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Biochemistry & Molecular Biology
Bo Liu, Zhengyu Jing, Xiaoming Zhang, Yuxin Chen, Shaoshuai Mao, Ravinder Kaundal, Yan Zou, Ge Wei, Ying Zang, Xinxin Wang, Wenyang Lin, Minghui Di, Yiwen Sun, Qin Chen, Yongqin Li, Jing Xia, Jianlong Sun, Chao-Po Lin, Xingxu Huang, Tian Chi
Summary: Here, we report the development of a transgenic platform called iMAP, which allows for simultaneous targeting of multiple genes throughout the mouse body, enabling high-throughput gene perturbation. Using this platform, we have successfully mapped a miniature Perturb-Atlas that provides valuable insights into gene functions.
Article
Biochemistry & Molecular Biology
David S. Wishart, Ray Kruger, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Rahil Doshi, Nitya Kehrtarpal, Omolola Fatokun, Daphnee Doucet, Ashley Zubkowski, Hayley Jackson, Gina Sykes, Miguel Ramirez-Gaona, Ana Marcu, Carin Li, Kristen Yee, Christiana Garros, Dorsa Yahya Rayat, Jeanne Coleongco, Tharuni Nandyala, Vasuk Gautam, Eponine Oler
Summary: PathBank is a database that provides comprehensive metabolite pathway information. With the latest update of PathBank 2.0, there have been significant improvements in the number, quality, and functionality of pathways, making it more useful for interpreting metabolomics data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Malcolm Fisher, Christina James-Zorn, Virgilio Ponferrada, Andrew J. Bell, Nivitha Sundararaj, Erik Segerdell, Praneet Chaturvedi, Nadia Bayyari, Stanley Chu, Troy Pells, Vaneet Lotay, Sergei Agalakov, Dong Zhuo Wang, Bradley Arshinoff, Saoirse Foley, Kamran Karimi, Peter D. Vize, Aaron M. Zorn
Summary: Xenbase is an online resource that integrates genomic and biological data from two laboratory frogs, Xenopus laevis and Xenopus tropicalis, to accelerate discovery and empower Xenopus research. It enhances the value of Xenopus data through curation, data integration, bioinformatics tools, and linking to human data and other model organisms. Xenbase also plays a crucial role in making Xenopus data interoperable and accessible to the broader biomedical community.
Article
Engineering, Civil
Qin Zhang, Rolf Moeckel, Kelly J. Clifton
Summary: Existing transport demand models lack the knowledge and experience in pedestrian modeling for health assessment. This paper presents the MITO/MoPeD model, which integrates fine-grained pedestrian modeling into an agent-based transport model, and applies it to the Munich metropolitan area. The model outperforms the existing Munich Model in simulating pedestrian travel behavior and addresses issues like overestimating physical activity volumes. The MITO/MoPeD model delivers more precise travel outcomes and has significant implications for pedestrian planning issues.
Article
Genetics & Heredity
Kim M. Rutherford, Midori A. Harris, Snezhana Oliferenko, Valerie Wood
Summary: The fission yeast Schizosaccharomyces japonicus has become an important system for studying cellular process evolution, utilizing similarities and differences with the established model organism Schizosaccharomyces pombe. By deploying open-source code and tools, JaponicusDB provides a central resource for S. japonicus researchers, supporting their studies and integration of new data.
Article
Microbiology
Christoph Elfmann, Bingyao Zhu, Tiago Pedreira, Ben Hossbach, Maria Lluch-Senar, Luis Serrano, Joerg Stuelke
Summary: The article introduces the significance of Mycoplasma pneumoniae and its database MycoWiki. As a minimal organism, M. pneumoniae can provide insights into the basic requirements for cellular life. MycoWiki integrates various data sources to facilitate the analysis of protein functions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yangyang Luo, Jingjing Guo, Jianguo Wen, Weiling Zhao, Kexin Huang, Yang Liu, Grant Wang, Ruihan Luo, Ting Niu, Yuzhou Feng, Haixia Xu, Pora Kim, Xiaobo Zhou
Summary: StemDriver is a comprehensive knowledgebase dedicated to annotating genes involved in determining the fate of hematopoietic stem cells. By analyzing single-cell RNA sequencing data, StemDriver has built a detailed lineage map of hematopoiesis, capturing the entire process from stem cell formation to mature cell development. The knowledgebase integrates data from 42 studies covering 14 tissue types, from embryonic to adult stages. Data undergo a standardized pipeline, including preprocessing, annotation, differential expression analysis, identification of differentiation-related gene categories, analysis of highly variable genes over pseudo-time, and exploration of gene regulatory networks. In total, StemDriver assesses the function of thousands of genes in human and mouse samples, and provides users with reference datasets and models for cell annotation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Kasturi Chakraborty, Palapuravan Anees, Sunaina Surana, Simona Martin, Jihad Aburas, Sandrine Moutel, Franck Perez, Sandhya P. Koushika, Paschalis Kratsios, Yamuna Krishnan
Summary: Nucleic acid nanodevices have great potential for logic-based therapeutic intervention and basic biology. By utilizing receptor-ligand interactions and biological barriers, these nanodevices can be targeted to specific cell types with subcellular precision in vivo, expanding their utility in biomedical applications and discovery biology.
Article
Genetics & Heredity
Feng Xu, Yifan Wang, Yunchao Ling, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yi Zhao, Haitao Zhao, Yungang He, Guoqing Zhang, Zhen Yang
Summary: MicroRNAs play important roles in gene expression regulation, and their dysregulation is widely reported in pathological cellular states. The dbDEMC database was constructed to store and query differentially expressed miRNAs (DEMs) in human cancers. The updated version, dbDEMC 3.0, contains more data entries and includes data from mice and rats. It provides a valuable resource for studying the molecular functions and regulatory mechanisms of DEMs in human cancers.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Alina Nicheperovich, Adrian M. Altenhoff, Christophe Dessimoz, Sina Majidian
Summary: Conservation of pathways and genes across species has allowed scientists to use non-human model organisms to gain a deeper understanding of human biology. The use of traditional model systems such as mice, rats, and zebrafish is costly and time-consuming, and raises ethical concerns. To address these issues, the Orthologous Matrix and Alternative Model Organism (OMAMO) software and web service provides users with the best non-complex organism for research based on orthologous relationships between humans and other species.
Article
Biochemistry & Molecular Biology
Jan Velecky, Marie Hamsikova, Jan Stourac, Milos Musil, Jiri Damborsky, David Bednar, Stanislav Mazurenko
Summary: Protein solubility is crucial for protein production and manufacturing yields. Understanding the structural determinants of solubility and the effects of mutations can help connect human diseases with protein aggregation. The SoluProtMut(DB) database contains extensive data on protein solubility changes upon mutations, serving as a valuable resource for researchers designing improved protein variants and developing machine learning tools. The database includes previously published datasets and additional data from recent studies, and it has been curated for machine learning applications.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Food Science & Technology
Paraskevi Koletsi, Geert F. Wiegertjes, Elisabeth A. M. Graat, Philip Lyons, Johan Schrama
Summary: This study examined the effects of dietary exposure to deoxynivalenol (DON) on juvenile rainbow trout. The results showed that DON intake reduced growth and caused liver and gastrointestinal tract damage. Restrictive exposure revealed time-dependent liver damage, while ad libitum exposure resulted in reduced growth.
Article
Biochemistry & Molecular Biology
Jingjing Jin, Peng Lu, Yalong Xu, Jiemeng Tao, Zefeng Li, Shuaibin Wang, Shizhou Yu, Chen Wang, Xiaodong Xie, Junping Gao, Qiansi Chen, Lin Wang, Wenxuan Pu, Peijian Cao
Summary: The emergence of single-cell sequencing has revolutionized transcriptomic and genomic research. The lack of a comprehensive database of cell markers for plant research community has been addressed by the development of PCMDB, providing a valuable resource for researchers to annotate cell types and predict the biological function of individual cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Michael Lynch, Bogi Trickovic, Christopher P. Kempes
Summary: Data from nearly 1000 species show that natural selection has an upper limit to the rates of biomass production across the Tree of Life. The relationship between maximum growth rates and organism size differs between bacteria and eukaryotes, and also between cyanobacteria and eukaryotes for phototrophs. These findings have implications for understanding the transition from prokaryotes to eukaryotes and the evolution of multicellularity in some eukaryotic groups.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Raul Eduardo Castillo-Medina, Tania Islas-Flores, Estefania Morales-Ruiz, Marco A. Villanueva
Summary: In this study, the coding and promoter region sequences of the SBiP1 protein from Symbiodinium microadriaticum CassKB8 were obtained and analyzed. It was found that SBiP1 is a member of the BiP/HSP70 family and its light-modulated phosphorylation/dephosphorylation likely functions as an activity switch for the chaperone. This light-induced modulation occurs relatively slow but is highly sensitive to the full spectrum of visible light.
Article
Rheumatology
Gloria Yiu, Tue K. Rasmussen, Bahareh Ajami, David J. Haddon, Alvina D. Chu, Stephanie Tangsombatvisit, Winston A. Haynes, Vivian Diep, Larry Steinman, James Faix, Paul J. Utz
ARTHRITIS & RHEUMATOLOGY
(2016)
Article
Biochemistry & Molecular Biology
Timothy E. Sweeney, Winston A. Haynes, Francesco Vallania, John P. Ioannidis, Purvesh Khatri
NUCLEIC ACIDS RESEARCH
(2017)
Article
Computer Science, Interdisciplinary Applications
Matt Griffin, Blake W. Nordstrom, Jon Scholes, Kate Joncas, Patrick Gordon, Elliott Krivenko, Winston Hayes, Roger Higdon, Elizabeth Stewart, Natali Kolker, Elizabeth Montague, Eugene Kolker
Article
Multidisciplinary Sciences
Aurelie Tomczak, Jonathan M. Mortensen, Rainer Winnenburg, Charles Liu, Dominique T. Alessi, Varsha Swamy, Francesco Vallania, Shane Lofgren, Winston Haynes, Nigam H. Shah, Mark A. Musen, Purvesh Khatri
SCIENTIFIC REPORTS
(2018)
Article
Computer Science, Software Engineering
Larissa Stanberry, Roger Higdon, Winston Haynes, Natali Kolker, William Broomall, Saliya Ekanayake, Adam Hughes, Yang Ruan, Judy Qiu, Eugene Kolker, Geoffrey Fox
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2014)
Article
Biochemical Research Methods
Roger Higdon, Elizabeth Stewart, Larissa Stanberry, Winston Haynes, John Choiniere, Elizabeth Montague, Nathaniel Anderson, Gregory Yandl, Imre Janko, William Broomall, Simon Fishilevich, Doron Lancet, Natali Kolker, Eugene Kolker
JOURNAL OF PROTEOME RESEARCH
(2014)
Article
Biochemical Research Methods
Eugene Kolker, Roger Higdon, Dean Welch, Andrew Bauman, Elizabeth Stewart, Winston Haynes, William Broomall, Natali Kolker
JOURNAL OF PROTEOMICS
(2011)
Correction
Biochemical Research Methods
Eugene Kolker, Roger Higdon, Phil Morgan, Margaret Sedensky, Dean Welch, Andrew Bauman, Elizabeth Stewart, Winston Haynes, William Broomall, Natali Kolker
JOURNAL OF PROTEOMICS
(2012)
Article
Multidisciplinary Sciences
Winston A. Haynes, Aurelie Tomczak, Purvesh Khatri
SCIENTIFIC REPORTS
(2018)
Article
Biochemical Research Methods
Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins, Eugene Kolker
PLOS COMPUTATIONAL BIOLOGY
(2013)
Article
Computer Science, Interdisciplinary Applications
Roger Higdon, Winston Haynes, Larissa Stanberry, Elizabeth Stewart, Gregory Yandl, Chris Howard, William Broomall, Natali Kolker, Eugene Kolker
Article
Multidisciplinary Sciences
Francesco Vallania, Andrew Tam, Shane Lofgren, Steven Schaffert, Tej D. Azad, Erika Bongen, Winston Haynes, Meia Alsup, Michael Alonso, Mark Davis, Edgar Engleman, Purvesh Khatri
NATURE COMMUNICATIONS
(2018)
Article
Immunology
Jennifer S. Chen, Ryan D. Chow, Eric Song, Tianyang Mao, Benjamin Israelow, Kathy Kamath, Joel Bozekowski, Winston A. Haynes, Renata B. Filler, Bridget L. Menasche, Jin Wei, Mia Madel Alfajaro, Wenzhi Song, Lei Peng, Lauren Carter, Jason S. Weinstein, Uthaman Gowthaman, Sidi Chen, Joe Craft, John C. Shon, Akiko Iwasaki, Craig B. Wilen, Stephanie C. Eisenbarth
Summary: This study found that both T-FH-dependent and -independent antibodies were induced against SARS-CoV-2 infection, vaccination, and influenza A virus infection. The T-FH-independent antibodies had reduced somatic hypermutation but were still high affinity and capable of neutralizing diverse spike-derived epitopes and variants of concern.
SCIENCE IMMUNOLOGY
(2022)
Article
Medicine, Research & Experimental
Winston A. Haynes, D. James Haddon, Vivian K. Diep, Avani Khatri, Erika Bongen, Gloria Yiu, Imelda Balboni, Christopher R. Bolen, Rong Mao, Paul J. Utz, Purvesh Khatri
