Article
Biochemistry & Molecular Biology
Adam Frankish, Silvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdan-Velez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcia Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J. Martin, Laura Martinez Gomez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: GENCODE provides high quality gene and transcript annotation for the human and mouse genomes, supported by experimental data, serving as a reference for genome biology and clinical genomics. The consortium generates data, develops tools and carries out analyses to support the identification and annotation of transcript structures and their function.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Peter Ebert, Peter A. Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Hops, Hufsah Ashraf, Nelson T. Chuang, Xiaofei Yang, Katherine M. Munson, Alexandra P. Lewis, Susan Fairley, Luke J. Tallon, Wayne E. Clarke, Anna O. Basile, Marta Byrska-Bishop, Andre Corvelo, Uday S. Evani, Tsung-Yu Lu, Mark J. P. Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M. Wenger, Maryam Ghareghani, William T. Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison A. Regier, Haley J. Abel, Ira M. Hall, Paul Flicek, Oliver Stegle, Mark B. Gerstein, Jose M. C. Tubio, Zepeng Mu, Yang Li, Xinghua Shi, Alex R. Hastie, Kai Ye, Zechen Chong, Ashley D. Sanders, Michael C. Zody, Michael E. Talkowski, Ryan E. Mills, Scott E. Devine, Charles Lee, Jan O. Korbel, Tobias Marschall, Evan E. Eichler
Summary: Through the use of long-read and strand-specific sequencing technologies, this study has achieved the de novo assembly of high-quality haplotype-resolved human genomes without the need for parent-child trio data. The research identified various forms of genetic variation, including structural variants and SV hotspots, and revealed the mechanisms of SV formation while providing SV candidates for adaptive selection within the human population.
Article
Biochemistry & Molecular Biology
Subin S. George, Maxim Pimkin, Vikram R. Paralkar
Summary: This study customized the genome assemblies of human and mouse to make them suitable for rDNA mapping and created annotation files for visualizing rDNA features in browsers. The customized genomes were validated for mapping known rDNA-binding proteins and a workflow for mapping chromatin immunoprecipitation-sequencing datasets was presented. The customized genome assemblies, annotation files, control tracks, and reference sequences have been deposited to GitHub.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Xiaoyu Zhuo, Alan Y. Du, Erica C. Pehrsson, Daofeng Li, Ting Wang
Summary: This study investigated the association between epigenomic differences between human and chimpanzee and lineage-specific indels, revealing that different types of indels are associated with specific epigenomic diversity between the two species.
Article
Biochemistry & Molecular Biology
Marzia Rossato, Luca Marcolungo, Luca De Antoni, Giulia Lopatriello, Elisa Bellucci, Gaia Cortinovis, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Valerio Di Vittori, Leonardo Vincenzi, Filippo Lucchini, Kirstin E. Bett, Larissa Ramsay, David James Konkin, Massimo Delledonne, Roberto Papa
Summary: High-throughput genotyping allows for the analysis of genetic diversity in large populations and genome-wide association studies. In this study, the researchers used CRISPR-Cas9 technology to remove repetitive elements in the lentil genome, thus focusing the sequencing data on coding and regulatory regions. This method significantly increased genotyping accuracy and the number of genotyped bases compared to non-depleted libraries.
Review
Biochemistry & Molecular Biology
Helena Vassilieff, Andrew D. W. Geering, Nathalie Choisne, Pierre-Yves Teycheney, Florian Maumus
Summary: The Caulimoviridae is a family of DNA viruses that infect plants, and their integration into plant genomes has resulted in the presence of endogenous caulimovirids (ECVs). Research on ECVs over the past 25 years has revealed the ecological diversity and macroevolution of Caulimoviridae, highlighting the need for further investigation into the impact of ECVs on plant biology and the evolutionary history of this viral family. The availability of plant genome sequences and new tools for genome annotation will greatly contribute to future research in this field.
Article
Multidisciplinary Sciences
Sanasar G. Babajanyan, Yuri I. Wolf, Andranik Khachatryan, Armen Allahverdyan, Purificacion Lopez-Garcia, Eugene V. Koonin
Summary: There are two fundamentally distinct types of biological evolutionary units, reproducers and replicators. Reproducers are cells and organelles that reproduce and maintain the physical continuity of compartments, while replicators are genetic elements that cooperate with reproducers for replication. Mathematical modeling suggests that the coordination between the birth-death process of genetic elements and the rate of cell division is essential for the success of genetic element-carrying cells in competition, with random, high-variance cell division being advantageous in preventing parasite takeover.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Editorial Material
Multidisciplinary Sciences
John T. Lovell, Jane Grimwood
Summary: A combination of state-of-the-art technologies has enabled researchers to generate the first complete human genome sequence, filling in the gaps in repetitive regions of the genome.
Article
Cell Biology
Xiaoying Fan, Ping Lu, Hongwei Wang, Shuhui Bian, Xinglong Wu, Yu Zhang, Yang Liu, Danqi Fu, Lu Wen, Jihui Hao, Fuchou Tang
Summary: This study used single-cell multiomics sequencing to uncover the epigenomic abnormality of pancreatic ductal adenocarcinoma (PDAC). The findings revealed differential DNA methylation and chromatin accessibility in cancer cells compared to normal epithelial cells, and identified novel candidate biomarkers associated with prognosis in PDAC patients.
Article
Microbiology
Stephany Flores Ramos, Silvio D. Brugger, Isabel Fernandez Escapa, Chelsey A. Skeete, Sean L. Cotton, Sara M. Eslami, Wei Gao, Lindsey Bomar, Tommy H. Tran, Dakota S. Jones, Samuel Minot, Richard J. Roberts, Christopher D. Johnston, Katherine P. Lemon
Summary: Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Comparative genome analysis of 28 strains collected over 20 years revealed highly conserved chromosomal synteny and identified defense mechanisms against mobile genetic elements. This suggests a potential role for D. pigrum as a therapeutic bacterium.
Review
Plant Sciences
Rebecca T. Batstone
Summary: Many important plant traits are influenced not only by the plant's genome, but also by genes within microbes and mobile genetic elements (MGEs) due to nested symbiosis. Understanding the evolution of plant traits is facilitated by combining quantitative genetic and functional genomics approaches to consider sources of nested genetic variation. Additionally, studying coevolution within nested symbiosis can help in designing or selecting for MGEs that promote plant health.
Article
Multidisciplinary Sciences
Bjarni Halldorsson, Hannes P. Eggertsson, Kristjan H. S. Moore, Hannes Hauswedell, Ogmundur Eiriksson, Magnus O. Ulfarsson, Gunnar Palsson, Marteinn T. Hardarson, Asmundur Oddsson, Brynjar O. Jensson, Snaedis Kristmundsdottir, Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Doruk Beyter, Guillaume Holley, Vinicius Tragante, Arnaldur Gylfason, Pall Olason, Florian Zink, Margret Asgeirsdottir, Sverrir T. Sverrisson, Brynjar Sigurdsson, Sigurjon A. Gudjonsson, Gunnar T. Sigurdsson, Gisli H. Halldorsson, Gardar Sveinbjornsson, Kristjan Norland, Unnur Styrkarsdottir, Droplaug N. Magnusdottir, Steinunn Snorradottir, Kari Kristinsson, Emilia Sobech, Helgi Jonsson, Arni J. Geirsson, Isleifur Olafsson, Palmi Jonsson, Ole Birger Pedersen, Christian Erikstrup, Soren Brunak, Sisse Rye Ostrowski, Gudmar Thorleifsson, Frosti Jonsson, Pall Melsted, Ingileif Jonsdottir, Thorunn Rafnar, Hilma Holm, Hreinn Stefansson, Jona Saemundsdottir, Daniel F. Gudbjartsson, Olafur T. Magnusson, Gisli Masson, Unnur Thorsteinsdottir, Agnar Helgason, Hakon Jonsson, Patrick Sulem, Kari Stefansson
Summary: A comprehensive understanding of how diversity in the human genome sequence affects phenotypic diversity relies on a reliable characterization of both sequences and phenotypic variation. In this study, whole-genome sequencing of 150,119 individuals from the UK Biobank was performed, leading to insights into the relationship between sequence variation and phenotypic traits. The analysis revealed rare variants with large effects, which were not previously identified through whole-exome sequencing and/or imputation studies.
Article
Biochemical Research Methods
Tianjiao Zhang, Liangyu Li, Hailong Sun, Dali Xu, Guohua Wang
Summary: This article introduces a deep learning framework called DeepICSH for identifying silencers in specific cells. DeepICSH leverages multiple biological data sources and a convolutional neural network to capture biologically relevant signal combinations associated with silencers. Through extensive experiments, DeepICSH has shown superior performance in silencer identification.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Fayrouz Hammal, Pierre de Langen, Aurelie Bergon, Fabrice Lopez, Benoit Ballester
Summary: ReMap 2022 provides manually curated, high-quality catalogs of regulatory regions from Human, Arabidopsis, Mouse, and Fly, including hundreds of transcription factors and regulators. The update also introduces new regulatory catalogs for Mouse and Fly, enriching research resources for scientists. Users can browse the four regulatory catalogs through track hubs at UCSC, Ensembl, and NCBI genome browsers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Anthony Fullam, Ivica Letunic, Thomas S. B. Schmidt, Quinten R. Ducarmon, Nicolai Karcher, Supriya Khedkar, Michael Kuhn, Martin Larralde, Oleksandr M. Maistrenko, Lukas Malfertheiner, Alessio Milanese, Joao Frederico Matias Rodrigues, Claudia Sanchis-Lopez, Christian Schudoma, Damian Szklarczyk, Shinichi Sunagawa, Georg Zeller, Jaime Huerta-Cepas, Christian von Mering, Peer Bork, Daniel R. Mende
Summary: The interpretation of 'omics data relies on well-annotated genomes. As the number of available microbial genomes increases, quality control and consistent annotation become crucial. proGenomes3 is a database containing 907,388 high-quality genomes with consistent annotation, including functional and taxonomic information.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Arpit Mishra, Mary Krishna Ekka, Souvik Maiti
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Review
Genetics & Heredity
Arpit Mishra, R. David Hawkins
Article
Biochemical Research Methods
Atul Kumar, Sanjiv Kumar, Dilip Kumar, Arpit Mishra, Rikeshwer P. Dewangan, Priyanka Shrivastava, Srinivasan Ramachandran, Bhupesh Taneja
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2013)
Article
Multidisciplinary Sciences
Arpit Mishra, Manika Vij, Dhirendra Kumar, Vibha Taneja, Anupam Kumar Mondal, Ankur Bothra, Vivek Rao, Munia Ganguli, Bhupesh Taneja
Article
Biochemistry & Molecular Biology
Bo Yu, Thomas H. Smith, Stephanie L. Battle, Shannon Ferrell, R. David Hawkins
Article
Biotechnology & Applied Microbiology
Chang Li, Arpit Suresh Mishra, Sucheol Gil, Meng Wang, Aphrodite Georgakopoulou, Thalia Papayannopoulou, R. David Hawkins, Andre Lieber
Article
Multidisciplinary Sciences
Sundaram Acharya, Arpit Mishra, Deepanjan Paul, Asgar Hussain Ansari, Mohd Azhar, Manoj Kumar, Riya Rauthan, Namrata Sharma, Meghali Aich, Dipanjali Sinha, Saumya Sharma, Shivani Jain, Arjun Ray, Suman Jain, Sivaprakash Ramalingam, Souvik Maiti, Debojyoti Chakraborty
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biology
Calvin Jon A. Leonen, Miho Shimada, Caroline E. Weller, Tomoyoshi Nakadai, Peter L. Hsu, Elizabeth L. Tyson, Arpit Mishra, Patrick M. M. Shelton, Martin Sadilek, R. David Hawkins, Ning Zheng, Robert G. Roeder, Champak Chatterjee
Summary: Post-translational modification of histones by the small ubiquitin-like modifier protein SUMO plays a key role in gene silencing, centromeric localization, and DNA repair in eukaryotes. The study demonstrated that H4K12su inhibits acetylation of H4 tail and methylation of H3K4 associated with transcription activation, as well as transcription mediated by RNA polymerase II. Cell-based assays confirmed the negative crosstalk between histone sumoylation and acetylation/methylation in human cells.
Article
Allergy
Naresh Doni Jayavelu, Matthew C. Altman, Basilin Benson, Matthew J. Dufort, Elizabeth R. Vanderwall, Lucille M. Rich, Maria P. White, Patrice M. Becker, Alkis Togias, Daniel J. Jackson, Jason S. Debley
Summary: This study found that individuals with allergic asthma are less susceptible to severe COVID-19 and identified mechanisms behind this protection. The researchers discovered that the replication of SARS-CoV-2 was lower in bronchial airway epithelial cells from children with allergic asthma, and that IL-13 treatment was effective in reducing viral replication in these cells. It was determined that the protection is likely attributed to the regulation of functional pathways related to ciliated epithelium, rather than ACE2 expression or mucus secretion pathways.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)
Meeting Abstract
Biotechnology & Applied Microbiology
Debojyoti Chakraborty, Souvik Maiti, Mohd Azhar, Deepanjan Paul, Sundaram Acharya, Rhythm Phutela, Asgar Hussain Ansari, Dipanjali Sinha, Manoj Kumar, Riya Rauthan, Meghali Aich, Saumya Sharma, Namrata Sharma, Arpit Mishra, Shivani Jain, Arjun Ray, Sivaprakash Ramalingam
Meeting Abstract
Biotechnology & Applied Microbiology
Chang Li, Arpit S. Mishra, Sucheol Gil, Pavel Sova, David Hawkins, Andre Lieber