Article
Biochemistry & Molecular Biology
Noemi del Toro, Anjali Shrivastava, Eliot Ragueneau, Birgit Meldal, Colin Combe, Elisabet Barrera, Livia Perfetto, Karyn How, Prashansa Ratan, Gautam Shirodkar, Odilia Lu, Balint Meszaros, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwinski, Sandra Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob
Summary: IntAct is a curated database of molecular interactions derived from scientific literature, containing over one million binary interactions curated by twelve global partners. The IMEx curation policy emphasizes fine-grained data and curation model to capture essential experimental details for interpretation of the molecular interaction data. Recently, IntAct has introduced a completely redeveloped website to present data in a more user-friendly and detailed way.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
James W. Saville, Dhiraj Mannar, Xing Zhu, Shanti S. Srivastava, Alison M. Berezuk, Jean-Philippe Demers, Steven Zhou, Katharine S. Tuttle, Inna Sekirov, Andrew Kim, Wei Li, Dimiter S. Dimitrov, Sriram Subramaniam
Summary: The Delta and Kappa variants of SARS-CoV-2, emerged in India in late 2020, demonstrate antibody escape and enhanced ACE2 binding, which contribute to their global dominance.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Bruno Merlin, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sa, Monica Silva de Oliveira, Larissa Maranhao Dias, Gislenne da Silva Moia, Victoria Cardoso dos Santos, Adonney Allan de Oliveira Veras
Summary: Manual curation of genome annotation is time-consuming and requires specialized labor, but is essential for adding complementary information to gene products. The CODON software streamlines this process and provides access to accurate database information and additional gene acronyms, metabolic pathways, and Gene Ontology terms.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Zhennan Zhao, Yufeng Xie, Bin Bai, Chunliang Luo, Jingya Zhou, Weiwei Li, Yumin Meng, Linjie Li, Dedong Li, Xiaomei Li, Xiaoxiong Li, Xiaoyun Wang, Junqing Sun, Zepeng Xu, Yeping Sun, Wei Zhang, Zheng Fan, Xin Zhao, Linhuan Wu, Juncai Ma, Odel Y. Li, Guijun Shang, Yan Chai, Kefang Liu, Peiyi Wang, George F. Gao, Jianxun Qi
Summary: Multiple SARS-CoV-2 Omicron sub-variants have emerged, with BA.5 becoming the dominant strain worldwide and BA.2.75 significantly increasing in some countries. The binding affinities between these sub-variants and ACE2 receptors in humans and closely related animals remain similar to previous variants of concern. However, a reverse mutation (R493Q) enhances the bindings to ACE2 receptors, suggesting an increased risk of cross-species transmission. Structural analysis reveals the molecular basis for receptor binding and broader interspecies recognition.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Tingting Li, Xiaojian Han, Chenjian Gu, Hangtian Guo, Huajun Zhang, Yingming Wang, Chao Hu, Kai Wang, Fengjiang Liu, Feiyang Luo, Yanan Zhang, Jie Hu, Wang Wang, Shenglong Li, Yanan Hao, Meiying Shen, Jingjing Huang, Yingyi Long, Shuyi Song, Ruixin Wu, Song Mu, Qian Chen, Fengxia Gao, Jianwei Wang, Shunhua Long, Luo Li, Yang Wu, Yan Gao, Wei Xu, Xia Cai, Di Qu, Zherui Zhang, Hongqing Zhang, Na Li, Qingzhu Gao, Guiji Zhang, Changlong He, Wei Wang, Xiaoyun Ji, Ni Tang, Zhenghong Yuan, Youhua Xie, Haitao Yang, Bo Zhang, Ailong Huang, Aishun Jin
Summary: Neutralizing antibodies targeting the receptor binding domain have shown remarkable efficacy against authentic SARS-CoV-2 and B.1.351 viruses. Two potent neutralizing antibodies, 58G6 and 510A5, demonstrate prophylactic efficacy and could be promising candidates to combat the prolonged COVID-19 pandemic.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Dhiraj Mannar, James W. Saville, Xing Zhu, Shanti S. Srivastava, Alison M. Berezuk, Steven Zhou, Katharine S. Tuttle, Andrew Kim, Wei Li, Dimiter S. Dimitrov, Sriram Subramaniam
Summary: The newly emerged SARS-CoV-2 variants, Beta and Gamma, exhibit key mutations that enhance spike protein affinity for ACE2 receptor and promote antibody evasion. By engineering spike proteins with these mutations and conducting structural analyses, the effects of different variants were studied in terms of increased ACE2 affinity and antibody evasion.
Article
Radiology, Nuclear Medicine & Medical Imaging
Jeroen Bleker, Thomas C. Kwee, Dennis Rouw, Christian Roest, Jaap Borstlap, Igle Jan de Jong, Rudi A. J. O. Dierckx, Henkjan Huisman, Derya Yakar
Summary: The deep learning masked auto-fixed volume of interest (DLM) segmentation method provides a more accurate radiomics diagnosis of clinically significant prostate cancer (CS PCa) compared to manual segmentation, while significantly reducing expert time investment.
EUROPEAN RADIOLOGY
(2022)
Article
Genetics & Heredity
Cristina Fortuno, Kristy Lee, Magali Olivier, Tina Pesaran, Phuong L. Mai, Kelvin C. de Andrade, Laura D. Attardi, Stephanie Crowley, D. Gareth Evans, Bing-Jian Feng, Ann K. M. Foreman, Megan N. Frone, Robert Huether, Paul A. James, Kelly McGoldrick, Jessica Mester, Bryce A. Seifert, Thomas P. Slavin, Leora Witkowski, Liying Zhang, Sharon E. Plon, Amanda B. Spurdle, Sharon A. Savage
Summary: Germline pathogenic variants in TP53 are associated with Li-Fraumeni syndrome, a cancer predisposition disorder inherited in an autosomal dominant pattern. Intense cancer surveillance for individuals with these variants can reduce cancer-related mortality. Accurate classification of germline variants is crucial for ensuring appropriate cancer surveillance recommendations.
Article
Cell Biology
Wenwe Li, Yaozong Chen, Jeemie Prevost, Irfan Ullah, Maoli Lu, Shang Yu Gong, Alexandra Tauzin, Romain Gasser, Dani Vezina, Sai Priya Anand, Guillaume Goyette, Debashree Chaterjee, Shilei Ding, William D. Tolbert, Michael W. Grunst, Yuxia Bo, Shijian Zhang, Jonathan Richard, Fei Zhou, Rick K. Huang, Lothar Esser, Allison Zeher, Marceline Cote, Priti Kumar, Joseph Sodroski, Di Xia, Pradeep D. Uchil, Marzena Pazgier, Andres Finzi, Walther Mothes
Summary: This study elucidates the structural basis and mode of action for two potent SARS-CoV-2 spike-neutralizing monoclonal antibodies. CV3-1 triggers shedding of the S1 subunit by binding to a loop structure in the receptor-binding domain (RBD), while CV3-25 inhibits membrane fusion by binding to an epitope in the stem helix region of the S2 subunit. Designing vaccine immunogens that incorporate conserved regions in the RBD and stem helix region could elicit pan-coronavirus protective immune responses.
Article
Multidisciplinary Sciences
Rebecca J. Rockett, Jenny Draper, Mailie Gall, Eby M. Sim, Alicia Arnott, Jessica E. Agius, Jessica Johnson-Mackinnon, Winkie Fong, Elena Martinez, Alexander P. Drew, Clement Lee, Christine Ngo, Marc Ramsperger, Andrew N. Ginn, Qinning Wang, Michael Fennell, Danny Ko, Linda Huston, Lukas Kairaitis, Edward C. Holmes, Matthew N. O'Sullivan, Sharon C-A Chen, Jen Kok, Dominic E. Dwyer, Vitali Sintchenko
Summary: The study reveals the co-infection of SARS-CoV-2 variants Omicron and Delta in two patients with chronic kidney disease, highlighting the importance of integrated genomic surveillance in vulnerable populations.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Barbara Zdrazil, Eloy Felix, Fiona Hunter, Emma J. Manners, James Blackshaw, Sybilla Corbett, Marleen de Veij, Harris Ioannidis, David Mendez Lopez, Juan F. Mosquera, Maria Paula Magarinos, Nicolas Bosc, Ricardo Arcila, Tevfik Kiziloren, Anna Gaulton, A. Patricia Bento, Melissa F. Adasme, Peter Monecke, Gregory A. Landrum, Andrew R. Leach
Summary: ChEMBL is a curated resource of bioactive molecules with drug-like properties. It has evolved significantly in size and diversity of data types over time. The inclusion of new datasets has expanded the bioactivity data available and added new features to ChEMBL.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Siling Wang, Hui Sun, Yali Zhang, Lunzhi Yuan, Yizhen Wang, Tianying Zhang, Shaojuan Wang, Jinlei Zhang, Hai Yu, Hualong Xiong, Zimin Tang, Liqin Liu, Yang Huang, Xiuting Chen, Tingting Li, Dong Ying, Chang Liu, Zihao Chen, Quan Yuan, Jun Zhang, Tong Cheng, Shaowei Li, Yi Guan, Qingbing Zheng, Zizheng Zheng, Ningshao Xia
Summary: The Omicron variant is highly resistant to vaccines and neutralizing antibodies, emphasizing the need for potent therapeutic antibodies. In this study, a panel of human antibodies from convalescent patients showed diverse neutralization abilities against Omicron. Three of these antibodies, XMA01, XMA04, and XMA09, were found to bind to the receptor-binding domains of both wild-type and Omicron spikes, allowing for broad neutralization. Furthermore, the combination of XMA01 and XMA04 demonstrated synergistic protection against Beta and Omicron variant infections in hamsters. These findings provide valuable insights for the development of antibody cocktails or universal vaccines against Omicron.
Article
Psychiatry
Marthe Ueland, Riad Hajdarevic, Olav Mella, Elin B. Strand, Daisy D. Sosa, Ola D. Saugstad, Oystein Fluge, Benedicte A. Lie, Marte K. Viken
Summary: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex disease with unknown etiology and pathogenesis. The immune system and genetic factors are believed to play a role in ME/CFS. A previous study reported association signals in the T cell receptor alpha (TRA) locus, which interacts with the human leucocyte antigen (HLA) molecules. However, our research did not find any reliable associations with variants in the TRA locus.
TRANSLATIONAL PSYCHIATRY
(2022)
Article
Biochemistry & Molecular Biology
Sophie M-C Gobeil, Rory Henderson, Victoria Stalls, Katarzyna Janowska, Xiao Huang, Aaron May, Micah Speakman, Esther Beaudoin, Kartik Manne, Dapeng Li, Rob Parks, Maggie Barr, Margaret Deyton, Mitchell Martin, Katayoun Mansouri, Robert J. Edwards, Amanda Eaton, David C. Montefiori, Gregory D. Sempowski, Kevin O. Saunders, Kevin Wiehe, Wilton Williams, Bette Korber, Barton F. Haynes, Priyamvada Acharya
Summary: The SARS-CoV-2 Omicron variant, aided by extensive spike protein mutation, has surpassed the previously dominant Delta variant. Cryo-EM structures of the Omicron and Delta spikes reveal the conformational impacts of mutations, with the Omicron spike showing a tightly packed RBD organization and increased flexibility at the fusion peptide site.
Article
Biochemistry & Molecular Biology
Juan Carlos Gonzalez-Sanchez, Mustafa F. R. Ibrahim, Ivo C. Leist, Kyle R. Weise, Robert B. Russell
Summary: Advances in DNA sequencing and proteomics require researchers to regularly examine thousands of gene/protein changes to identify those relevant for potential clinical applications or biological insights. The developed tool, Mechnetor, allows users to explore and visualize integrated mechanistic data for proteins or interactions of interest, providing a finer resolution interaction network for immediate clues on intervention points or mechanistic understanding. The tool is demonstrated with topical examples in human genetic diseases and cancer genomics.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Elisabeth A. Rosenthal, Brian H. Shirts, Laura M. Amendola, Martha Horike-Pyne, Peggy D. Robertson, Fuki M. Hisama, Robin L. Bennett, Michael O. Dorschner, Deborah A. Nickerson, Ian B. Stanaway, Rami Nassir, Kathy T. Vickers, Christopher Li, William M. Grady, Ulrike Peters, Gail P. Jarvik
Article
Genetics & Heredity
James M. Havrilla, Brent S. Pedersen, Ryan M. Layer, Aaron R. Quinlan
Article
Biochemistry & Molecular Biology
Leandros Boukas, James M. Havrilla, Peter F. Hickey, Aaron R. Quinlan, Hans T. Bjornsson, Kasper D. Hansen
Article
Biochemical Research Methods
Jordan A. Berg, Jonathan R. Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Medical Informatics
Jacqueline Peng, Mengge Zhao, James Havrilla, Cong Liu, Chunhua Weng, Whitney Guthrie, Robert Schultz, Kai Wang, Yunyun Zhou
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2020)
Article
Multidisciplinary Sciences
Michael J. Cormier, Jonathan R. Belyeu, Brent S. Pedersen, Joseph Brown, Johannes Koester, Aaron R. Quinlan
Summary: With the rapid increase in genomic data, researchers face challenges in integrating datasets and annotations. By developing the fast and reproducible GGD method, researchers can install standardized data recipes easily, saving time and improving research reproducibility.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Jonathan R. Belyeu, Thomas A. Sasani, Brent S. Pedersen, Aaron R. Quinlan
Summary: Unfazed is a command-line tool for determining the parental gamete of origin for de novo mutations from DNA sequencing data, achieving a high success rate by chaining reads into haplotype groups to increase the search space for informative sites.
Article
Genetics & Heredity
James M. Havrilla, Cong Liu, Xiangchen Dong, Chunhua Weng, Kai Wang
Summary: PhenCards is a database and web server that integrates previously disconnected biomedical knowledge related to human clinical phenotypes. Users can query phenotype terms or clinical notes to obtain information on disease, drugs, genes, and more.
Article
Genetics & Heredity
James Margolin Havrilla, Mengge Zhao, Cong Liu, Chunhua Weng, Ingo Helbig, Elizabeth Bhoj, Kai Wang
Summary: This study successfully developed a method for characterizing the phenotypic spectrum of individuals with Down syndrome using natural language processing techniques and electronic health records data. It also identified phenotypic terms that were not significantly associated with Down syndrome.
Article
Clinical Neurology
Mengge Zhao, James Havrilla, Jacqueline Peng, Madison Drye, Maddie Fecher, Whitney Guthrie, Birkan Tunc, Robert Schultz, Kai Wang, Yunyun Zhou
Summary: By using natural language processing techniques, ASD phenotypic terms were identified and curated from high-quality unstructured clinical notes in the electronic health record of 8499 individuals with ASD, 8177 individuals with non-ASD psychiatric disorders, and 8482 individuals without a documented psychiatric disorder. A total of 3336 ASD terms linking to 1943 unique medical concepts were identified, and clustering analysis showed their potential use in differentiating individuals with ASD from those with other psychiatric disorders.
JOURNAL OF NEURODEVELOPMENTAL DISORDERS
(2022)
Article
Cell Biology
Paul J. Bonthuis, Susan Steinwand, Cornelia N. Stacher Horndli, Jared Emery, Wei-Chao Huang, Stephanie Kravitz, Elliott Ferris, Christopher Gregg
Summary: Noncanonical genomic imprinting can cause biased expression of one parental allele in a tissue, but the functional relevance of such biases is unclear. Using machine learning, we investigated the ethological roles of noncanonical imprinting in dopa decarboxylase and tyrosine hydroxylase, and found distinct effects of maternal and paternal alleles on foraging behavior, operating through specific subsets of cells.
Article
Medical Informatics
James M. Havrilla, Anbumalar Singaravelu, Dennis M. Driscoll, Leonard Minkovsky, Ingo Helbig, Livija Medne, Kai Wang, Ian Krantz, Bimal R. Desai
Summary: This research developed a point-of-care web application called PheNominal, embedded within the EHR workflow, for capturing standardized phenotype data. Using this application greatly improves the efficiency of collecting patient phenotype data in busy clinical workflows and reduces manual errors in the process.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2022)
Article
Genetics & Heredity
Mengge Zhao, James M. Havrilla, Li Fang, Ying Chen, Jacqueline Peng, Cong Liu, Chao Wu, Mahdi Sarmady, Pablo Botas, Julian Isla, Gholson J. Lyon, Chunhua Weng, Kai Wang
NAR GENOMICS AND BIOINFORMATICS
(2020)