Search Results - "F1000 research"

Sustainable data analysis with Snakemake [version 2; peer review: 2 approved] by Mölder, Felix, Jablonski, Kim Philipp, Letcher, Brice, Hall, Michael B, Tomkins-Tinch, Christopher H, Sochat, Vanessa, Forster, Jan, Lee, Soohyun, Twardziok, Sven O, Kanitz, Alexander, Wilm, Andreas, Holtgrewe, Manuel, Rahmann, Sven, Nahnsen, Sven, Köster, Johannes

“…Data analysis often entails a multitude of heterogeneous steps, from the application of various command line tools to the usage of scripting languages like R…”
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Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates [version 2; peer review: 3 approved] by Chen, Yu Wai, Yiu, Chin-Pang Bennu, Wong, Kwok-Yin

“…We prepared the three-dimensional model of the SARS-CoV-2 (aka 2019-nCoV) 3C-like protease (3CL pro) using the crystal structure of the highly similar (96%…”
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Ulcerative colitis: Recent advances in the understanding of disease pathogenesis [version 1; peer review: 2 approved] by Porter, Ross J, Kalla, Rahul, Ho, Gwo-Tzer

“…Inflammatory bowel diseases are common, complex, immune-mediated conditions with a sharply rising global prevalence. While major advances since 2000 have…”
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Benchmarking of long-read assemblers for prokaryote whole genome sequencing [version 1; peer review: 4 approved] by Wick, Ryan R, Holt, Kathryn E

“…Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be…”
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'The long tail of Covid-19' - The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients [version 1; peer review: 2 approved] by Doykov, Ivan, Hällqvist, Jenny, Gilmour, Kimberly C, Grandjean, Louis, Mills, Kevin, Heywood, Wendy E

“…'Long Covid', or medical complications associated with post SARS-CoV-2 infection, is a significant post-viral complication that is being more and more commonly…”
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The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: a living systematic review [version 1; peer review: 1 approved, 2 approved with reservations] by John, Ann, Okolie, Chukwudi, Eyles, Emily, Webb, Roger T, Schmidt, Lena, McGuiness, Luke A, Olorisade, Babatunde K, Arensman, Ella, Hawton, Keith, Kapur, Nav, Moran, Paul, O'Connor, Rory C, O'Neill, Siobhan, Higgins, Julian P.T, Gunnell, David

“…Background: The COVID-19 pandemic has caused morbidity and mortality, as well as, widespread disruption to people's lives and livelihoods around the world…”
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Epidemiology of mental health problems in COVID-19: a review [version 1; peer review: 2 approved] by Hossain, Md Mahbub, Tasnim, Samia, Sultana, Abida, Faizah, Farah, Mazumder, Hoimonty, Zou, Liye, McKyer, E. Lisako J, Ahmed, Helal Uddin, Ma, Ping

“…The novel coronavirus disease 2019 (COVID-19) has become a pandemic affecting health and wellbeing globally. In addition to the physical health, economic, and…”
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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: 2 approved] by Garcia, Maxime, Juhos, Szilveszter, Larsson, Malin, Olason, Pall I, Martin, Marcel, Eisfeldt, Jesper, DiLorenzo, Sebastian, Sandgren, Johanna, Díaz De Ståhl, Teresita, Ewels, Philip, Wirta, Valtteri, Nistér, Monica, Käller, Max, Nystedt, Björn

“…Whole-genome sequencing (WGS) is a fundamental technology for research to advance precision medicine, but the limited availability of portable and…”
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Understanding the role of neutrophils in chronic inflammatory airway disease [version 1; peer review: 2 approved] by Jasper, Alice E, McIver, William J, Sapey, Elizabeth, Walton, Georgia M

“…Airway neutrophilia is a common feature of many chronic inflammatory lung diseases and is associated with disease progression, often regardless of the…”
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Recent advances in vasoactive intestinal peptide physiology and pathophysiology: focus on the gastrointestinal system [version 1; peer review: 4 approved] by Iwasaki, Mari, Akiba, Yasutada, Kaunitz, Jonathan D

“…Vasoactive intestinal peptide (VIP), a gut peptide hormone originally reported as a vasodilator in 1970, has multiple physiological and pathological effects on…”
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Large-scale sequence comparisons with sourmash [version 1; peer review: 2 approved] by Pierce, N. Tessa, Irber, Luiz, Reiter, Taylor, Brooks, Phillip, Brown, C. Titus

“…The sourmash software package uses MinHash-based sketching to create "signatures", compressed representations of DNA, RNA, and protein sequences, that can be…”
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SARS-CoV-2 and the role of fomite transmission: a systematic review [version 2; peer review: 2 approved] by Onakpoya, Igho J, Heneghan, Carl J, Spencer, Elizabeth A, Brassey, Jon, Plüddemann, Annette, Evans, David H, Conly, John M, Jefferson, Tom

“…Background: SARS-CoV-2 RNA has been detected in fomites which suggests the virus could be transmitted via inanimate objects. However, there is uncertainty…”
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ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations [version 1; peer review: 1 approved, 2 approved with reservations] by Kandlikar, Gaurav S, Gold, Zachary J, Cowen, Madeline C, Meyer, Rachel S, Freise, Amanda C, Kraft, Nathan J.B, Moberg-Parker, Jordan, Sprague, Joshua, Kushner, David J, Curd, Emily E

“…Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education,…”
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GFF Utilities: GffRead and GffCompare by Pertea, Geo, Pertea, Mihaela

“…GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats used by bioinformatics programs to represent and exchange information…”
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FastQ Screen: A tool for multi-genome mapping and quality control by Wingett, Steven W., Andrews, Simon

“…DNA sequencing analysis typically involves mapping reads to just one reference genome.  Mapping against multiple genomes is necessary, however, when the genome…”
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Current understanding of Alzheimer's disease diagnosis and treatment [version 1; peer review: 2 approved] by Weller, Jason, Budson, Andrew

“…Alzheimer's disease is the most common cause of dementia worldwide, with the prevalence continuing to grow in part because of the aging world population. This…”
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Visualize omics data on networks with Omics Visualizer, a Cytoscape App [version 1; peer review: 2 approved] by Legeay, Marc, Doncheva, Nadezhda T., Morris, John H., Jensen, Lars Juhl

“…Cytoscape is open-source software used to analyze and visualize biological networks. In addition to being able to import networks from a variety of sources,…”
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The importance of understanding individual differences in Down syndrome [version 1; peer review: 2 approved] by Karmiloff-Smith, Annette, Al-Janabi, Tamara, D'Souza, Hana, Groet, Jurgen, Massand, Esha, Mok, Kin, Startin, Carla, Fisher, Elizabeth, Hardy, John, Nizetic, Dean, Tybulewicz, Victor, Strydom, Andre

“…In this article, we first present a summary of the general assumptions about Down syndrome (DS) still to be found in the literature. We go on to show how new…”
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Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China [version 2; peer review: 2 approved] by Kruse, Robert L

“…A novel coronavirus (2019-nCoV) originating in Wuhan, China presents a potential respiratory viral pandemic to the world population. Current efforts are…”
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Intensive care unit-acquired weakness: unanswered questions and targets for future research [version 1; peer review: 3 approved] by Piva, Simone, Fagoni, Nazzareno, Latronico, Nicola

“…Intensive care unit-acquired weakness (ICU-AW) is the most common neuromuscular impairment in critically ill patients. We discuss critical aspects of ICU-AW…”
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