cran: cowplot | Projects | Ecosyste.ms: Papers

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.1038/s41598-020-76683-1

Revisiting potential associations between brain morphology, fear acquisition and extinction through new data and a literature review
Cited by: 7
Author(s): Mana R. Ehlers, Janne Nold, Manuel Kuhn, Maren Klingelhöfer-Jens, Tina B. Lonsdorf
Software Mentions: 44
Published: about 4 years ago

10.1186/s40462-020-00219-5

No room to roam: King Cobras reduce movement in agriculture
Cited by: 27
Author(s): Benjamin Michael Marshall, Matt Crane, Inês Silva, Colin Thomas Strine, Max Dolton Jones, Cameron Wesley Hodges, Pongthep Suwanwaree, Taksin Artchawakom, Surachit Waengsothorn, Matt Goode
Software Mentions: 31
Published: over 4 years ago

10.3390/microorganisms9051094

Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance
Cited by: 16
Author(s): Alfredo Mari, Tim Roloff, Madlen Stange, Kirstine Kobberøe Søgaard, Erblin Asllanaj, Gerardo Tauriello, Leila T. Alexander, Michael Schweitzer, Karoline Leuzinger, Alexander Gensch, Aurélien Emmanuel Martinez, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Parham Sendi, Manuel Battegay, Catia Marzolini, Helena M. B. Seth-Smith, Torsten Schwede, Hans H. Hirsch, Adrian Egli
Software Mentions: 27
Published: over 3 years ago

10.1186/s13073-021-00910-1

Landscape and selection of vaccine epitopes in SARS-CoV-2
Cited by: 21
Author(s): Christof C. Smith, Kelly Olsen, Kaylee M. Gentry, Maria J. Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric D. Routh, Julia Kodysh, Timothy J. O’Donnell, Carsten Haber, Kirsten Heiß, Volker Stadler, Erik Garrison, Adam Sandor, Jenny P.-Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark T. Heise, Benjamin G. Vincent, Alex Rubinsteyn
Software Mentions: 27
Published: over 3 years ago

10.3389/fcell.2020.577125

Development of a Metastasis-Related Immune Prognostic Model of Metastatic Colorectal Cancer and Its Usefulness to Immunotherapy
Cited by: 11
Author(s): Zhiwen Luo, Xiao Chen, Yefan Zhang, Zhen Huang, Hong Zhao, Jianjun Zhao, Zhiyu Li, Jianguo Zhou, Jianmei Liu, Jianqiang Cai, Xinyu Bi
Software Mentions: 26
Published: almost 4 years ago

10.3390/s20247188

Which Are the Central Aspects of Infant Sleep? The Dynamics of Sleep Composites across Infancy
Cited by: 17
Author(s): Sarah F. Schoch, Reto Huber, Malcolm Kohler, Salomé Kurth
Software Mentions: 26
Published: about 4 years ago

10.3390/ani9070417

Talking to Dogs: Companion Animal-Directed Speech in a Stress Test
Cited by: 9
Author(s): Raffaela Lesch, Kurt Kotrschal, Iris Schöberl, Andrea Beetz, Judith Solomon, W. Tecumseh Fitch
Software Mentions: 25
Published: over 5 years ago

10.1038/s41598-020-74015-x

Rural–urban scaling of age, mortality, crime and property reveals a loss of expected self-similar behaviour
Cited by: 7
Author(s): Jack Sutton, Golnaz Shahtahmassebi, Haroldo V. Ribeiro, Quentin S. Hanley
Software Mentions: 24
Published: about 4 years ago

10.1037/rev0000169

Simultaneous consonance in music perception and composition.
Cited by: 47
Author(s): Peter M. C. Harrison, Marcus T. Pearce
Software Mentions: 23
Published: almost 5 years ago

10.7554/eLife.70086

Gaps in global wildlife trade monitoring leave amphibians vulnerable
Cited by: 22
Author(s): Alice C. Hughes, Benjamin Michael Marshall, Colin Thomas Strine
Software Mentions: 23
Published: over 3 years ago

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.7554/eLife.43966

Unified single-cell analysis of testis gene regulation and pathology in five mouse strains
Cited by: 91
Author(s): Min Jung, Daniel Wells, Jannette Rusch, Suhaira Ahmad, Jonathan Marchini, Simon Myers, Donald F. Conrad
Software Mentions: 22
Published: over 5 years ago

10.1093/molbev/msaa288

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: about 4 years ago

10.3390/cells8091045

Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate Uptake
Cited by: 12
Author(s): Fabian Kern, Nicole Ludwig, Christina Backes, Esther Maldener, Tobias Fehlmann, Artur Suleymanov, Eckart Meese, Anne Hecksteden, Andreas Keller, Tim Meyer
Software Mentions: 21
Published: over 5 years ago

10.1093/gigascience/giaa026

ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data
Cited by: 13
Author(s): Stephen R. Piccolo, Terry J. Lee, Erica Suh, Kimball T Hill
Software Mentions: 21
Published: over 4 years ago

10.7717/peerj.11742

Lots of movement, little progress: a review of reptile home range literature
Cited by: 19
Author(s): Matthew Crane, Inês Silva, Benjamin Michael Marshall, Colin Thomas Strine
Software Mentions: 21
Published: over 3 years ago

10.3389/fimmu.2021.632333

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice
Cited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: almost 4 years ago

10.7554/eLife.51254

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
Cited by: 102
Author(s): Christopher Jackson, Dayanne M. Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham
Software Mentions: 20
Published: almost 5 years ago

10.7717/peerj.5794

beadplexr: reproducible and automated analysis of multiplex bead assays
Cited by: 4
Author(s): Ulrik Stervbo, Timm H. Westhoff, Nina Babel
Software Mentions: 20
Published: about 6 years ago

10.1186/s12866-021-02282-3

Associations between the gut microbiome and metabolome in early life
Cited by: 14
Author(s): Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal Pathmasiri, Susan McRitche, Susan Sumner, H. Robert Frost, Anne G. Hoen
Software Mentions: 19
Published: over 3 years ago

10.1084/jem.20201795

Diagnostic blood RNA profiles for human acute spinal cord injury
Cited by: 21
Author(s): Nikos Kyritsis, Abel Torres-Espín, Patrick G. Schupp, J. Russell Huie, Austin Chou, Xuan Duong Fernandez, Libby Thomas, Rachel Tsolinas, Debra D. Hemmerle, Lisa U. Pascual, Vineeta Singh, Jonathan Z. Pan, Jason F. Talbott, William D. Whetstone, John F. Burke, Anthony M DiGiorgio, Philip Weinstein, Geoffrey T. Manley, Sanjay S. Dhall, Adam R. Ferguson, Michael C. Oldham, Jacqueline C. Bresnahan, Michael S. Beattie
Software Mentions: 19
Published: almost 4 years ago

10.1093/molbev/msaa311

A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance
Cited by: 15
Author(s): Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola, Jason P. Andras, Jan Engelstädter, Dieter Ebert
Software Mentions: 19
Published: about 4 years ago

10.1371/journal.pone.0244384

Metropolitan age-specific mortality trends at borough and neighborhood level: The case of Mexico City
Cited by: 2
Author(s): Karol Baca-López, Cristóbal Fresno, Jesús Espinal-Enríquez, Miriam V. Flores-Merino, Miguel A. Camacho-López, Enrique Hernández‐Lemus
Software Mentions: 18
Published: almost 4 years ago

10.3390/genes12030413

Spt4 Promotes Pol I Processivity and Transcription Elongation
Cited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: almost 4 years ago

10.1371/journal.pbio.3000673

“Frozen evolution” of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
Cited by: 15
Author(s): David Pascall, Kyriaki Nomikou, Emmanuel Bréard, Stéphan Zientara, Ana da Silva Filipe, Bernd Hoffmann, Maude Jacquot, Joshua B. Singer, Kris De Clercq, Anette Bøtner, Corinne Sailleau, Cyril Viarouge, Carrie Batten, Giantonella Puggioni, Ciriaco Ligios, Giovanni Savini, Piet A. van Rijn, Peter Mertens, Roman Biek, Massimo Palmarini
Software Mentions: 18
Published: over 4 years ago

10.1002/eap.1898

Spatiotemporal prediction of wildfire size extremes with Bayesian finite sample maxima
Cited by: 40
Author(s): Maxwell B. Joseph, Matthew W. Rossi, Nathan Mietkiewicz, Adam L. Mahood, Megan E. Cattau, Lise A. St. Denis, R. Chelsea Nagy, Virginia Iglesias, John T. Abatzoglou, Jennifer K. Balch
Software Mentions: 17
Published: over 5 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: almost 4 years ago

10.12688/wellcomeopenres.16458.2

MethylDetectR: a software for methylation-based health profiling
Cited by: 14
Author(s): Robert F. Hillary, Riccardo E. Marioni
Software Mentions: 17
Published: over 3 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 6 years ago

10.1001/jamanetworkopen.2020.37227

Trends in US Pediatric Hospital Admissions in 2020 Compared With the Decade Before the COVID-19 Pandemic
Cited by: 115
Author(s): Jonathan Pelletier, Jaskaran Rakkar, Alicia K. Au, Dana Y. Fuhrman, Robert S. B. Clark, Christopher M. Horvat
Software Mentions: 17
Published: almost 4 years ago

10.1038/s41598-020-80340-y

Universal principles underlying segmental structures in parrot song and human speech
Cited by: 6
Author(s): Dan C. Mann, W. Tecumseh Fitch, Hsiao‐Wei Tu, Marisa Hoeschele
Software Mentions: 17
Published: almost 4 years ago

10.3389/fimmu.2020.565730

Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
Cited by: 22
Author(s): Marco Antônio M. Pretti, Rômulo Gonçalves Galvani, Gustavo Fioravanti Vieira, Adriana Bonomo, Martín Bonamino, Mariana Boroni
Software Mentions: 17
Published: about 4 years ago

10.1093/molbev/msab006

Compatibility of Evolutionary Responses to Constituent Antibiotics Drive Resistance Evolution to Drug Pairs
Cited by: 14
Author(s): Leonie Johanna Jahn, Daniel Simon, Mia Jensen, Charles B. Bradshaw, Mostafa Mostafa Hashim Ellabaan, Morten Otto Alexander Sommer
Software Mentions: 16
Published: almost 4 years ago

10.1371/journal.pone.0231982

Rapid processing of neutral and angry expressions within ongoing facial stimulus streams: Is it all about isolated facial features?
Cited by: 2
Author(s): Antonio Schettino, Emanuele Porcu, Christopher Gundlach, Christian Keitel, Matthias Müller
Software Mentions: 16
Published: over 4 years ago

10.3389/fcell.2020.596679

Development and Validation of a Combined Ferroptosis and Immune Prognostic Classifier for Hepatocellular Carcinoma
Cited by: 77
Author(s): Yang Liu, Xi Zhang, Junjun Zhang, Juan Tan, Jie Li, Zewen Song
Software Mentions: 16
Published: almost 4 years ago

10.1093/conphys/coaa131

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols
Cited by: 3
Author(s): Björn Illing, Andrea Severati, Justin Hochen, Paul M. Boyd, Paulin Raison, Rachel Mather, Adam T. Downie, Jodie L. Rummer, Frederieke J. Kroon, Craig Humphrey
Software Mentions: 16
Published: almost 4 years ago

10.3389/fimmu.2021.668391

A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma
Cited by: 21
Author(s): Yuhan Sun, Alexander James Sedgwick, Yaseelan Palarasah, Stefano Mangiola, Alexander D. Barrow
Software Mentions: 15
Published: over 3 years ago

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: over 3 years ago

10.1128/mBio.02120-17

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients
Cited by: 95
Author(s): Matthew K. Doherty, Tao Ding, Charlie C. Koumpouras, Shannon Telesco, Calixte S. Monast, Anuk Das, Carrie Brodmerkel, Patrick D. Schloss
Software Mentions: 15
Published: over 6 years ago

10.1007/s00204-021-03031-1

Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neurons
Cited by: 26
Author(s): Dominik Loser, María G. Hinojosa, John D. Blum, Jasmin Schaefer, Markus Brüll, Ylva Johansson, Ilinca Suciu, Karin Grillberger, Timm Danker, Clemens Möller, Iain Gardner, Gerhard Ecker, Susanne Hougaard Bennekou, Anna Forsby, Udo Kraushaar, Marcel Leist
Software Mentions: 15
Published: over 3 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 years ago

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: about 4 years ago

10.3389/fgene.2021.559998

Gene Size Matters: An Analysis of Gene Length in the Human Genome
Cited by: 55
Author(s): Inês Lopes, Gulam Altab, Priyanka Raina, João Pedro de Magalhães
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-020-03860-4

Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: about 4 years ago

10.1038/s41598-019-46510-3

Differential prognostic impact of platelet-derived growth factor receptor expression in NSCLC
Cited by: 19
Author(s): Thomas K. Kilvaer, Mehrdad Rakaee, Turid Hellevik, Jørg Vik, Luigi De Petris, Tom Dønnem, Carina Strell, Arne Östman, Lill-Tove Busund, Iñigo Martínez-Zubiaurre
Software Mentions: 15
Published: over 5 years ago

10.3389/fimmu.2020.606164

Six Immune Associated Genes Construct Prognostic Model Evaluate Low-Grade Glioma
Cited by: 32
Author(s): Yin Qiu Tan, Yun Tao Li, Teng Feng Yan, Yang Xu, Bao Hui Liu, Ji An Yang, Yang Xue, Qianxue Chen, Hong Bo Zhang
Software Mentions: 14
Published: about 4 years ago

10.1007/s00204-020-02956-3

Human neuronal signaling and communication assays to assess functional neurotoxicity
Cited by: 13
Author(s): Dominik Loser, Jasmin Schaefer, Timm Danker, Clemens Möller, Markus Brüll, Ilinca Suciu, Anna‐Katharina Ückert, Stefanie Klima, Marcel Leist, Udo Kraushaar
Software Mentions: 14
Published: about 4 years ago

10.7554/eLife.53392

ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair
Cited by: 23
Author(s): Daniel Wells, Emmanuelle Bitoun, Daniela Moralli, Gang Zhang, Anjali Gupta Hinch, Julia Jankowska, Peter Donnelly, Catherine Green, Simon Myers
Software Mentions: 14
Published: over 4 years ago

10.7150/jca.55970

Characteristics of Infiltrating Immune Cells and a Predictive Immune Model for Cervical Cancer
Cited by: 11
Author(s): Ruanmin Zou, Ruihong Gu, Xinbing Yu, Yingying Hu, Ji Hee Yu, Xiangyang Xue, Xueqiong Zhu
Software Mentions: 14
Published: almost 4 years ago

10.1002/ece3.7135

Invasive <i>Impatiens glandulifera</i>: A driver of changes in native vegetation?
Cited by: 5
Author(s): Judith Bieberich, Stefanie Müller, Heike Feldhaar, Marianne Lauerer
Software Mentions: 14
Published: almost 4 years ago

10.3390/insects10100321

Evaluation of NEON Data to Model Spatio-Temporal Tick Dynamics in Florida
Cited by: 5
Author(s): Geraldine Klarenberg, Samantha M. Wisely
Software Mentions: 14
Published: about 5 years ago

10.3389/fpsyg.2020.564083

Correlates of Health-Protective Behavior During the Initial Days of the COVID-19 Outbreak in Norway
Cited by: 54
Author(s): Janis Zickfeld, Thomas W. Schubert, Anders Kuvaas Herting, Jon Grahe, Kate Faasse
Software Mentions: 14
Published: about 4 years ago

10.1098/rspb.2021.0552

Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome
Cited by: 9
Author(s): Xavier A. Harrison, Allan D. McDevitt, Jenny C. Dunn, Sarah M. Griffiths, Chiara Benvenuto, Richard Birtles, Jean P. Boubli, Kevin Bown, Calum Bridson, Darren R. Brooks, Samuel S. Browett, Ruth F. Carden, Julian Chantrey, Friederike Clever, Ilaria Coscia, Katie L. Edwards, Nicolas Ferry, Ian Goodhead, Andrew Highlands, Jane Hopper, Joseph A. Jackson, Robert Jehle, Mariane da Cruz Kaizer, Tony King, Jessica M. D. Lea, Jessica L Lenka, Alexandra McCubbin, Jack McKenzie, Bárbara Lins Caldas de Moraes, Denise O'Meara, Poppy Pescod, Richard F. Preziosi, Jennifer K. Rowntree, Susanne Shultz, Matthew J. Silk, Jennifer E. Stockdale, William O. C. Symondson, Mariana Villalba de la Peña, Susan L. Walker, Michael D. Wood, Rachael E. Antwis
Software Mentions: 14
Published: over 3 years ago

10.1186/s12859-021-03970-7

stochprofML: stochastic profiling using maximum likelihood estimation in R
Cited by: 3
Author(s): Lisa Amrhein, Christiane Fuchs
Software Mentions: 14
Published: almost 4 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.1038/s41398-021-01596-0

Autoantibody profiles associated with clinical features in psychotic disorders
Cited by: 6
Author(s): August Jernbom Falk, Cherrie Galletly, David R. Just, Catherine Toben, Bernhard T. Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg, Klaus Oliver Schubert
Software Mentions: 13
Published: over 3 years ago

10.1186/s13227-020-0147-0

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus
Cited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: almost 5 years ago

10.1186/s13073-021-00893-z

Destination shapes antibiotic resistance gene acquisitions, abundance increases, and diversity changes in Dutch travelers
Cited by: 18
Author(s): Alaric W. D’Souza, Manish Boolchandani, Sanket Patel, Gianluca Galazzo, Jarne M. van Hattem, Maris S Arcilla, Damian C. Melles∗, Menno D. de Jong, Constance Schultsz, Gautam Dantas, John Penders
Software Mentions: 13
Published: over 3 years ago

10.3390/cancers11010091

The Potential Mechanism of Bufadienolide-Like Chemicals on Breast Cancer via Bioinformatics Analysis
Cited by: 5
Author(s): Yingbo Zhang, Xiaomin Tang, Yuxin Pang, Luqi Huang, Dan Wang, Chao Yuan, Xuan Hu, Liping Qu
Software Mentions: 13
Published: almost 6 years ago

10.3390/v13061184

Age and Infectious Dose Significantly Affect Disease Progression after RHDV2 Infection in Naïve Domestic Rabbits
Cited by: 13
Author(s): Robyn N. Hall, Tegan King, Tiffany W. O’Connor, Andrew J. Read, Jane Arrow, Katherine Trought, Janine A. Duckworth, M. Treuting Piper, Tanja Strive
Software Mentions: 13
Published: over 3 years ago

10.3389/fonc.2021.583547

Alternative Splicing Events in Tumor Immune Infiltration in Colorectal Cancer
Cited by: 5
Author(s): Shi Jian-yu, Yan-yan Bi, Bo Yu, Qingfeng Wang, Teng Dan, WU Dong-ning
Software Mentions: 13
Published: over 3 years ago

10.1186/s13059-020-02001-7

Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing
Cited by: 7
Author(s): Jinyan Huang, Lijun Bai, Bowen Cui, Liang Wu, Liwen Wang, Zhiyin An, Shulin Ruan, Yue Yu, Xianyang Zhang, Jun Chen
Software Mentions: 13
Published: over 4 years ago

10.1128/AEM.01225-21

Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek
Cited by: 7
Author(s): Anna Cäcilia Ingham, Tinna Ravnholt Urth, Raphael N. Sieber, Marc Stegger, Sofie Marie Edslev, Øystein Angen, Anders Rhod Larsen
Software Mentions: 13
Published: over 3 years ago

10.7554/eLife.61980

Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues
Cited by: 43
Author(s): Andrew W. DeVilbiss, Zhiyu Zhao, Misty S. Martin-Sandoval, Jessalyn M. Ubellacker, Alpaslan Tasdogan, Michalis Agathocleous, Thomas P. Mathews, Sean J. Morrison
Software Mentions: 13
Published: almost 4 years ago

10.1186/s12864-019-5700-7

RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq data
Cited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 5 years ago

10.1038/s42003-021-02335-3

A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues
Cited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pcbi.1007859

Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease
Cited by: 10
Author(s): Christine Tataru, Maude M. David
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pcbi.1008896

Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities
Cited by: 8
Author(s): Gil J. B. Henriques, Simon van Vliet, Michael Doebeli
Software Mentions: 13
Published: over 3 years ago

10.3389/fmicb.2021.616013

Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab
Cited by: 7
Author(s): Wencong Shi, Gaoya Su, Mingcong Li, Bing Wang, Runmao Lin, Yang Yu-tian, Tao Wei, Bo Zhou, Zheng Gao
Software Mentions: 13
Published: almost 4 years ago

10.1002/ece3.7130

QuoVidi: An open‐source web application for the organization of large‐scale biological treasure hunts
Cited by: 8
Author(s): Guillaume Lobet, Charlotte Descamps, Lola Leveau, Alain Guillet, Jean-François Rees
Software Mentions: 12
Published: almost 4 years ago

10.3389/fonc.2019.01361

Development and Validation of an RNA-Seq-Based Prognostic Signature in Neuroblastoma
Cited by: 28
Author(s): Jianguo Zhou, Bo Liang, Sanli Jin, Hui-Ling Liao, Guocheng Du, Long Cheng, Hu Ma, Udo S. Gaipl
Software Mentions: 12
Published: about 5 years ago

10.1038/s41396-018-0251-5

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals
Cited by: 56
Author(s): Amanda C. Perofsky, Rebecca J. Lewis, Lauren Ancel Meyers
Software Mentions: 12
Published: over 6 years ago

10.1371/journal.pone.0239197

Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures
Cited by: 13
Author(s): Weston R. Bodily, Brian H. Shirts, Tom Walsh, Süleyman Gülsüner, Mary‐Claire King, Alyssa Parker, Moom R. Roosan, Stephen R. Piccolo
Software Mentions: 12
Published: about 4 years ago

10.1111/1462-2920.14621

Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes
Cited by: 22
Author(s): Pavla Debeljak, Ève Toulza, Sara Beier, Stéphane Blain, Ingrid Obernosterer
Software Mentions: 12
Published: over 5 years ago

10.1155/2021/4743971

Exploration of the Immune-Related Signatures and Immune Infiltration Analysis in Melanoma
Cited by: 0
Author(s): Ai-lan Li, Yong‐Mei Zhu, Lai-qiang Gao, Shuyue Wei, Mingtao Wang, Qiang Ma, Yuanna Zheng, Jianhua Li, Qingfeng Wang
Software Mentions: 12
Published: almost 4 years ago

10.1093/gigascience/giab011

The case for using mapped exonic non-duplicate reads when reporting RNA-sequencing depth: examples from pediatric cancer datasets
Cited by: 2
Author(s): Holly C. Beale, Jacquelyn Roger, Matthew Cattle, Liam T. McKay, Drew Thompson, Katrina Learned, A. Geoffrey Lyle, Ellen Kephart, R. Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R. Salama, David Haussler, Olena M. Vaske
Software Mentions: 12
Published: almost 4 years ago

10.1534/g3.120.401527

rdmc: An Open Source R Package Implementing Convergent Adaptation Models of Lee and Coop (2017)
Cited by: 2
Author(s): Silas Tittes
Software Mentions: 12
Published: over 4 years ago

10.1038/s41598-020-69239-w

Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish
Cited by: 14
Author(s): Yipeng Liang, Axel Meyer, Claudius F. Kratochwil
Software Mentions: 12
Published: over 4 years ago

10.7554/eLife.55529

Smchd1 is a maternal effect gene required for genomic imprinting
Cited by: 22
Author(s): Iromi Wanigasuriya, Quentin Gouil, Sarah Kinkel, Andrés Tapia del Fierro, Tamara Beck, Ellise A Roper, Kelsey Breslin, Jessica M Stringer, Karla J. Hutt, Heather Lee, Andrew Keniry, Matthew E. Ritchie, Marnie E. Blewitt
Software Mentions: 12
Published: about 4 years ago

10.3390/genes9120569

NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
Cited by: 13
Author(s): Eduardo Zúñiga-León, Ulises Carrasco-Navarro, Francisco Fierro
Software Mentions: 12
Published: about 6 years ago

10.7554/eLife.52465

Navigating the garden of forking paths for data exclusions in fear conditioning research
Cited by: 87
Author(s): Tina B. Lonsdorf, Maren Klingelhöfer-Jens, Marta Andreatta, Tom Beckers, Anastasia Chalkia, Anna Gerlicher, Valerie L. Jentsch, Shira Meir Drexler, Gaëtan Mertens, Jan Richter, Rachel Sjouwerman, Julia Wendt, Christian J. Merz
Software Mentions: 12
Published: about 5 years ago

10.12688/f1000research.12874.2

Measuring evolutionary rates of proteins in a structural context
Cited by: 5
Author(s): Dariya K. Sydykova, Benjamin R. Jack, Scott R. Spielman, Claus O. Wilke
Software Mentions: 12
Published: almost 7 years ago

10.3389/fimmu.2021.647832

Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection
Cited by: 9
Author(s): Thyago Leal-Calvo, Bruna Letícia Martins, Daniele Ferreira de Faria Bertoluci, Patrícia Sammarco Rosa, Rodrigo Mendes de Camargo, G. Germano, Vânia Niéto Brito de Souza, Ana Carla Pereira Latini, Milton Ozório Moraes
Software Mentions: 12
Published: over 3 years ago

10.3389/fonc.2021.690324

Predictive Nomogram and Risk Factors for Lymph Node Metastasis in Bladder Cancer
Cited by: 11
Author(s): Zijian Tian, Lingfeng Meng, Xin Wang, Tongxiang Diao, Mao‐Lin Hu, Miao Wang, Yaqun Zhang, Ming Liu
Software Mentions: 12
Published: over 3 years ago

10.1007/s00431-021-04147-3

Sleep behavior of infants with infantile hemangioma treated with propranolol—a cohort study
Cited by: 6
Author(s): Martin Theiler, Nicole Knöpfel, Susanne Heydt, Agnes Schwieger‐Briel, Isabelle Luchsinger, Alexandra Smith, Kristin Kernland‐Lang, Regula Waelchli, Kathrin Neuhaus, Malcolm Kohler, Ralph Gnannt, Sarah F. Schoch, Lisa Weibel, Salomé Kurth
Software Mentions: 11
Published: over 3 years ago

10.1186/s42523-020-00066-0

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary
Cited by: 16
Author(s): Rebecca J. Stevick, Anton F. Post, Marta Gómez-Chiarri
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12913-021-06509-x

Importance of patient bed pathways and length of stay differences in predicting COVID-19 hospital bed occupancy in England
Cited by: 20
Author(s): Quentin J. Leclerc, Naomi M. Fuller, Ruth H. Keogh, Karla Díaz-Ordaz, Richard Sekula, Malcolm G Semple, J Kenneth Baillie, Malcolm G Semple, Peter Openshaw, Gail Carson, Beatrice Alex, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Meera Chand, Graham Cooke, Annemarie B Docherty, Jake Dunning, Ana da Silva Filipe, Tom Fletcher, Christopher Green, Ewen M Harrison, Julian A. Hiscox, Antonia Ho, Peter Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Wei Shen Lim, Alexander J. Mentzer, Laura Merson, Alison Meynert, Mahdad Noursadeghi, Shona C. Moore, Massimo Palmarini, William A. Paxton, Georgios Pollakis, Nicholas Price, Andrew Rambaut, David L. Robertson, Clark D Russell, Vanessa Sancho‐Shimizu, Janet T. Scott, Thushan I. de Silva, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, D.I. Stuart, Charlotte Summers, Richard S. Tedder, Emma C. Thomson, A. A. Roger Thompson, Ryan S. Thwaites, Lance Turtle, Maria Zambon, Hayley Hardwick, Chloe Donohue, Ruth Lyons, Fiona Griffiths, Wilna Oosthuyzen, Lisa Norman, Riinu Pius, Tom Drake, Cameron J Fairfield, Stephen R Knight, Kenneth A McLean, Derek Murphy, Catherine Shaw, Jo Ann Dalton, James Lee, Daniel Plotkin, Michelle Girvan, Eglė Savičiūtė, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Claire Petersen, Scott Mullaney, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, William Greenhalf, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, J. A. Armstrong, Milton Ashworth, Innocent G Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W. A. Catterall, Jordan Clark, Emily Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, L. W. Fisher, Terry Foster, Isabel García-Dorival, Philip Gunning, Catherine Hartley, Antonia Ho, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A Livoti, Maria Elisabetta Mancini, Sarah E. McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce M. Mitchell, Ellen Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, Paul Ridley, Debby Sales, Victoria Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Ana Alegria, Brian Angus, Abdul Ashish, D. Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John C. Berridge, Nicola Best, Pieter Bothma, David Brealey, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, David Chadwick, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Samir Dervisevic, Phil Donnison, Sam Douthwaite, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Cariad Evans, Alice C Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Sanjeev Garg, Atul Garg, Effrossyni Gkrania‐Klotsas, Jo Godden, Arthur R. Goldsmith, Clive Graham, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, M.C. Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamás Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Michael MacMahon, Emily Macnaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary L. Mills, Jane Minton, Mariyam Mirfenderesky, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig C. Morris, Katherine Mortimore, Samuel Moses, Mbiye Mpenge, Rohinton Mulla, Michael V. Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Igor Otahal, Mark Pais, Selva Panchatsharam, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Frank A. Post, David J. Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Brendan Ryan, Taranprit Saluja, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamás Szakmány, Kate Tatham, Thomas Jo, Chris Thompson, Robert J. Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Andrew Ustianowski, Nick Vallotton, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Meme Wijesinghe, Martin Williams, Lawrence A. Wilson, Sarah Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wooton, Andrew Workman, Bryan Yates, Peter Young, Matthew Quaife, Christopher Jarvis, Sophie Meakin, Billy J Quilty, Kiesha Prem, C. Julian Villabona-Arenas, Fiona Yueqian Sun, Kaja Abbas, Megan Auzenbergs, Amy Gimma, Damien C. Tully, Katharine Sherratt, Alicia Roselló, Nicholas Davies, Yang Liu, Rachel Lowe, Hamish Gibbs, Naomi R. Waterlow, W. John Edmunds, David Simons, Graham Medley, James D. Munday, Stefan Flasche, Frank Sandmann, Alicia Showering, Rosalind M Eggo, Yung-Wai Desmond Chan, Carl A. B. Pearson, Adam J. Kucharski, Anna M Foss, Timothy Russell, Nikos I. Bosse, Mark Jit, Sam Abbott, Jack Williams, Akira Endo, Samuel Clifford, Georgia R. Gore-Langton, Petra Klepac, Oliver J. Brady, Joel Hellewell, Sebastian Funk, Kevin van Zandvoort, Rosanna C. Barnard, Emily Nightingale, Thibaut Jombart, Katherine E. Atkins, Simon R. Procter, Gwenan M. Knight
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-021-89020-x

Gene-environment dependencies lead to collider bias in models with polygenic scores
Cited by: 29
Author(s): Evelina T. Akimova, Richard Breen, David M. Brazel, Melinda Mills
Software Mentions: 11
Published: over 3 years ago

10.1099/mgen.0.000503

Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago

10.1002/ece3.6904

Light might suppress both types of sound‐evoked antipredator flight in moths
Cited by: 2
Author(s): Theresa Hügel, Holger R. Goerlitz
Software Mentions: 11
Published: about 4 years ago

10.1007/s11306-016-1090-x

Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis
Cited by: 6
Author(s): Elisabete Carvalho, Pietro Franceschi, Antje Feller, Lorena Herrera, L. Palmieri, Panagiotis Arapitsas, Samantha Riccadonna, Stefan Martens
Software Mentions: 11
Published: over 8 years ago

10.3389/fmicb.2021.633659

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast
Cited by: 14
Author(s): Maria Luis de Vilar Correia Brito Bôto, Catarina Magalhães, Rafaela Perdigão, Diogo A. M. Alexandrino, Joana P. Fernandes, Ana M. Bernabéu, Sandra Ramos, Maria F. Carvalho, Miguel Semedo, Julie LaRoche, C. Marisa R. Almeida, Ana P. Mucha
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0180791

A validation of 11 body-condition indices in a giant snake species that exhibits positive allometry
Cited by: 29
Author(s): Bryan G. Falk, Ray W. Snow, Robert N. Reed
Software Mentions: 11
Published: over 7 years ago

10.1038/s41598-018-32681-y

Medicinal value of sunflower pollen against bee pathogens
Cited by: 77
Author(s): Jonathan J. Giacomini, Jessica Leslie, David R. Tarpy, Evan C. Palmer‐Young, Rebecca E. Irwin, Lynn S. Adler
Software Mentions: 10
Published: about 6 years ago

10.18632/aging.203257

Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: over 3 years ago

10.1186/s13071-020-04461-z

Oviposition of Aedes japonicus japonicus (Diptera: Culicidae) and associated native species in relation to season, temperature and land use in western Germany
Cited by: 12
Author(s): Linus Früh, Helge Kampen, Marcel B. Koban, Nadja Pernat, Günter A. Schaub, Doreen Werner
Software Mentions: 10
Published: about 4 years ago

10.1371/journal.pone.0216723

A metadata approach to evaluate the state of ocean knowledge: Strengths, limitations, and application to Mexico
Cited by: 10
Author(s): Juliano Palacios‐Abrantes, Andrés M. Cisneros‐Montemayor, Miguel Á. Cisneros-Mata, Laura Rodríguez, Francisco Arreguı́n-Sánchez, Verónica Aguilar, Santiago Domínguez-Sánchez, Stuart Fulton, Raquel López-Sagástegui, Héctor Reyes‐Bonilla, Rocío Rivera-Campos, Silvia Salas, Nuno Simões, William W. L. Cheung
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-017-09303-0

The impact of immigration on microbial community composition in full-scale anaerobic digesters
Cited by: 111
Author(s): Rasmus Hansen Kirkegaard, Simon Jon McIlroy, Jannie Munk Kristensen, Marta Nierychlo, Søren Michael Karst, Morten Simonsen Dueholm, Mads Albertsen, Per Halkjær Nielsen
Software Mentions: 10
Published: over 7 years ago

10.3389/fmicb.2020.01190

Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk
Cited by: 14
Author(s): Christopher Maier, Christopher Huptas, Mario von Neubeck, Stephen W. Scherer, Mareike Wenning, Genia Lücking
Software Mentions: 10
Published: over 4 years ago

Projects: cran: cowplot

Papers Mentioning cowplot 298