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

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

10.1371/journal.pone.0251194

A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses
Cited by: 15
Author(s): Heidi Seibold, Severin Czerny, Siona Decke, Roman Dieterle, Thomas Eder, Steffen Fohr, Nico Hahn, Rabea Hartmann, Christoph Heindl, Philipp Kopper, Dario Lepke, Verena Loidl, Maximilian Mandl, Sarah Musiol, Jessica Peter, Alexander Piehler, Elio Rojas, Stefanie Schmid, Hannah Schmidt, Melissa Schmoll, Lennart Schneider, Xiao-Yin To, Viêt Anh Tran, Antje Völker, Moritz Wagner, Joshua Wagner, Maria Waize, Hannah Wecker, Rui Yang, Simone Zellner, Malte Nalenz
Software Mentions: 46
Published: over 3 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

10.12688/f1000research.9973.2

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.15252/msb.20209539

Predictive features of gene expression variation reveal mechanistic link with differential expression
Cited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 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

10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago

10.1111/cobi.13492

Matching expert range maps with species distribution model predictions
Cited by: 18
Author(s): Kumar P. Mainali, Trevor J. Hefley, Leslie Ries, William F. Fagan
Software Mentions: 26
Published: over 4 years ago

10.1186/s12859-017-1905-4

ADAGE signature analysis: differential expression analysis with data-defined gene sets
Cited by: 15
Author(s): Jie Tan, Matthew Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene
Software Mentions: 25
Published: about 7 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: over 4 years ago

10.1155/2021/8020879

Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network Mechanism
Cited by: 10
Author(s): Jin Zhang, Fei Xiao, Guangliang Qiang, Zhenrong Zhang, Qianli Ma, Hao Yang, H. Rosie Xing, Chaoyang Liang
Software Mentions: 22
Published: about 3 years ago

10.3390/cancers13092163

Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Software Mentions: 20
Published: over 3 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

10.3390/ijms21186652

Identification of Gastritis Subtypes by Convolutional Neuronal Networks on Histological Images of Antrum and Corpus Biopsies
Cited by: 15
Author(s): Georg Steinbuß, Katharina Kriegsmann, Mark Kriegsmann
Software Mentions: 19
Published: about 4 years ago

10.1371/journal.pone.0247002

Chainchecker: An application to visualise and explore transmission chains for Ebola virus disease
Cited by: 2
Author(s): Katy A. M. Gaythorpe, Aaron Morris, Natsuko Imai, Miles Stewart, Jeffrey S. Freeman, Mary J. Choi
Software Mentions: 19
Published: almost 4 years ago

10.1080/17453674.2020.1846956

Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size
Cited by: 7
Author(s): Yosef Tyson, Christer Hillman, Norbert Majenburg, Olof Sköldenberg, Ola Rolfson, Johan Kärrholm, Maziar Mohaddes, Nils P Hailer
Software Mentions: 16
Published: about 4 years ago

10.1128/MRA.00129-19

omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Cited by: 12
Author(s): Connor R. Tiffany, Andreas J. Bäumler
Software Mentions: 16
Published: over 5 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: over 3 years ago

10.1186/s13059-020-02020-4

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians
Cited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: over 4 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

10.3390/genes12071044

CircIMPACT: An R Package to Explore Circular RNA Impact on Gene Expression and Pathways
Cited by: 3
Author(s): Alessia Buratin, Enrico Gaffo, Anna Dal Molin, Stefania Bortoluzzi
Software Mentions: 15
Published: over 3 years ago

10.1371/journal.pbio.3000581

PlotTwist: A web app for plotting and annotating continuous data
Cited by: 43
Author(s): Joachim Goedhart
Software Mentions: 14
Published: almost 5 years ago

10.1371/journal.pone.0248202

Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils
Cited by: 1
Author(s): Ava Mackay-Smith, Mary Kate Dornon, R.E. Lucier, Annalisa Okimoto, Flavia Mendonca de Sousa, Marcela Silvina Rodriguero, Viviana A. Confalonieri, Analía Alicia Lanteri, Andrea S. Sequeira
Software Mentions: 14
Published: over 3 years ago

10.1186/s42523-020-00027-7

Domesticated equine species and their derived hybrids differ in their fecal microbiota
Cited by: 18
Author(s): Joan E. Edwards, A. Schennink, Faith Burden, Stuart A. Long, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Edoardo Saccenti, Hauke Smidt
Software Mentions: 14
Published: over 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: almost 4 years ago

10.1186/s13059-020-02233-7

tidybulk: an R tidy framework for modular transcriptomic data analysis
Cited by: 22
Author(s): Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A. Doyle, Anthony T. Papenfuss
Software Mentions: 13
Published: almost 4 years ago

10.1186/s42523-020-0023-1

Multi-kingdom characterization of the core equine fecal microbiota based on multiple equine (sub)species
Cited by: 31
Author(s): Joan E. Edwards, Sudarshan A. Shetty, Pim van den Berg, Faith Burden, D.A. van Doorn, W.F. Pellikaan, J. Dijkstra, Hauke Smidt
Software Mentions: 13
Published: almost 5 years ago

10.1128/AEM.01096-17

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data
Cited by: 58
Author(s): Laura M. Carroll, Jasna Kovač, Robert W. Miller, Martin Wiedmann
Software Mentions: 13
Published: about 7 years ago

10.3390/ijms21134674

The Inflammasome Adaptor Protein ASC in Mild Cognitive Impairment and Alzheimer’s Disease
Cited by: 37
Author(s): Xavier O. Scott, Marisa E. Stephens, Marie C. Desir, W. Dalton Dietrich, Robert W. Keane, Juan Pablo de Rivero Vaccari
Software Mentions: 13
Published: over 4 years ago

10.1371/journal.pone.0212669

Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects
Cited by: 3
Author(s): Robin Gradin, Malin Lindstedt, Henrik J. Johansson
Software Mentions: 13
Published: over 5 years ago

10.12688/f1000research.8967.2

An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: over 6 years ago

10.1186/s12920-017-0303-0

Classifying cancer genome aberrations by their mutually exclusive effects on transcription
Cited by: 8
Author(s): Jonathan Dayton, Stephen R. Piccolo
Software Mentions: 12
Published: almost 7 years ago

10.1093/aobpla/plz054

tealeaves: an R package for modelling leaf temperature using energy budgets
Cited by: 26
Author(s): Christopher D. Muir
Software Mentions: 12
Published: about 5 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: about 4 years ago

10.1371/journal.pone.0156293

Cryopreservation of Human Mucosal Leukocytes
Cited by: 14
Author(s): Sean M. Hughes, Zhiquan Shu, Claire Levy, April L. Ferre, Heather Hartig, Cifeng Fang, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, Kristina M. Adams Waldorf, Ronald S. Veazey, Anja Germann, Hagen von Briesen, M. Juliana McElrath, Charlene S. Dezzutti, Elizabeth Sinclair, Chris A. R. Baker, Barbara L. Shacklett, Dayong Gao, Florian Hladik
Software Mentions: 12
Published: over 8 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: over 6 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

10.3389/fnut.2021.676026

Food Sources Contributing to Intake of Choline and Individual Choline Forms in a Norwegian Cohort of Patients With Stable Angina Pectoris
Cited by: 8
Author(s): Anthea Van Parys, Therese Karlsson, Kathrine J. Vinknes, Trond E. Olsen, Jannike Øyen, Jutta Dierkes, Ottar Nygård, Vegard Lysne
Software Mentions: 11
Published: over 3 years ago

10.12688/wellcomeopenres.15477.2

Feasibility of informing syndrome-level empiric antibiotic recommendations using publicly available antibiotic resistance datasets
Cited by: 5
Author(s): Quentin J. Leclerc, Nichola R. Naylor, Alexander M. Aiken, Francesc Español i Coll, Gwenan M. Knight
Software Mentions: 11
Published: over 4 years ago

10.1128/mSphere.00743-20

Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull ( <i>Chroicocephalus novaehollandiae</i> ) Reveals the Acquisition of Multidrug Resistance Plasmids
Cited by: 17
Author(s): Max L. Cummins, Martina L. Sanderson-Smith, Peter Newton, Nicholas Carlile, David N. Phalen, Kimberly Maute, Leigh G. Monahan, Bethany J. Hoye, Steven P. Djordjevic
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0238160

Diagnostic and prognostic value of hematological and immunological markers in COVID-19 infection: A meta-analysis of 6320 patients
Cited by: 138
Author(s): Rami M. Elshazli, Eman A. Toraih, Abdelaziz Elgaml, Mohammed El‐Mowafy, Mohamed El-Mesery, Mohamed N. Amin, Mohammad Hussein, Mary Killackey, Manal S. Fawzy, Emad Kandil
Software Mentions: 10
Published: over 4 years ago

10.1186/s13071-020-04319-4

Retrospective analysis of feline intestinal parasites: trends in testing positivity by age, USA geographical region and reason for veterinary visit
Cited by: 7
Author(s): Sarah Sweet, Donald Szlosek, Donald J. McCrann, Michael J. Coyne, David Kincaid, Evan Hegarty
Software Mentions: 10
Published: about 4 years ago

10.1038/s41598-019-45491-7

The future of coffee and cocoa agroforestry in a warmer Mesoamerica
Cited by: 58
Author(s): Kauê de Sousa, Maarten van Zonneveld, Milena Holmgren, Roeland Kindt, Jenny C. Ordóñez
Software Mentions: 10
Published: over 5 years ago

10.7717/peerj.7907

motoRneuron: an open-source R toolbox for time-domain motor unit analyses
Cited by: 0
Author(s): Andrew J. Tweedell, Matthew S. Tenan
Software Mentions: 10
Published: almost 5 years ago

10.1186/s11689-021-09360-7

Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-018-1597-8

plyranges: a grammar of genomic data transformation
Cited by: 62
Author(s): Stuart Lee, Dianne Cook, Michael C. Lawrence
Software Mentions: 9
Published: almost 6 years ago

10.1371/journal.pbio.3000202

PlotsOfData—A web app for visualizing data together with their summaries
Cited by: 394
Author(s): Marten Postma, Joachim Goedhart
Software Mentions: 9
Published: over 5 years ago

10.1038/s41598-019-53903-x

Proteome characterization of used nesting material and potential protein sources from group housed male mice, Mus musculus
Cited by: 16
Author(s): Amanda J. Barabas, Uma K. Aryal, Brianna N. Gaskill
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-020-76603-3

VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots
Cited by: 230
Author(s): Joachim Goedhart, Martijn S. Luijsterburg
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-021-95185-2

The food patterns of a multicenter cohort of Brazilian nulliparous pregnant women
Cited by: 3
Author(s): Maria J Miele, Renato Teixeira Souza, Iracema de Mattos Paranhos Calderon, Francisco Edson de Lucena Feitosa, Débora Farias Batista Leite, Edilberto A. Rocha Filho, Janete Vettorazzi, Jussara Mayrink, Karayna Gil Fernandes, Matias C. Vieira, Rodolfo C. Pacagnella, José Guilherme Cecatti
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0226069

Short-term treatment with a peroxisome proliferator-activated receptor α agonist influences plasma one-carbon metabolites and B-vitamin status in rats
Cited by: 3
Author(s): Vegard Lysne, Bodil Bjørndal, Mari Lausund Grinna, Øivind Midttun, Per Magne Ueland, Rolf K. Berge, Jutta Dierkes, Ottar Nygård, Elin Strand
Software Mentions: 9
Published: almost 5 years ago

10.1186/s12867-018-0111-x

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Cited by: 4
Author(s): Paola M. Boggiatto, Daniel Fitzsimmons, Darrell O. Bayles, David P. Alt, Catherine E. Vrentas, Steven C. Olsen
Software Mentions: 9
Published: over 6 years ago

10.1186/s13071-021-04678-6

A 3-year retrospective analysis of canine intestinal parasites: fecal testing positivity by age, U.S. geographical region and reason for veterinary visit
Cited by: 14
Author(s): Sarah Sweet, Evan Hegarty, Donald J. McCrann, Michael J. Coyne, Dave Kincaid, Donald Szlosek
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-70596-9

Identification of potential diagnostic gene biomarkers in patients with osteoarthritis
Cited by: 13
Author(s): Xinling Wang, Yu Yang, Yong Huang, Zhu Ming-shuang, Rigao Chen, Zhanghui Liao, Shipeng Yang
Software Mentions: 8
Published: over 4 years ago

10.3897/BDJ.8.e47018

Rapid Least Concern: towards automating Red List assessments
Cited by: 25
Author(s): Steven P. Bachman, Barnaby E. Walker, Sara Bárrios, Alison Copeland, Justin Moat
Software Mentions: 8
Published: almost 5 years ago

10.3390/v11060492

Culex torrentium: A Potent Vector for the Transmission of West Nile Virus in Central Europe
Cited by: 33
Author(s): Stéphanie Jansen, Anna Heitmann, Renke Lühken, Mayke Leggewie, Michelle Helms, Marlis Badusche, Giada Rossini, Jonas Schmidt‐Chanasit, Egbert Tannich
Software Mentions: 8
Published: over 5 years ago

10.1093/eurheartj/ehaa756

Midlife blood pressure is associated with the severity of white matter hyperintensities: analysis of the UK Biobank cohort study
Cited by: 56
Author(s): Karolina Wartolowska, Alastair Webb
Software Mentions: 8
Published: almost 4 years ago

10.12688/f1000research.18002.1

Epidemic curves made easy using the R package incidence
Cited by: 38
Author(s): Zhian N. Kamvar, Jun Cai, Juliet R. C. Pulliam, Jakob Schumacher, Thibaut Jombart
Software Mentions: 8
Published: almost 6 years ago

10.3389/fpsyg.2020.579545

When Large-Scale Assessments Meet Data Science: The Big-Fish-Little-Pond Effect in Fourth- and Eighth-Grade Mathematics Across Nations
Cited by: 4
Author(s): Ze Wang
Software Mentions: 8
Published: about 4 years ago

10.1001/jamanetworkopen.2021.15985

Assessment of Effectiveness of 1 Dose of BNT162b2 Vaccine for SARS-CoV-2 Infection 13 to 24 Days After Immunization
Cited by: 92
Author(s): Gabriel Chodick, Lilac Tene, Tal Patalon, Sivan Gazit, Amir Ben‐Tov, Dani Cohen, Khitam Muhsen
Software Mentions: 8
Published: over 3 years ago

10.1186/s40478-021-01240-4

Experimental colitis promotes sustained, sex-dependent, T-cell-associated neuroinflammation and parkinsonian neuropathology
Cited by: 26
Author(s): Madelyn C. Houser, W. Michael Caudle, Jianjun Chang, George T. Kannarkat, Yuan Yang, Sean D. Kelly, Danielle Oliver, Valerie Joers, Kathleen M. Shannon, Ali Keshavarzian, Malú G. Tansey
Software Mentions: 8
Published: over 3 years ago

10.1161/HYPERTENSIONAHA.121.17403

Blood Pressure Determinants of Cerebral White Matter Hyperintensities and Microstructural Injury: UK Biobank Cohort Study
Cited by: 13
Author(s): Karolina Wartolowska, Alastair Webb
Software Mentions: 8
Published: over 3 years ago

10.5696/2156-9614-10.27.200912

Levels of PM10 and PM2.5 and Respiratory Health Impacts on School-Going Children in Kenya
Cited by: 8
Author(s): Faridah Hussein Were, Godfrey A. Wafula, Cromwel B Lukorito, Timothy Kamanu
Software Mentions: 8
Published: about 4 years ago

10.3758/s13428-017-0862-1

Estimating psychological networks and their accuracy: A tutorial paper
Cited by: 1,743
Author(s): Sacha Epskamp, Denny Borsboom, Eiko I. Fried
Software Mentions: 7
Published: over 7 years ago

10.7150/jca.49707

Cancer-associated fibroblasts in gastric cancer affect malignant progression via the CXCL12-CXCR4 axis
Cited by: 20
Author(s): Qin Yan, Fang Wang, Hengli Ni, Yao Liu, Yuan Yin, Xinyi Zhou, Guihua Gao, Qing Li, Xiaowei Qi, Jianming Li
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.ppat.1008864

Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates
Cited by: 14
Author(s): Duncan Ndungu Ndegwa, Prasun Kundu, Jessica B. Hostetler, Alejandro Marín-Menéndez, Theo Sanderson, Kioko Mwikali, Lisa Verzier, Rachael Coyle, Sophie H. Adjalley, Julian C. Rayner
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0245626

Diversity of microbial communities and soil nutrients in sugarcane rhizosphere soil under water soluble fertilizer
Cited by: 20
Author(s): Huan Niu, Ziqin Pang, Nyumah Fallah, Yongmei Zhou, Caifang Zhang, Chaohua Hu, Wenxiong Lin, Zhaonian Yuan
Software Mentions: 7
Published: almost 4 years ago

10.1186/s12940-018-0413-y

Statistical software for analyzing the health effects of multiple concurrent exposures via Bayesian kernel machine regression
Cited by: 423
Author(s): Jennifer F. Bobb, Birgit Claus Henn, Linda Valeri, Brent A. Coull
Software Mentions: 7
Published: over 6 years ago

10.3389/fpsyg.2018.02358

East Asian Young and Older Adult Perceptions of Emotional Faces From an Age- and Sex-Fair East Asian Facial Expression Database
Cited by: 13
Author(s): Yu-Zhen Tu, Dai-Jie Lin, Atsunobu Suzuki, Joshua Oon Soo Goh
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12891-020-03889-9

High blood pressure and overweight in children with Legg-Calvé-Perthes disease: a nationwide population-based cohort study
Cited by: 6
Author(s): Gabriella B. Mörlin, Yasmin D. Hailer
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0204076

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Cited by: 62
Author(s): Kris A. Christensen, Eric B. Rondeau, David R. Minkley, Jong S. Leong, Cameron M. Nugent, Roy G. Danzmann, Moira M. Ferguson, Agnieszka Stadnik, Robert H. Devlin, Robin Muzzerall, Michael G. Edwards, William S. Davidson, Ben F. Koop
Software Mentions: 7
Published: about 6 years ago

10.3390/vetsci7030138

Cattle Manure Trade Network Analysis and the Relevant Spatial Pathways in an Endemic Area of Foot and Mouth Disease in Northern Thailand
Cited by: 0
Author(s): Chalutwan Sansamur, Anuwat Wiratsudakul, Arisara Charoenpanyanet, Veerasak Punyapornwithaya
Software Mentions: 7
Published: about 4 years ago

10.1155/2019/8047627

Short-Term Activation of Peroxisome Proliferator-Activated Receptors<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi>α</mml:mi></mml:mrow></mml:math>and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:mi>γ</mml:mi></mml:mrow></mml:math>Induces Tissue-Specific Effects on Lipid Metabolism and Fatty Acid Composition in Male Wistar Rats
Cited by: 18
Author(s): Elin Strand, Vegard Lysne, Mari Lausund Grinna, Pavol Bohov, Asbjørn Svardal, Ottar Nygård, Rolf K. Berge, Bodil Bjørndal
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.6792

Timing and ecological priority shaped the diversification of sedges in the Himalayas
Cited by: 9
Author(s): Uzma Uzma, Pedro Jiménez‐Mejías, Rabia Amir, Muhammad Qasim Hayat, Andrew L. Hipp
Software Mentions: 7
Published: over 5 years ago

10.1093/bioinformatics/bty088

SecretSanta: flexible pipelines for functional secretome prediction
Cited by: 10
Author(s): Anna Gogleva, Hajk-Georg Drost, Sebastián Schornack
Software Mentions: 7
Published: almost 7 years ago

10.7717/peerj.2823

An extensive comparison of species-abundance distribution models
Cited by: 65
Author(s): Elita Baldridge, David J. Harris, Xiao Xiao, Ethan White
Software Mentions: 7
Published: almost 8 years ago

10.1080/17453674.2020.1749810

Fate of patients with slipped capital femoral epiphysis (SCFE) in later life: risk of obesity, hypothyroidism, and death in 2,564 patients with SCFE compared with 25,638 controls
Cited by: 4
Author(s): Yasmin D. Hailer
Software Mentions: 6
Published: over 4 years ago

10.1186/s13071-019-3606-5

Comparative analysis of subsampling methods for large mosquito samples
Cited by: 3
Author(s): Linda Jaworski, Stéphanie Jansen, Wolf Peter Pfitzner, Matthias Beck, Norbert Becker, Jonas Schmidt‐Chanasit, Ellen Kiel, Renke Lühken
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-018-25588-1

Alterations in Cell Motility, Proliferation, and Metabolism in Novel Models of Acquired Temozolomide Resistant Glioblastoma
Cited by: 29
Author(s): Deanna Tiek, Janice D. Rone, Garrett T. Graham, Evan L. Pannkuk, Bassem R. Haddad, Rebecca B. Riggins
Software Mentions: 6
Published: over 6 years ago

10.1186/s12931-019-1144-5

Mass spectrometry imaging as a tool for evaluating the pulmonary distribution of exogenous surfactant in premature lambs
Cited by: 7
Author(s): Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Francesca Ricci, Francesca Boscaro, Barbara Pioselli, Valentina Mileo, Xabier Murgia, Federico Bianco, Fabrizio Salomone, Augusto F. Schmidt, Noah H. Hillman, Matthew W. Kemp, Alan H. Jobe
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0237881

Identification of key odorants in honeysuckle by headspace-solid phase microextraction and solvent-assisted flavour evaporation with gas chromatography-mass spectrometry and gas chromatograph-olfactometry in combination with chemometrics
Cited by: 6
Author(s): Keran Su, Xin Zhang, Shao-Quan Liu, LiHui Jia, Benjamin Lassabliere, Kim Huey Ee, Aileen Pua, Rui Min Vivian Goh, Jingcan Sun, Bin Yu, XiaoXue Hu
Software Mentions: 6
Published: over 4 years ago

10.3390/vaccines9070694

Impact of Transcriptome and Gut Microbiome on the Response of HIV-1 Infected Individuals to a Dendritic Cell-Based HIV Therapeutic Vaccine
Cited by: 6
Author(s): Roque Pastor-Ibáñez, Francisco Díez-Fuertes, Sonsoles Sánchez-Palomino, José Alcamı́, Montserrat Plana, David Torrents, Lorna Leal, Felipe García
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.8141

Experimental evaluation of genomic DNA degradation rates for the pathogen <i>Pseudogymnoascus destructans</i> (Pd) in bat guano
Cited by: 5
Author(s): Jenny Urbina, Tara Chestnut, Donelle Schwalm, Jenn Allen, Taal Levi
Software Mentions: 5
Published: almost 5 years ago

10.1093/gigascience/gix101

LAGOS-NE: a multi-scaled geospatial and temporal database of lake ecological context and water quality for thousands of US lakes
Cited by: 97
Author(s): Patricia A. Soranno, Linda C. Bacon, Michael Beauchene, Karen E. Bednar, Edward G. Bissell, Claire Boudreau, Marvin G. Boyer, Mary T. Bremigan, Stephen R. Carpenter, J. Carr, Kendra Spence Cheruvelil, Samuel T. Christel, Matt Claucherty, Sarah M. Collins, Joseph D. Conroy, John A. Downing, Jed Dukett, C. Emi Fergus, Christopher T. Filstrup, Clara Funk, María J. González, Linda T. Green, Corinna Gries, John D. Halfman, Stephen K. Hamilton, Paul C. Hanson, Emily Norton Henry, Elizabeth Herron, Celeste Hockings, James R. Jackson, Kari Jacobson-Hedin, Lorraine L. Janus, William A. Jones, John R. Jones, Caroline M. Keson, Katelyn B. S. King, Scott A. Kishbaugh, Jean‐François Lapierre, Barbara Lathrop, Jo A. Latimore, Yuehlin Lee, Noah R. Lottig, Jason Lynch, Leslie J. Matthews, William H. McDowell, Karen Moore, Brian P. Neff, Sarah J. Nelson, Samantha Oliver, Michael L. Pace, Donald C. Pierson, Autumn Poisson, Amina I. Pollard, David M. Post, Paul O. Reyes, Donald O. Rosenberry, Karen M. Roy, Lars G. Rudstam, Orlando Sarnelle, Nancy J. Schuldt, Catherine Scott, Nicholas K. Skaff, Nicole J. Smith, Nick R. Spinelli, Joseph Stachelek, Emily H. Stanley, John L. Stoddard, Scott B. Stopyak, Craig A. Stow, Jason Tallant, Pang‐Ning Tan, Anthony P. Thorpe, Michael J. Vanni, Tyler Wagner, Gretchen Watkins, Kathleen C. Weathers, Katherine E. Webster, Jeffrey D. White, Marcy K. Wilmes, Shuai Yuan
Software Mentions: 5
Published: about 7 years ago

10.3390/vaccines8030438

Distinct miRNA Profile of Cellular and Extracellular Vesicles Released from Chicken Tracheal Cells Following Avian Influenza Virus Infection
Cited by: 4
Author(s): Kelsey O’Dowd, Mehdi Emam, Mohamed Reda El Khili, Amin Emad, Eveline M. Ibeagha‐Awemu, Carl A. Gagnon, Neda Barjesteh
Software Mentions: 5
Published: over 4 years ago

10.3390/metabo9060113

Cerebral Vitamin B5 (D-Pantothenic Acid) Deficiency as a Potential Cause of Metabolic Perturbation and Neurodegeneration in Huntington’s Disease
Cited by: 46
Author(s): Stefano Patassini, Paul Begley, Jiaolong Xu, Stephanie J. Church, Nina Kureishy, Suzanne J. Reid, Henry J. Waldvogel, Richard L.M. Faull, Russell G. Snell, Richard D. Unwin, Garth J. S. Cooper
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-018-0163-y

Genetically engineered minipigs model the major clinical features of human neurofibromatosis type 1
Cited by: 44
Author(s): Sara Isakson, Anthony E. Rizzardi, Alexander W. Coutts, Daniel F. Carlson, Mark N. Kirstein, James E. Fisher, Jérémie Vitte, Kyle Williams, G. Elizabeth Pluhar, Sonika Dahiya, Brigitte C. Widemann, Eva Dombi, Tilat A. Rizvi, Nancy Ratner, Ludwine Messiaen, Anat Stemmer‐Rachamimov, Scott C. Fahrenkrug, David H. Gutmann, Marco Giovannini, Christopher L. Moertel, David A. Largaespada, Adrienne L. Watson
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.6486

Modulating pain thresholds through classical conditioning
Cited by: 17
Author(s): Juliane Traxler, Victoria J. Madden, G. Lorimer Moseley, Johan W.S. Vlaeyen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-27314-3

Sample tracking in microbiome community profiling assays using synthetic 16S rRNA gene spike-in controls
Cited by: 16
Author(s): Dieter M. Tourlousse, Akiko Ohashi, Yuji Sekiguchi
Software Mentions: 4
Published: over 6 years ago

10.1155/2021/3621677

A Data Mining-Based Analysis of Core Herbs on Different Patterns (Zheng) of Non-Small Cell Lung Cancer
Cited by: 2
Author(s): Xiangjun Qi, Zehuai Guo, Qianying Chen, Wanning Lan, Zhuangzhong Chen, Wenmin Chen, Lizhu Lin
Software Mentions: 4
Published: over 3 years ago

10.1186/s13063-021-05171-2

Passive Immunity Trial for Our Nation (PassITON): study protocol for a randomized placebo-control clinical trial evaluating COVID-19 convalescent plasma in hospitalized adults
Cited by: 13
Author(s): Wesley H. Self, Thomas G. Stewart, Allison P. Wheeler, Wissam El Atrouni, Amanda J. Bistran-Hall, Jonathan D. Casey, Vince D. Cataldo, James D. Chappell, Claudia S. Cohn, Jessica Collins, Mark R. Denison, Marjolein de Wit, S. Dixon, Abhijit Duggal, Terri Edwards, Magali J. Fontaine, Adit A. Ginde, Michelle Harkins, Thelma Harrington, Estelle S. Harris, Daanish Hoda, Tina S. Ipe, Stuti J. Jaiswal, Nicholas J. Johnson, Alan E. Jones, Maryrose Laguio-Vila, Christopher J. Lindsell, Jason Mallada, Manoj J. Mammen, Ryan A. Metcalf, Elizabeth Middleton, Simon Mucha, Hollis R. O’Neal, Sonal Pannu, Jill M. Pulley, Xinhua Qiao, Jay S. Raval, Jillian P. Rhoads, Harry Schrager, Carl Shanholtz, Nathan I. Shapiro, Stephen Schrantz, Isaac Thomsen, Krista Vermillion, Gordon R. Bernard, Todd W. Rice
Software Mentions: 4
Published: over 3 years ago

10.3389/fnhum.2021.622224

Predicting Student Performance Using Machine Learning in fNIRS Data
Cited by: 10
Author(s): Amanda Yumi Ambriola Oku, João Ricardo Sato
Software Mentions: 4
Published: almost 4 years ago

10.3389/fncel.2021.629279

Validation of Induced Microglia-Like Cells (iMG Cells) for Future Studies of Brain Diseases
Cited by: 24
Author(s): Atoshi Banerjee, Yujie Lu, Kenny Do, Travis Mize, Xiaogang Wu, Xiangning Chen, Jingchun Chen
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.9893.2

exprso: an R-package for the rapid implementation of machine learning algorithms
Cited by: 12
Author(s): Thomas P. Quinn, Daniel S. Tylee, Stephen J. Glatt
Software Mentions: 4
Published: almost 7 years ago

10.1007/s10661-019-8042-7

Surveying the arable plant diversity of conventionally managed farmland: a comparison of methods
Cited by: 3
Author(s): Alexander Wietzke, Christoph Leuschner
Software Mentions: 4
Published: almost 5 years ago

10.3390/v11070674

Evidence for West Nile Virus and Usutu Virus Infections in Wild and Resident Birds in Germany, 2017 and 2018
Cited by: 79
Author(s): Friederike Michel, Michael Sieg, Dominik Fischer, Markus Keller, Martin Eiden, Maximilian Reuschel, Volker Schmidt, Rebekka Schwehn, Monika Rinder, Sylvia Urbaniak, Kerstin Müller, Martina Schmoock, Renke Lühken, Patrick Wysocki, Christine Fast, Michael Lierz, Rüdiger Korbel, Thomas W. Vahlenkamp, Martin H. Groschup, Ute Ziegler
Software Mentions: 4
Published: over 5 years ago

10.3390/nu12113450

Metabolomic and Metataxonomic Fingerprinting of Human Milk Suggests Compositional Stability over a Natural Term of Breastfeeding to 24 Months
Cited by: 7
Author(s): Natalie Shenker, Alvaro Perdones‐Montero, Adam Burke, Sarah Stickland, Julie A. K. McDonald, Kate Alexander-Hardiman, James M. Flanagan, Zoltan Takáts, Simon Cameron
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-69830-1

Clinical outcomes and prognostic factors of robotic assisted rectal cancer resection alone versus robotic rectal cancer resection with natural orifice extraction: a matched analysis
Cited by: 7
Author(s): Dongning Liu, Rui Luo, Zhikai Wan, Weiquan Zhu, Peng He, Shanping Ye, Cheng Tang, Lei Xiong, Taiyuan Li
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-92912-7

MYD88, NFKB1, and IL6 transcripts overexpression are associated with poor outcomes and short survival in neonatal sepsis
Cited by: 12
Author(s): Nouran B. AbdAllah, Eman A. Toraih, Essam Al Ageeli, Hala F. Elhagrasy, Nawal S. Gouda, Manal S. Fawzy, Ghada M. Helal
Software Mentions: 4
Published: over 3 years ago