Article
Multidisciplinary Sciences
Andrea Piserchio, Kimberly J. Long, Luke S. Browning, Amanda L. Bohanon, Eta A. Isiorho, Kevin N. Dalby, Ranajeet Ghose
Summary: Protein translation, a high-energy process, requires robust regulation under energy-deprived conditions. The eEF-2K plays a crucial role in this regulation by suppressing translational elongation through phosphorylation of eEF-2. It has been suggested that eEF-2K's response to energy levels is mediated by AMPK and the mTOR pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Surgery
Ying-Chun Jheng, Yen-Po Wang, Hung-En Lin, Kuang-Yi Sung, Yuan-Chia Chu, Huann-Sheng Wang, Jeng-Kai Jiang, Ming-Chih Hou, Fa-Yauh Lee, Ching-Liang Lu
Summary: The study aimed to develop a CNN-based algorithm, GUTAID, for recognizing different colon lesions and anatomical landmarks. Through training and validating AI classifiers, a successful CNN algorithm was established with high accuracy in identifying colonic abnormalities and landmarks.
SURGICAL ENDOSCOPY AND OTHER INTERVENTIONAL TECHNIQUES
(2022)
Article
Mathematical & Computational Biology
Michela Chiara Caprani, John Healy, Orla Slattery, Joan O'Keeffe
Summary: The paper introduces a promising two-tier ensemble of machine learning models that successfully predicts AMPs from marine macroalgae, identifying 39 putative AMP sequences.
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES
(2021)
Review
Biochemical Research Methods
Pamela M. Rezende, Joicymara S. Xavier, David B. Ascher, Gabriel R. Fernandes, Douglas E. Pires
Summary: With the rapid increase in biological data generation, databases have become an important resource for guiding innovation and biological insights. Automatic data classification is often necessary for hierarchical biological data sets, with different approaches such as "Local" and "Global" methods being available. Consideration of different components within hierarchical datasets is crucial for determining appropriate classification schemes.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Siming Zhang, Qifeng Tu, Xiaowei Qian, Junpei Wang, Chao Ma, Liu Yang, Yan Liu, Ronghua Wu, Mei Liu
Summary: In this study, the knockout of the Kif15 gene was found to significantly inhibit tumor growth, and this inhibition was related to the activation of the immune system.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Ho-Jin Gwak, Mina Rho
Summary: A hierarchical BERT model named ViBE was developed to detect eukaryotic viruses from metagenome sequencing data and classify them at the order level, outperforming state-of-the-art alignment-based and alignment-free methods for virus identification.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Oncology
Antje Schaefer, Channing J. Der
Summary: RAS and RHO GTPases play significant roles as signaling nodes that regulate cellular processes and cancer development. While RAS mutations are widely present in various human cancers, mutations in RAC1 and RHOA are associated with specific cancer types. Unlike RAS and RAC1, RHOA may function as both an oncogene and a tumor suppressor.
Article
Biochemistry & Molecular Biology
Manjeet Kumar, Sushama Michael, Jesus Alvarado-Valverde, Andras Zeke, Tamas Lazar, Juliana Glavina, Eszter Nagy-Kanta, Juan Mac Donagh, Zsofia E. Kalman, Stefano Pascarelli, Nicolas Palopoli, Laszlo Dobson, Carmen Florencia Suarez, Kim Van Roey, Izabella Krystkowiak, Juan Esteban Griffin, Anurag Nagpal, Rajesh Bhardwaj, Francesca Diella, Balint Meszaros, Kellie Dean, Norman E. Davey, Rita Pancsa, Lucia B. Chemes, Toby J. Gibson
Summary: Short Linear Motifs (SLiMs) are the smallest structural and functional components of modular eukaryotic proteins, and they are also the most abundant, especially when considering post-translational modifications. SLiMs are found throughout the cell as part of regulatory processes and are extensively mimicked by intracellular pathogens.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Rasmus Freter, Paola Falletta, Omid Omrani, Mahdi Rasa, Katharine Herbert, Francesco Annunziata, Alberto Minetti, Anna Krepelova, Lisa Adam, Sandra Kaeppel, Tina Ruediger, Zhao-Qi Wang, Colin R. Goding, Francesco Neri
Summary: The authors have developed a fluorescent Optical Stem Cell Activity Reporter (OSCAR) to assess RNA polymerase II activity and identify dormant cell populations in intestinal epithelial cells in vivo, providing a tool for a better understanding of dormant stem cell biology.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Simon Orozco-Arias, Luis Humberto Lopez-Murillo, Mariana S. Candamil-Cortes, Maradey Arias, Paula A. Jaimes, Alexandre Rossi Paschoal, Reinel Tabares-Soto, Gustavo Isaza, Romain Guyot
Summary: LTR-retrotransposons, the most abundant repeat sequences in plant genomes, are important for evolution and biodiversity. However, their identification and classification remain challenging. Inpactor2 is a fast and accurate tool that can create reference libraries for LTR-retrotransposons in a short time. It uses a hybrid approach and takes advantage of multi-core and GPU architectures to decrease execution times.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Plant Sciences
Yingying Gao, Xiaochen Wang, Xianju Liu, Zhenchang Liang
Summary: This study identified 163 Vv2OGD superfamily members from the grape genome, and found that 37 of them are related to hormone biosynthesis and metabolism process. These genes play important roles in regulating hormone levels during grape berry development. Some of these genes are also responsive to hormone treatments, indicating their involvement in the ripening process. Overall, this study provides valuable insights into the mechanism of hormone regulation during grape berry development.
Article
Biochemistry & Molecular Biology
John Nguyen, Johannes Pettmann, Philipp Kruger, Omer Dushek
Summary: The study found that among co-stimulation TNF receptor superfamily members, 4-1BB and CD27 increased cytokine production in CD8(+) T cells, but only 4-1BB could prolong the duration of cytokine production. CD27 co-stimulation could enhance the expression of 4-1BB and GITR, leading to synergy between co-stimulation receptors.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Chemistry, Physical
Sohrab R. Daemi, Chun Tan, Thomas G. Tranter, Thomas M. M. Heenan, Aaron Wade, Luis Salinas-Farran, Alice Llewellyn, Xuekun Lu, Alessia Matruglio, Daniel J. L. Brett, Rhodri Jervis, Paul R. Shearing
Summary: This study presents a novel approach that combines convolutional neural networks to analyze the microstructure of battery electrodes. The method accurately locates and segments each particle, and classifies them while detecting flaws. This analysis pipeline is significant for battery research and other fields.
Article
Multidisciplinary Sciences
Susanne Gottfried, Siaosi M. B. M. J. Koloamatangi, Clement Daube, Anja H. Schiemann, Evelyn Sattlegger
Summary: Protein kinase Gcn2 is found in almost all eukaryotic cells and plays a role in cellular response to amino acid starvation and other biological functions. Gcn2 binds to its effector protein Gcn1 to phosphorylate and stimulate cellular response to starvation, and disruption of Gcn1-Gcn2 interaction may impair cell growth.
Article
Biology
Eshwar R. Tammineni, Lourdes Figueroa, Carlo Manno, Disha Varma, Natalia Kraeva, Carlos A. Ibarra, Amira Klip, Sheila Riazi, Eduardo Rios, Mark T. Nelson
Summary: Calcium ion movements between cellular stores and the cytosol regulate muscle contraction and play a crucial role in glycemia regulation. Chronic elevation of calcium stress has been suggested to contribute to the progression from hyperglycemia to insulin resistance. This study uncovers the mechanisms underlying this progression, including the activation of GSK3 beta and proteolysis of junctophilin1 in muscle cells derived from patients with malignant hyperthermia-susceptible (MHS) and multiple myopathies.
Article
Microbiology
Bruno Perichon, Sylvie Goussard, Violaine Walewski, Lenka Krizova, Gustavo Cerqueira, Cheryl Murphy, Michael Feldgarden, Jennifer Wortman, Dominique Clermont, Alexandr Nemec, Patrice Courvalin
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2014)
Article
Microbiology
Diane O. Inglis, Jonathan Binkley, Marek S. Skrzypek, Martha B. Arnaud, Gustavo C. Cerqueira, Prachi Shah, Farrell Wymore, Jennifer R. Wortman, Gavin Sherlock
Article
Evolutionary Biology
Marie Touchon, Jean Cury, Eun-Jeong Yoon, Lenka Krizova, Gustavo C. Cerqueira, Cheryl Murphy, Michael Feldgarden, Jennifer Wortman, Dominique Clermont, Thierry Lambert, Catherine Grillot-Courvalin, Alexandr Nemec, Patrice Courvalin, Eduardo P. C. Rocha
GENOME BIOLOGY AND EVOLUTION
(2014)
Article
Genetics & Heredity
Christopher A. Desjardins, Gustavo C. Cerqueira, Jonathan M. Goldberg, Julie C. Dunning Hotopp, Brian J. Haas, Jeremy Zucker, Jose M. C. Ribeiro, Sakina Saif, Joshua Z. Levin, Lin Fan, Qiandong Zeng, Carsten Russ, Jennifer R. Wortman, Doran L. Fink, Bruce W. Birren, Thomas B. Nutman
Article
Biochemistry & Molecular Biology
Martha B. Arnaud, Gustavo C. Cerqueira, Diane O. Inglis, Marek S. Skrzypek, Jonathan Binkley, Marcus C. Chibucos, Jonathan Crabtree, Clinton Howarth, Joshua Orvis, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock, Jennifer R. Wortman
NUCLEIC ACIDS RESEARCH
(2012)
Article
Biochemistry & Molecular Biology
Gustavo C. Cerqueira, Martha B. Arnaud, Diane O. Inglis, Marek S. Skrzypek, Gail Binkley, Matt Simison, Stuart R. Miyasato, Jonathan Binkley, Joshua Orvis, Prachi Shah, Farrell Wymore, Gavin Sherlock, Jennifer R. Wortman
NUCLEIC ACIDS RESEARCH
(2014)
Article
Multidisciplinary Sciences
Doyle V. Ward, Dirk Gevers, Georgia Giannoukos, Ashlee M. Earl, Barbara A. Methe, Erica Sodergren, Michael Feldgarden, Dawn M. Ciulla, Diana Tabbaa, Cesar Arze, Elizabeth Appelbaum, Leigh Aird, Scott Anderson, Tulin Ayvaz, Edward Belter, Monika Bihan, Toby Bloom, Jonathan Crabtree, Laura Courtney, Lynn Carmichael, David Dooling, Rachel L. Erlich, Candace Farmer, Lucinda Fulton, Robert Fulton, Hongyu Gao, John A. Gill, Brian J. Haas, Lisa Hemphill, Otis Hall, Susanna G. Hamilton, Theresa A. Hepburn, Niall J. Lennon, Vandita Joshi, Cristyn Kells, Christie L. Kovar, Divya Kalra, Kelvin Li, Lora Lewis, Shawn Leonard, Donna M. Muzny, Elaine Mardis, Kathie Mihindukulasuriya, Vincent Magrini, Michelle O'Laughlin, Craig Pohl, Xiang Qin, Keenan Ross, Matthew C. Ross, Yu-Hui A. Rogers, Navjeet Singh, Yue Shang, Katarzyna Wilczek-Boney, Jennifer R. Wortman, Kim C. Worley, Bonnie P. Youmans, Shibu Yooseph, Yanjiao Zhou, Patrick D. Schloss, Richard Wilson, Richard A. Gibbs, Karen E. Nelson, George Weinstock, Todd Z. DeSantis, Joseph F. Petrosino, Sarah K. Highlander, Bruce W. Birren
Article
Multidisciplinary Sciences
Vivien G. Dugan, Scott J. Emrich, Gloria I. Giraldo-Calderon, Omar S. Harb, Ruchi M. Newman, Brett E. Pickett, Lynn M. Schriml, Timothy B. Stockwell, Christian J. Stoeckert, Dan E. Sullivan, Indresh Singh, Doyle V. Ward, Alison Yao, Jie Zheng, Tanya Barrett, Bruce Birren, Lauren Brinkac, Vincent M. Bruno, Elizabet Caler, Sinead Chapman, Frank H. Collins, Christina A. Cuomo, Valentina Di Francesco, Scott Durkin, Mark Eppinger, Michael Feldgarden, Claire Fraser, W. Florian Fricke, Maria Giovanni, Matthew R. Henn, Erin Hine, Julie Dunning Hotopp, Ilene Karsch-Mizrachi, Jessica C. Kissinger, Eun Mi Lee, Punam Mathur, Emmanuel F. Mongodin, Cheryl I. Murphy, Garry Myers, Daniel E. Neafsey, Karen E. Nelson, William C. Nierman, Julia Puzak, David Rasko, David S. Roos, Lisa Sadzewicz, Joana C. Silva, Bruno Sobral, R. Burke Squires, Rick L. Stevens, Luke Tallon, Herve Tettelin, David Wentworth, Owen White, Rebecca Will, Jennifer Wortman, Yun Zhang, Richard H. Scheuermann
Letter
Multidisciplinary Sciences
Yonatan H. Grad, Marc Lipsitch, Allison D. Griggs, Brian J. Haas, Terrance P. Shea, Caryn McCowan, Anna Montmayeur, Michael FitzGerald, Jennifer R. Wortman, Karen A. Krogfelt, Edouard Bingen, Francois-Xavier Weill, Erhard Tietze, Antje Flieger, Eric S. Lander, Chad Nusbaum, Bruce W. Birren, Deborah T. Hung, William P. Hanage
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Multidisciplinary Sciences
Yonatan H. Grad, Marc Lipsitch, Michael Feldgarden, Harindra M. Arachchi, Gustavo C. Cerqueira, Michael FitzGerald, Paul Godfrey, Brian J. Haas, Cheryl I. Murphy, Carsten Russ, Sean Sykes, Bruce J. Walker, Jennifer R. Wortman, Sarah Young, Qiandong Zeng, Amr Abouelleil, James Bochicchio, Sara Chauvin, Timothy DeSmet, Sharvari Gujja, Caryn McCowan, Anna Montmayeur, Scott Steelman, Jakob Frimodt-Moller, Andreas M. Petersen, Carsten Struve, Karen A. Krogfelt, Edouard Bingen, Francois-Xavier Weill, Eric S. Lander, Chad Nusbaum, Bruce W. Birren, Deborah T. Hung, William P. Hanage
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Article
Microbiology
Kelli L. Palmer, Paul Godfrey, Allison Griggs, Veronica N. Kos, Jeremy Zucker, Christopher Desjardins, Gustavo Cerqueira, Dirk Gevers, Suzanne Walker, Jennifer Wortman, Michael Feldgarden, Brian Haas, Bruce Birren, Michael S. Gilmore
Article
Microbiology
Veronica N. Kos, Christopher A. Desjardins, Allison Griggs, Gustavo Cerqueira, Andries Van Tonder, Matthew T. G. Holden, Paul Godfrey, Kelli L. Palmer, Kip Bodi, Emmanuel F. Mongodin, Jennifer Wortman, Michael Feldgarden, Trevor Lawley, Steven R. Gill, Brian J. Haas, Bruce Birren, Michael S. Gilmore
Article
Microbiology
Yonatan H. Grad, Paul Godfrey, Gustavo C. Cerquiera, Patricia Mariani-Kurkdjian, Malika Gouali, Edouard Bingen, Terrence P. Shea, Brian J. Haas, Allison Griggs, Sarah Young, Qiandong Zeng, Marc Lipsitch, Matthew K. Waldor, Franois-Xavier Weill, Jennifer R. Wortman, William P. Hanage
Article
Microbiology
Francois Lebreton, Willem van Schaik, Abigail Manson McGuire, Paul Godfrey, Allison Griggs, Varun Mazumdar, Jukka Corander, Lu Cheng, Sakina Saif, Sarah Young, Qiandong Zeng, Jennifer Wortman, Bruce Birren, Rob J. L. Willems, Ashlee M. Earl, Michael S. Gilmore