Article
Computer Science, Software Engineering
Markus Rittenbruch, Kellie Vella, Margot Brereton, James M. Hogan, Daniel Johnson, Julian Heinrich, Sean O'Donoghue
Summary: Genomic research requires collaboration across different disciplines, and visualisation plays a crucial role in facilitating this collaboration. Visualisations are used for question formation, hypothesis confirmation, and as a communication tool. The specific interactions and work patterns within a group also impact how visualisations are used.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Editorial Material
Microbiology
Taj Azarian
Summary: Population genomic analysis is a powerful tool to understand the evolutionary history and success factors of pathogens. This article demonstrates the utility of pathogen genomic data by elucidating the origin of methicillin-resistant Staphylococcus aureus ST239. The availability of representative genomic data and associated metadata is crucial for these analyses.
Article
Computer Science, Information Systems
Rongrong Liu, Birgitta Dresp-Langley
Summary: The study utilizes expert grip force data to investigate the surgical operations in robot-assisted minimally invasive endoscopic surgery, finding that individual grip force is influenced by task specificity. Two data analysis strategies are employed to explore this phenomenon.
Article
Nuclear Science & Technology
Patrick Talou
Summary: The scientific method heavily relies on uncertain knowledge, with Massimo Salvatores making significant contributions to nuclear technologies. Advances in machine learning and computational capabilities are increasing confidence in predicting key nuclear metrics.
ANNALS OF NUCLEAR ENERGY
(2021)
Review
Biochemistry & Molecular Biology
Zbigniew J. Krol, Paula Dobosz, Antonina Slubowska, Magdalena Mroczek
Summary: Initially, exome sequencing was expected to uncover the genetic basis of most heritable diseases. However, attention has shifted to the non-coding sequences that make up 98% of the genome and have important regulatory functions. The release of whole-genome sequencing datasets, including underrepresented populations, and the recognition of the importance of local databases have further enhanced the potential of genomic databases in diagnostics, therapies, and various fields of research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Gen-ichiro Arimura
Summary: Plants under threat from herbivores can devise survival strategies by sensing and responding to elicitors secreted by herbivores. These elicitors activate diverse plant defense mechanisms, increasing resistance to herbivores. Insights into the cellular pathways involved in plant-herbivore interactions are leading to potential agricultural applications.
TRENDS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Ziqi Deng, Jorge Botas, Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Jordi Burguet-Castell, Jaime Huerta-Cepas
Summary: PhyloCloud is an online platform designed to host and index large collections of phylogenetic trees, providing seamless access to analyses and operations, as well as custom annotations and multiple sequence alignments.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Vasundra Toure, Asmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
Summary: Causal molecular interactions are crucial for computational modeling and predicting biological behaviors. Different biological interests have led to various ways of describing and annotating these interactions, making it challenging to efficiently explore and utilize the data. Understanding the variety of data formats, biological process representations, and exchange procedures is important in extracting and downloading causal interaction data.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Luc Cornet, Denis Baurain
Summary: The decreasing cost of sequencing and the increasing availability of publicly available genomes have created a need for automated software to assess genomic contamination. In the past six years, 18 programs have been published, each with its own strengths and weaknesses. This article reviews and benchmarks six of these programs, providing researchers with guidance in selecting appropriate tools for specific applications. It also highlights the future challenges in contamination detection.
Review
Genetics & Heredity
Kirsten Seale, Steve Horvath, Andrew Teschendorff, Nir Eynon, Sarah Voisin
Summary: This article reviews the changes in DNA methylation during aging and the statistical tools used to quantify them. It also explores the evidence linking DNA methylation to aging phenotypes and strategies for extending healthspan and lifespan. Finally, it discusses theories on the mechanistic causes of epigenetic aging.
NATURE REVIEWS GENETICS
(2022)
Article
Computer Science, Information Systems
Salah Al-Obaidi, Hiba Al-Khafaji, Charith Abhayaratne
Summary: In this paper, a method based on handcrafted features is proposed to analyze neuromorphic vision sensor data streams for human action recognition. The method outperformed existing methods in terms of accuracy rates for different datasets.
Article
Ethics
Christopher Gyngell, Fiona Lynch, Danya Vears, Hilary Bowman-Smart, Julian Savulescu, John Christodoulou
Summary: Genomic sequencing is increasingly used in paediatric medicine for screening, research, and treatment. Storing genomic data for future clinical use brings ethical challenges related to privacy, consent, justice, and equality. This paper explores the ethical case for storing genomic data as a lifetime health resource and argues for a future where genomic data is sequentially interrogated throughout one's lifespan.
JOURNAL OF MEDICAL ETHICS
(2023)
Article
Multidisciplinary Sciences
Zhenyu Zhang, Kyle Hernandez, Jeremiah Savage, Shenglai Li, Dan Miller, Stuti Agrawal, Francisco Ortuno, Louis M. Staudt, Allison Heath, Robert L. Grossman
Summary: The goal of National Cancer Institute's Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and clinical data to support precision medicine through data sharing and collaborative analysis. The initial dataset includes various data types from NCI TCGA and TARGET projects, and data production started in June 2015 using an OpenStack-based private cloud. The GDC has analyzed more than 50,000 raw sequencing data inputs and generated different data types using the latest human genome reference build GRCh38, which are available for download and exploratory analysis at GDC Data Portal and Legacy Archive.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Piotr Minkiewicz, Malgorzata Darewicz, Anna Iwaniak, Marta Turlo
Summary: Phosphorylation is a crucial modification for amino acids, peptides, and proteins, improving the functional properties of foods. This publication introduces a simple code for annotating phosphopeptide sequences, discussing the location and diversity of phosphate residues, as well as translating the biological code into SMILES. Possible errors associated with the proposed code and SMILES representations are also addressed, with potential for future extensions to describe other modifications.
Review
Plant Sciences
Rodrigo Siqueira Reis, Yves Poirier
Summary: In plants, thousands of genes are associated with antisense transcription, producing noncoding RNAs that play diverse roles in gene regulation. The evidence suggests that antisense transcription is not primarily involved in gene silencing, but has a broad and diverse function in gene regulation. A framework for the functional dissection of antisense transcripts is proposed to move beyond the gene silencing paradigm.
TRENDS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman El-Sayed, Cathy H. Wu
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Marcela K. Tello-Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser, Guy Naamati, Electra Tapanari, Nuno Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D. Stein, Robert Petryszak, Irene Papatheodorou, Paul J. Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas Roca, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
NUCLEIC ACIDS RESEARCH
(2018)
Article
Allergy
Steve Jupe, Keith Ray, Corina Duenas Roca, Thawfeek Varusai, Veronica Shamovsky, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2018)
Article
Multidisciplinary Sciences
Liang-Chin Huang, Karen E. Ross, Timothy R. Baffi, Harold Drabkin, Krzysztof J. Kochut, Zheng Ruan, Peter D'Eustachio, Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A. Natale, Cynthia Smith, Pascale Gaudet, Alexandra C. Newton, Cathy Wu, Natarajan Kannan
SCIENTIFIC REPORTS
(2018)
Article
Biochemical Research Methods
Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
S. Carbon, E. Douglass, N. Dunn, B. Good, N. L. Harris, S. E. Lewis, C. J. Mungall, S. Basu, R. L. Chisholm, R. J. Dodson, E. Hartline, P. Fey, P. D. Thomas, L. P. Albou, D. Ebert, M. J. Kesling, H. Mi, A. Muruganujian, X. Huang, S. Poudel, T. Mushayahama, J. C. Hu, S. A. LaBonte, D. A. Siegele, G. Antonazzo, H. Attrill, N. H. Brown, S. Fexova, P. Garapati, T. E. M. Jones, S. J. Marygold, G. H. Millburn, A. J. Rey, V. Trovisco, G. dos Santos, D. B. Emmert, K. Falls, P. Zhou, J. L. Goodman, V. B. Strelets, J. Thurmond, M. Courtot, D. Osumi-Sutherland, H. Parkinson, P. Roncaglia, M. L. Acencio, M. Kuiper, A. Laegreid, C. Logie, R. C. Lovering, R. P. Huntley, P. Denny, N. H. Campbell, B. Kramarz, V. Acquaah, S. H. Ahmad, H. Chen, J. H. Rawson, M. C. Chibucos, M. Giglio, S. Nadendla, R. Tauber, M. J. Duesbury, N. Del-Toro, B. H. M. Meldal, L. Perfetto, P. Porras, S. Orchard, A. Shrivastava, Z. Xie, H. Y. Chang, R. D. Finn, A. L. Mitchell, N. D. Rawlings, L. Richardson, A. Sangrador-Vegas, J. A. Blake, K. R. Christie, M. E. Dolan, H. J. Drabkin, D. P. Hill, L. Ni, D. Sitnikov, M. A. Harris, S. G. Oliver, K. Ruther-Ford, V. Wood, J. Hayles, J. Bahler, A. Lock, E. R. Bolton, J. De Pons, M. Dwinell, G. T. Hayman, S. J. F. Laulederkind, M. Shimoyama, M. Tutaj, S. -J. Wang, P. D'Eustachio, L. Matthews, J. P. Balhoff, S. A. Aleksander, G. Binkley, B. L. Dunn, J. M. Cherry, S. R. Engel, F. Gondwe, K. Karra, K. A. MacPherson, S. R. Miyasato, R. S. Nash, P. C. Ng, T. K. Sheppard, A. V. P. Shrivatsav, M. Simison, M. S. Skrzypek, S. Weng, E. D. Wong, M. Feuermann, P. Gaudet, E. Bakker, T. Z. Berardini, L. Reiser, S. Subramaniam, E. Huala, C. Arighi, A. Auchincloss, K. Axelsen, G. Argoud-Puy, A. Bateman, B. Bely, M. -C. Blatter, E. Boutet, L. Breuza, A. Bridge, R. Britto, H. Bye-A-Jee, C. Casals-Casas, E. Coudert, A. Estreicher, L. Famiglietti, P. Garmiri, G. Georghiou, A. Gos, N. Gruaz-Gumowski, E. Hatton-Ellis, U. Hinz, C. Hulo, A. Ignatchenko, F. Jungo, G. Keller, K. Laiho, P. Lemercier, D. Lieberherr, Y. Lussi, A. Mac-Dougall, M. Magrane, M. J. Martin, P. Masson, D. A. Natale, N. Hyka-Nouspikel, I. Pedruzzi, K. Pichler, S. Poux, C. Rivoire, M. Rodriguez-Lopez, T. Sawford, E. Speretta, A. Shypitsyna, A. Stutz, S. Sundaram, M. Tognolli, N. Tyagi, K. Warner, R. Zaru, C. Wu, A. D. Diehl, J. Chan, J. Cho, S. Gao, C. Grove, M. C. Harrison, K. Howe, R. Lee, J. Mendel, H. -M. Muller, D. Raciti, K. Van Auken, M. Berriman, L. Stein, P. W. Sternberg, D. Howe, S. Toro, M. Westerfield
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Sushma Naithani, Parul Gupta, Justin Preece, Peter D'Eustachio, Justin L. Elser, Priyanka Garg, Daemon A. Dikeman, Jason Kiff, Justin Cook, Andrew Olson, Sharon Wei, Marcela K. Tello-Ruiz, Antonio Fabregat Mundo, Alfonso Munoz-Pomer, Suhaib Mohammed, Tiejun Cheng, Evan Bolton, Irene Papatheodorou, Lincoln Stein, Doreen Ware, Pankaj Jaiswal
NUCLEIC ACIDS RESEARCH
(2020)
Article
Cell Biology
Thawfeek Mohamed Varusai, Steven Jupe, Cristoffer Sevilla, Lisa Matthews, Marc Gillespie, Lincoln Stein, Guanming Wu, Peter D'Eustachio, Emmanouil Metzakopian, Henning Hermjakob
Summary: The 21st century has revealed much about the fundamental cellular process of autophagy, with Reactome playing a vital role as a freely available knowledgebase to aid researchers in studying autophagy mechanisms and conducting data analysis.
Article
Plant Sciences
Sushma Naithani, Bijayalaxmi Mohanty, Justin Elser, Peter D'Eustachio, Pankaj Jaiswal
Summary: Modeling biological processes and genetic-regulatory networks using in silico approaches is valuable for understanding how genes and variations result in specific traits. This study constructed a network of 57 transcription factors to explore gene-gene interactions in seed germination and coleoptile elongation under submergence. The network incorporates co-expression data and experimental evidence, and is publicly accessible to facilitate re-analysis of OMICs data and accelerate crop improvement.
Article
Biochemistry & Molecular Biology
Parul Gupta, Justin Elser, Elizabeth Hooks, Peter D'Eustachio, Pankaj Jaiswal, Sushma Naithani
Summary: Plant Reactome is a freely accessible, comprehensive plant pathway knowledgebase that provides reference pathways from rice and gene-orthology-based pathway projections to 129 additional species. Users can analyze and visualize omics data, such as gene expression, gene-gene interaction, proteome, and metabolome data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Marija Milacic, Deidre Beavers, Patrick Conley, Chuqiao Gong, Marc Gillespie, Johannes Griss, Robin Haw, Bijay Jassal, Lisa Matthews, Bruce May, Robert Petryszak, Eliot Ragueneau, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Ralf Stephan, Krishna Tiwari, Thawfeek Varusai, Joel Weiser, Adam Wright, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
Summary: Reactome is a knowledgebase that provides manually curated molecular details of human biological processes, allowing for the discovery of functional relationships and annotation of cell- and tissue-specific pathways.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Marcela K. Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari, Vivek Kumar, Bruno Contreras-Moreira, Guy Naamati, Nancy George, Justin Cook, Daniel Bolser, Peter D'Eustachio, Lincoln D. Stein, Amit Gupta, Weijia Xu, Jennifer Regala, Irene Papatheodorou, Paul J. Kersey, Paul Flicek, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Summary: Gramene is a knowledge-base focused on comparative functional analyses of genomic and pathway data for model plants and major crops, supporting agricultural researchers worldwide. They are committed to open access and reproducible science, continuously updating and expanding their content.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Mathematical & Computational Biology
Guilherme Viteri, Lisa Matthews, Thawfeek Varusai, Marc Gillespie, Marija Milacic, Justin Cook, Joel Weiser, Solomon Shorser, Konstantinos Sidiropoulos, Antonio Fabregat, Robin Haw, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2019)
Article
Biochemical Research Methods
Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo Marin-Garcia, Peipei Ping, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob