Article
Biochemistry & Molecular Biology
Yao Lu, Guangyan Zhou, Jessica Ewald, Zhiqiang Pang, Tanisha Shiri, Jianguo Xia
Summary: Microbiome studies have become routine in various scientific fields, requiring user-friendly bioinformatics tools to analyze complex multi-omics datasets. MicrobiomeAnalyst 2.0 is introduced here as a comprehensive tool for statistical analysis, visualization, functional interpretation, and integrative analysis of microbiome data. It features three new modules for data processing, metabolomics profiling, and statistical meta-analysis, along with other improvements such as support for multi-factor analysis and interactive visualizations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Leonardo Vinicius Monteiro de Assis, Paulo Newton Tonolli, Maria Nathalia Moraes, Mauricio S. Baptista, Ana Maria de Lauro Castrucci
Summary: Human skin responses to sunlight involve both the beneficial and harmful effects of UV and visible light, which require a comprehensive understanding of the interactions of photons in the skin and the regulatory role of the light-sensing protein opsins.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS
(2021)
Review
Microbiology
John P. DeLong, Maitham A. Al-Sammak, Zeina T. Al-Ameeli, David D. Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack
Summary: This review discusses the traits of viral cells and viral particles, as well as how to categorize virus phenotypes; the foundational goal in biology is understanding how phenotypes emerge from genotypes; identifying the features that constitute a virus's phenotype is crucial for comprehensive interpretation of viral genome sequences and for advancing our understanding of viral evolution and ecology.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Dachuan Zhang, Ye Tian, Yu Tian, Huadong Xing, Sheng Liu, Haoyang Zhang, Shaozhen Ding, Pengli Cai, Dandan Sun, Tong Zhang, Yanhong Hong, Hongkun Dai, Weizhong Tu, Junni Chen, Aibo Wu, Qian-Nan Hu
Summary: The article introduces a new platform that integrates data-driven computational methods with experimental validation to predict toxin biotransformation and discover new metabolites. This platform will help explore the "dark matter" of toxin metabolites and promote the discovery of detoxification enzymes.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
Aleksandr Ianevski, Ronja M. Simonsen, Vegard Myhre, Tanel Tenson, Valentyn Oksenych, Magnar Bjoras, Denis E. Kainov
Summary: Viruses can cause outbreaks in humans and have economic and health burdens. Broad-spectrum antivirals (BSAs) and BSA-containing drug combinations (BCCs) are immediate therapeutic options for virus identification and vaccine development. DrugVirus.info 2.0 provides an integrative portal for exploration and analysis of BSAs and BCCs, expanding the database and functionality for antiviral drug development.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Horticulture
Tokurou Shimizu
Summary: Developing varieties with diverse features, improving overall fruit quality, and quickly releasing them are difficult to achieve in conventional breeding. Genomics-assisted breeding can enhance breeding efficiency and help solve this breeding trilemma. Selecting new premium quality hybrids is possible by integrating genomics-assisted breeding technique.
Article
Health Care Sciences & Services
Weijie Zhang, Christine Wendt, Russel Bowler, Craig P. Hersh, Sandra E. Safo
Summary: In biomedical research, the integrative sparse singular value decomposition (iSSVD) method is effective in detecting meaningful biclusters in both single-view and multi-view data analyses.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2022)
Article
Computer Science, Software Engineering
Bipul Mohanto, A. B. M. Tariqul Islam, Enrico Gobbetti, Oliver Staadt
Summary: Foveated rendering adapts the image synthesis process to the user's gaze, utilizing the limitations of the human visual system to provide high-quality visual experiences at reduced costs. Despite significant progress, there are still open research problems in this field.
COMPUTERS & GRAPHICS-UK
(2022)
Article
Biochemistry & Molecular Biology
Florian Schmidt, Alexander Marx, Nina Baumgarten, Marie Hebel, Martin Wegner, Manuel Kaulich, Matthias S. Leisegang, Ralf P. Brandes, Jonathan Goeke, Jilles Vreeken, Marcel H. Schulz
Summary: STITCHIT is a novel approach to dissect epigenetic variation in a gene-specific manner for the detection of regulatory elements (REMs) without relying on peak calls in individual samples, leading to a more accurate and refined REM detection compared to standard methods across multiple samples. The approach also predicts thousands of putative REMs, suggesting a large portion of the regulome might be uncharted water.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Plant Sciences
Anjana Thottapillil, Sania Kouser, Subrahmanya Kumar Kukkupuni, Chethala N. Vishnuprasad
Summary: Diabetes is a multifactorial disease requiring a holistic and systemic approach for successful management. The principles of Ayurveda and modern biomedicine overlap at a gut centred view of diabetes management, highlighting the central role of the gut in postprandial glucose disposal and whole body glucose homeostasis. Integrating holistic and reductionist perspectives can offer novel strategies for the multi-targeted management of diabetes.
JOURNAL OF ETHNOPHARMACOLOGY
(2021)
Article
Multidisciplinary Sciences
Sarmistha Das, Indranil Mukhopadhyay
Summary: The study introduces a statistical model TiMEG for identifying disease-associated biomarkers in a case-control paradigm, specifically in the presence of missing omics data. By utilizing the inter-relationship among multiple omics data, TiMEG is able to capture weaker signals that remain unidentified in single-omic analysis or common imputation-based methods. Application of TiMEG on a real tuberous sclerosis dataset successfully identified functionally relevant genes in the disease pathway.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Neda Shokraneh, Mariam Arab, Maxwell Libbrecht
Summary: In this study, we propose an integrated approach to annotate genomic domains using both 1D functional genomic signals and Hi-C measurements of genome-wide 3D interactions without the use of a pairwise prior. By using graph embedding to learn structural features corresponding to each genomic region and inputting learned structural features along with functional genomic signals to a SAGA algorithm, our domain types recapitulate well-known subcompartments with an additional granularity that distinguishes a combination of the spatial and functional states of the genomic regions.
Review
Plant Sciences
Minhang Yuan, Bruno Pok Man Ngou, Pingtao Ding, Xin Xiu-Fan
Summary: Plants have innate immune responses to resist pathogen attacks, involving pattern-recognition receptors (PRRs) and nucleotide-binding domain leucine-rich repeat containing receptors (NLRs) that lead to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Despite different activation mechanisms, PTI and ETI converge into similar downstream responses, with evidence of interactions and shared components between PRR-mediated and NLR-mediated signaling cascades. Future research on signal collaboration between PRR-initiated and NLR-initiated immunity will provide a more comprehensive understanding of the plant immune system.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Marcus Mendes, Jarjapu Mahita, Nina Blazeska, Jason Greenbaum, Brendan Ha, Kelly Wheeler, Jiyao Wang, Deborah Shackelford, Alessandro Sette, Bjoern Peters
Summary: The Immune Epitope Database (IEDB) is a database that catalogs T cell, B cell, and major histocompatibility complex ligand information in the context of infectious disease, allergy, autoimmunity, and transplantation. IEDB-3D is an important component of this database, which provides three-dimensional structural data on T cell receptors, antibodies, and pairwise residue interactions between immune receptors and antigens. With the release of IEDB-3D 2.0, a new 3D viewer experience and epitope mapping system have been implemented, allowing for better visualization of epitope data and highlighting immunogenic regions of antigens.
Article
Biochemical Research Methods
Harold Durufle, Merwann Selmani, Philippe Ranocha, Elisabeth Jamet, Christophe Dunand, Sebastien Dejean
Summary: This article introduces a powerful framework for managing and analyzing multi-omics heterogeneous data for integrative analysis. By using the mixOmics package and studying the model plant Arabidopsis thaliana, novel conclusions on the biological system were achieved.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik
Article
Microbiology
Harris Onywera, Anna-Lise Williamson, Luca Cozzuto, Sarah Bonnin, Zizipho Z. A. Mbulawa, David Coetzee, Julia Ponomarenko, Tracy L. Meiring
Article
Biochemistry & Molecular Biology
Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, Adam Godzik
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Mayya Sedova, Adam Godzik
Article
Genetics & Heredity
Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva Maria Novoa
FRONTIERS IN GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Thomas Conrad, Evgenia Ntini, Benjamin Lang, Luca Cozzuto, Jesper B. Andersen, Jens U. Marquardt, Julia Ponomarenko, Gian Gaetano Tartaglia, Ulf A. Vang Orom
Review
Medicine, General & Internal
Harris Onywera, Anna-Lise Williamson, Julia Ponomarenko, Tracy L. Meiring
FRONTIERS IN MEDICINE
(2020)
Article
Biochemistry & Molecular Biology
Mayya Sedova, Lukasz Jaroszewski, Mallika Iyer, Zhanwen Li, Adam Godzik
Summary: There is a significant gap between the number of proteins characterized only by their amino acid sequence and those with structurally characterized by direct experiment. To bridge this gap, homology-based inference and modeling are used to predict the structures of uncharacterized proteins. The use of different templates with distinct structural flexibility can provide more informative results depending on the research questions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Microbiology
Jesse R. Willis, Susana Iraola-Guzman, Ester Saus, Ewa Ksiezopolska, Luca Cozzuto, Luis A. Bejarano, Nuria Andreu-Somavilla, Miriam Alloza-Trabado, Anna Puig-Sola, Andrea Blanco, Elisabetta Broglio, Carlo Carolis, Jochen Hecht, Julia Ponomarenko, Toni Gabaldon
Summary: This study found differences in the oral microbiome of individuals with Down syndrome (DS), characterized by low salivary pH, less microbial diversity, and specific levels of certain bacterial species. More research is needed to determine if these differences are related to oral pathology in DS.
JOURNAL OF ORAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik
Summary: The mutation patterns in the SARS-CoV-2 virus genomes are closely linked to the structure and function of the proteins they encode, with highly mutated regions corresponding to more easily adaptable structural regions. Understanding these patterns is important for developing tools like antibodies, vaccines, and drugs to target conserved genomic regions due to natural selection.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Marciela M. DeGrace, Elodie Ghedin, Matthew B. Frieman, Florian Krammer, Alba Grifoni, Arghavan Alisoltani, Galit Alter, Rama R. Amara, Ralph S. Baric, Dan H. Barouch, Jesse D. Bloom, Louis-Marie Bloyet, Gaston Bonenfant, Adrianus C. M. Boon, Eli A. Boritz, Debbie L. Bratt, Traci L. Bricker, Liliana Brown, William J. Buchser, Juan Manuel Carreno, Liel Cohen-Lavi, Tamarand L. Darling, Meredith E. Davis-Gardner, Bethany L. Dearlove, Han Di, Meike Dittmann, Nicole A. Doria-Rose, Daniel C. Douek, Christian Drosten, Venkata-Viswanadh Edara, Ali Ellebedy, Thomas P. Fabrizio, Guido Ferrari, Will M. Fischer, William C. Florence, Ron A. M. Fouchier, John Franks, Adolfo Garcia-Sastre, Adam Godzik, Ana Silvia Gonzalez-Reiche, Aubree Gordon, Bart L. Haagmans, Peter J. Halfmann, David D. Ho, Michael R. Holbrook, Yaoxing Huang, Sarah L. James, Lukasz Jaroszewski, Trushar Jeevan, Robert M. Johnson, Terry C. Jones, Astha Joshi, Yoshihiro Kawaoka, Lisa Kercher, Marion P. G. Koopmans, Bette Korber, Eilay Koren, Richard A. Koup, Eric B. LeGresley, Jacob E. Lemieux, Mariel J. Liebeskind, Zhuoming Liu, Brandi Livingston, James P. Logue, Yang Luo, Adrian B. McDermott, Margaret J. McElrath, Victoria A. Meliopoulos, Vineet D. Menachery, David C. Montefiori, Barbara Muehlemann, Vincent J. Munster, Jenny E. Munt, Manoj S. Nair, Antonia Netzl, Anna M. Niewiadomska, Sijy O'Dell, Andrew Pekosz, Stanley Perlman, Marjorie C. Pontelli, Barry Rockx, Morgane Rolland, Paul W. Rothlauf, Sinai Sacharen, Richard H. Scheuermann, Stephen D. Schmidt, Michael Schotsaert, Stacey Schultz-Cherry, Robert A. Seder, Mayya Sedova, Alessandro Sette, Reed S. Shabman, Xiaoying Shen, Pei-Yong Shi, Maulik Shukla, Viviana Simon, Spencer Stumpf, Nancy J. Sullivan, Larissa B. Thackray, James Theiler, Paul G. Thomas, Sanja Trifkovic, Sina Tureli, Samuel A. Turner, Maria A. Vakaki, Harm van Bakel, Laura A. VanBlargan, Leah R. Vincent, Zachary S. Wallace, Li Wang, Maple Wang, Pengfei Wang, Wei Wang, Scott C. Weaver, Richard J. Webby, Carol D. Weiss, David E. Wentworth, Stuart M. Weston, Sean P. J. Whelan, Bradley M. Whitener, Samuel H. Wilks, Xuping Xie, Baoling Ying, Hyejin Yoon, Bin Zhou, Tomer Hertz, Derek J. Smith, Michael S. Diamond, Diane J. Post, Mehul S. Suthar
Summary: The SAVE program is a real-time risk assessment initiative established by the National Institute of Allergy and Infectious Diseases to address the public health threat posed by the emergence of SARS-CoV-2 variants. Its goal is to evaluate the potential impact of these variants on transmission, virulence, and immunity induced through infection or vaccination.
Article
Biochemistry & Molecular Biology
Mallika Iyer, Lukasz Jaroszewski, Mayya Sedova, Adam Godzik
Summary: The study found that proteins undergoing similar conformational changes have similar difference distance maps (DDMs), and this similarity can be quantified by the correlation between the DDMs. By comparing the DDMs of homologous protein pairs, it was discovered that large-scale conformational changes show a high level of conservation across a broad range of sequence identities.
Article
Biochemistry & Molecular Biology
Arghavan Alisoltani, Xinru Qiu, Lukasz Jaroszewski, Mayya Sedova, Mallika Iyer, Adam Godzik
Summary: Both gender and smoking have an impact on cancer prevalence and outcomes. This study aimed to investigate the gender-specific effects of smoking on tumor immune microenvironment. The results showed that smoking had different effects on immune subtypes and cell populations in male and female cancer patients. It also indicated that smoking influenced gene expression profiles differently based on immune cell type and gender.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2023)
Article
Immunology
Sam Turner, Arghavan Alisoltani, Debbie Bratt, Liel Cohen-Lavi, Bethany L. Dearlove, Christian Drosten, Will M. Fischer, Ron A. M. Fouchier, Ana Silvia Gonzalez-Reiche, Lukasz Jaroszewski, Zain Khalil, Eric LeGresley, Marc Johnson, Terry C. Jones, Barbara Muehlemann, David O'Connor, Mayya Sedova, Maulik Shukla, James Theiler, Zachary S. Wallace, Hyejin Yoon, Yun Zhang, Harm van Bakel, Marciela M. Degrace, Elodie Ghedin, Adam Godzik, Tomer Hertz, Bette Korber, Jacob Lemieux, Anna M. Niewiadomska, Diane J. Post, Morgane Rolland, Richard Scheuermann, Derek J. Smith
Summary: Since late 2020, SARS-CoV-2 variants with competitive and phenotypic differences have been regularly emerging, sometimes having the potential to escape immunity. The Early Detection group of the US National Institutes of Health uses bioinformatics to monitor and prioritize the most relevant variants for experimental characterization. Their success includes identifying major variants and providing updated information for phenotypic investigations.
EMERGING INFECTIOUS DISEASES
(2023)
Meeting Abstract
Immunology
Arghavan Alisoltanidehkordi, Xinru Qiu, Lukasz Jaroszewski, Mayya Sedova, Mallika Iyer, Zhanwen Li, Adam Godzik
JOURNAL OF IMMUNOLOGY
(2021)