío Redondo-Rodriguez, Laura Cano-García, Laura Cano-García, Francisco J. Tinahones, Francisco J. Tinahones, Francisco J. Tinahones, Francisco J. Tinahones, Antonio Fernández-Nebro, Antonio Fernández-Nebro, Antonio Fernández-Nebro

“…The gut microbiota was analyzed using 16S rRNA gene sequencing; bioinformatics analysis was performed using QIIME2, and its functionality was inferred through PICRUSt. …”
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Case of phenotype of optic nerve atrophy due to mutation in С19orf12 gene (neurodegeneration with the brain iron accumulation (nbia)) by M.E. Ivanova, V.V. Kadyshev, D.S. Atarshchikov, I.V. Zolnikova, N.P. Akchurina, N.K. Serova, F.A. Konovalov, E.R. Lozier, E.A. Pomerantseva, N.V. Vetrova, D. Barh, L.M. Balashova, J.M. Salmasi

“…Burdenko National Medical Research Center of Neurosurgery, Moscow, Russian <br> Federation</b> </p> <p> <b>⁶Independent Clinical Bioinformatics Laboratory, Moscow, Russian Federation</b> </p> <p> <b>⁷Center for Genetics and Reproductive Medicine “Genetiko”, Moscow, Russian <br> Federation</b> </p> <p> <b>⁸Institute of Integrative Omics and Applied Biotechnology (IIOAB), Bangalore, India</b> </p> <p> <b>⁹ Non-profit partnership International Scientific and Practical Center for the Proliferation <br> of Tissues of Russia, Moscow, Russian Federation</b> </p> <p> <b>¹⁰Pirogov Russian National Research Medical University, Moscow, Russian Federation</b> </p> <p> <i>The article describes the clinical case of optic atrophy due to a homozygous mutation in exon 3 of the C19orf12 gene (chr19: 30193863AACAGCCCCCCG&gt; A, rs515726204), the frequency of which in the ExAC control sample is 0.0074. …”
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Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis by Salsabeel Yousuf, Hao Luo, Meiyin Zeng, Lei Chen, Tengfei Ma, Xiaofang Li, Maosheng Zheng, Xin Zhou, Liang Chen, Jiao Xi, Hongye Lu, Huiluo Cao, Xiaoya Ma, Bian Bian, Pengfan Zhang, Jiqiu Wu, Renyou Gan, Baolei Jia, Linyang Sun, Zhicheng Ju, Yunyun Gao, Waqar Afzal Malik, Chuang Ma, Hujie Lyu, Yahui Li, Huiyu Hou, Yuanping Zhou, Defeng Bai, Yao Wang, Haifei Yang, Jiani Xun, Shengda Du, Tianyuan Zhang, Xiulin Wan, Kai Peng, Shanshan Xu, Tao Wen, Tong Chen, Yong‐Xin Liu

“…However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. …”
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Designing a comprehensive behaviour change intervention to promote and monitor exclusive use of liquefied petroleum gas stoves for the Household Air Pollution Intervention Network... by J Jaime Miranda, William Checkley, Kyle Steenland, Vanessa Burrowes, Kirk R Smith, Aris Papageorghiou, Abigail Jones, Ghislaine Rosa, Anaité Díaz-Artiga, Gurusamy Thangavel, Kalpana Balakrishnan, Joshua P Rosenthal, Thomas F Clasen, Steven A Harvey, Amit Verma, Kendra N. Williams, Lisa M. Thompson, Zoe Sakas, Mayari Hengstermann, Ashlinn Quinn, Elisa Puzzolo, Jennifer Peel, Vigneswari Aravindalochanan, Dana Boyd Barr, Alejandra Bussalleu, Devan Campbell, Eduardo Canuz, Adly Castañaza, Howard Chang, Yunyun Chen, Marilú Chiang, Maggie L Clark, Rachel Craik, Mary Crocker, Victor Davila-Roman, Lisa de las Fuentes, Oscar De León, Ephrem Dusabimana, Lisa Elon, Juan Gabriel Espinoza, Irma Sayury Pineda Fuentes, Sarada Garg, Dina Goodman, Savannah Gupton, Meghan Hardison, Stella Hartinger, Phabiola M Herrera, Shakir Hossen, Penelope Howards, Lindsay Jaacks, Shirin Jabbarzadeh, Michael A Johnson, Katherine Kearns, Miles Kirby, Jacob Kremer, Margaret A Laws, Pattie Lenzen, Jiawen Liao, Amy E Lovvorn, Fiona Majorin, Eric McCollum, John McCracken, Julia N McPeek, Rachel Meyers, Erick Mollinedo, Lawrence Moulton, Krishnendu Mukhopadhyay, Luke Naeher, Abidan Nambajimana, Durairaj Natesan, Florien Ndagijimana, Azhar Nizam, Jean de Dieu Ntivuguruzwa, Ricardo Piedrahita, Ajay Pillarisetti, Naveen Puttaswamy, Sarah Rajkumar, Usha Ramakrishnan, Rengaraj Ramasami, Davis Reardon, Barry Ryan, Sudhakar Saidam, Sankar Sambandam, Jeremy A Sarnat, Suzanne Simkovich, Sheela S Sinharoy, Damien Swearing, Ashley Toenjes, Lindsay Underhill, Jean Damascene Uwizeyimana, Viviane Valdes, Kayla Valentine, Lance Waller, Megan Warnock, Wenlu Ye, Bonnie Young

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Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes by Peter Vo, Denise M. Imai-Leonard, Benjamin Yang, Andrew Briere, Andy Shao, M. Isabel Casanova, David Adams, Takanori Amano, Oana Amarie, Zorana Berberovic, Lynette Bower, Robert Braun, Steve Brown, Samantha Burrill, Soo Young Cho, Sharon Clementson-Mobbs, Abigail D’Souza, Mary Dickinson, Mohammad Eskandarian, Ann M. Flenniken, Helmut Fuchs, Valerie Gailus-Durner, Jason Heaney, Yann Hérault, Martin Hrabe de Angelis, Chih-Wei Hsu, Shundan Jin, Russell Joynson, Yeon Kyung Kang, Haerim Kim, Hiroshi Masuya, Hamid Meziane, Steve Murray, Ki-Hoan Nam, Hyuna Noh, Lauryl M. J. Nutter, Marcela Palkova, Jan Prochazka, Miles Joseph Raishbrook, Fabrice Riet, Jennifer Ryan, Jason Salazar, Zachery Seavey, John Richard Seavitt, Radislav Sedlacek, Mohammed Selloum, Kyoung Yul Seo, Je Kyung Seong, Hae-Sol Shin, Toshihiko Shiroishi, Michelle Stewart, Karen Svenson, Masaru Tamura, Heather Tolentino, Uchechukwu Udensi, Sara Wells, Jacqueline White, Amelia Willett, Janine Wotton, Wolfgang Wurst, Atsushi Yoshiki, The International Mouse Phenotyping Consortium, Louise Lanoue, K. C. Kent Lloyd, Brian C. Leonard, Michel J. Roux, Colin McKerlie, Ala Moshiri

“…Conclusions We identified 213 mouse genes that resulted in statistically significant abnormal corneal phenotypes in knockout mice, many of which have not previously been implicated in corneal pathology. Bioinformatic analyses implicated candidate genes in several signaling pathways which are potential therapeutic targets.…”
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Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders by Filipe Zimmer Dezordi, José Valter Joaquim Silva Júnior, Terimar Facin Ruoso, Angela Giovana Batista, Pedro Mesquita Fonseca, Larissa Paim Bernardo, Richard Steiner Salvato, Tatiana Schäffer Gregianini, Thaísa Regina Rocha Lopes, Eduardo Furtado Flores, Rudi Weiblen, Patrícia Chaves Brites, Mônica de Medeiros Silva, João Batista Teixeira da Rocha, Gustavo de Lima Barbosa, Lais Ceschini Machado, Alexandre Freitas da Silva, Marcelo Henrique Santos Paiva, Matheus Filgueira Bezerra, Tulio de Lima Campos, Tiago Gräf, Daniel Angelo Sganzerla Graichen, Elgion Lucio da Silva Loreto, Gabriel da Luz Wallau

“…SARS-CoV-2 whole genome amplification and sequencing were performed using high-throughput Illumina sequencing. Bioinformatics analysis encompassed the development of scripts and tools to perform subsampling taking into account epidemiological information to reduce sequencing disparities bias among the regions/countries, genome assembly, and large-scale alignment and phylogenetic reconstruction. …”
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Changes in laboratory value improvement and mortality rates over the course of the pandemic: an international retrospective cohort study of hospitalised patients infected with SARS... by Ramakanth Kavuluru, Xuan Wang, Paul Avillach, Florence Bourgeois, Kee Yuan Ngiam, Gabriel A Brat, Isaac Kohane, Tianxi Cai, Yuk-Lam Ho, Yuan Luo, Harrison G Zhang, Kelly Cho, Vincent Benoit, Antoine Neuraz, Chuan Hong, Sehi L'Yi, Griffin Weber, Bryce W Q Tan, Alba Gutiérrez-Sacristán, Clara-Lea Bonzel, Nathan P Palmer, Alberto Malovini, Valentina Tibollo, Meghan R Hutch, Molei Liu, Riccardo Bellazzi, Luca Chiovato, Fernando J Sanz Vidorreta, Trang T Le, William Yuan, Bertrand Moal, Michele Morris, David A Hanauer, Sarah Maidlow, Kavishwar Wagholikar, Shawn Murphy, Hossein Estiri, Adeline Makoudjou, Patric Tippmann, Jeffery Klann, Robert W Follett, Nils Gehlenborg, Gilbert S Omenn, Zongqi Xia, Arianna Dagliati, Shyam Visweswaran, Lav P Patel, Danielle L Mowery, Emily R Schriver, Malarkodi Jebathilagam Samayamuthu, Sara Lozano-Zahonero, Daniela Zöller, Amelia L M Tan, Byorn W L Tan, John H Holmes, Petra Schubert, Brett K. Beaulieu-Jones, Miguel Pedrera-Jiménez, Noelia García-Barrio, Pablo Serrano-Balazote, Andrew South

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Blood immunophenotyping of multiple sclerosis patients at diagnosis identifies a classical monocyte subset associated to disease evolution by Stéphane Rodriguez, Stéphane Rodriguez, Laura Couloume, Juliette Ferrant, Juliette Ferrant, Nicolas Vince, Marion Mandon, Marion Mandon, Rachel Jean, Rachel Jean, Celine Monvoisin, Simon Leonard, Simon Le Gallou, Simon Le Gallou, Nayane S. B. Silva, Nayane S. B. Silva, Sonia Bourguiba-Hachemi, David Laplaud, David Laplaud, Alexandra Garcia, Romain Casey, Romain Casey, Romain Casey, Romain Casey, Helene Zephir, Anne Kerbrat, Gilles Edan, Emmanuelle Lepage, Eric Thouvenot, Eric Thouvenot, Aurelie Ruet, Aurelie Ruet, Guillaume Mathey, Guillaume Mathey, Pierre-Antoine Gourraud, Pierre-Antoine Gourraud, Karin Tarte, Karin Tarte, Celine Delaloy, Patricia Amé, Patricia Amé, Mikael Roussel, Mikael Roussel, Laure Michel, Laure Michel, Laure Michel

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A Meta-Analysis of Tea Drinking and Risk of Parkinson's Disease by Feng-Jiao Li, Hong-Fang Ji, Liang Shen

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Novel Genes Potentially Involved in Fibroblasts of Diabetic Wound by Weirong Zhu, Qin Fang, Zhao Liu, Qiming Chen

“…In this study, we sought to screen out the novel genes which act important roles in diabetic fibroblasts through bioinformatic methods. A total of 811 and 490 differentially expressed genes (DEGs) between diabetic and normal fibroblasts were screened out in GSE49566 and GSE78891, respectively. …”
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A Genomic‐Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi by Holly V. Nelson, Arthur Georges, Katherine A. Farquharson, Elspeth A. McLennan, Jane L. DeGabriel, Katherine Belov, Carolyn J. Hogg

“…In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. …”
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Long Noncoding RNAs-Related Diseases, Cancers, and Drugs by Jen-Yang Tang, Jin-Ching Lee, Yung-Ting Chang, Ming-Feng Hou, Hurng-Wern Huang, Chih-Chuang Liaw, Hsueh-Wei Chang

“…Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized. The improving knowledge of the lncRNA regulatory network has implications not only in gene expression, diseases, and cancers, but also in the development of lncRNA-based pharmacology.…”
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Systematic multiomics analysis and in vitro experiments suggest that ITGA5 could serve as a promising therapeutic target for ccRCC by Xiangxian Che, Xi Tian, Zhenda Wang, Shuxuan Zhu, Shiqi Ye, Yue Wang, Yihan Chen, Yiyun Huang, Aihetaimujiang Anwaier, Peifeng Yao, Yijia Chen, Keting Wu, Yifei Liu, Wenhao Xu, Hailiang Zhang, Dingwei Ye

“…In vitro experiments and bioinformatical analysis identified ITGA5 function as predominantly cell proliferation, migration, angiogenesis, and macrophage recruitment. …”
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Molecular Basis of Inhibitory Activities of Berberine against Pathogenic Enzymes in Alzheimer's Disease by Hong-Fang Ji, Liang Shen

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