10.1186/s13104-017-2607-8

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks
Cited by: 28
Author(s): Θεοδόσιος Θεοδοσίου, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C. Kyrpides, Pantelis G. Bagos, Ioannis Iliopoulos, Georgios A. Pavlopoulos
Software Mentions: 11
Published: about 9 years ago

10.1038/s41598-018-31154-6

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis
Cited by: 156
Author(s): Hendrik Nolte, Thomas MacVicar, Frederik Tellkamp, Marcus Krüger
Software Mentions: 11
Published: about 8 years ago

10.3389/fgene.2019.01380

Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma Multiforme
Cited by: 6
Author(s): Runzhi Huang, Zhenyu Li, Chen Li, Guanghua Wang, Penghui Yan, Li P, Jiaqi Wang, Xiaolong Zhu, Peng Hu, Junfang Zhang, Zhengyan Chang, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pcbi.1002276

BeadArray Expression Analysis Using Bioconductor
Cited by: 50
Author(s): Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch
Software Mentions: 11
Published: almost 15 years ago

10.18632/aging.202957

Integrative analysis identifies key mRNA biomarkers for diagnosis, prognosis, and therapeutic targets of HCV-associated hepatocellular carcinoma
Cited by: 8
Author(s): Yongqiang Zhang, Yuqin Tang, Chengbin Guo, Gen Li
Software Mentions: 11
Published: over 5 years ago

10.1186/s12885-019-5965-x

Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response
Cited by: 32
Author(s): Marta Lucchetta, Isabelle da Piedade, Mohamed Mounir, Marina Vabistsevits, Thilde Terkelsen, Elena Papaleo
Software Mentions: 11
Published: about 7 years ago

10.1186/s12894-019-0479-z

Where is the limit of prostate cancer biomarker research? Systematic investigation of potential prognostic and diagnostic biomarkers
Cited by: 2
Author(s): Anika Kremer, Tobias Kremer, Glen Kristiansen, Yuri Tolkach
Software Mentions: 11
Published: over 7 years ago

10.3389/fonc.2020.570654

Prognostic Role of Tumor Mutation Burden Combined With Immune Infiltrates in Skin Cutaneous Melanoma Based on Multi-Omics Analysis
Cited by: 16
Author(s): Junya Yan, Xiaowen Wu, Jiayi Yu, Yanyan Zhu, Shundong Cang
Software Mentions: 11
Published: almost 6 years ago

10.1186/s40168-019-0658-x

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Cited by: 124
Author(s): Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Jesse Connell, Jung‐Jin Lee, Bryton Fett, Frederic D. Bushman, Kyle Bittinger
Software Mentions: 11
Published: over 7 years ago

10.3389/fmicb.2018.02301

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach
Cited by: 38
Author(s): Wen Chen, Graham Wilkes, Izhar U. H. Khan, Katarina Pintar, Joseph P. Thomas, C. André Lévesque, Julie T. Chapados, Edward Topp, David R. Lapen
Software Mentions: 11
Published: almost 8 years ago

10.1038/s41598-019-48495-5

Latent-period stool proteomic assay of multiple sclerosis model indicates protective capacity of host-expressed protease inhibitors
Cited by: 9
Author(s): Carlos Gutiérrez González, Stephanie Tankou, Laura M. Cox, Ellen P. Casavant, Howard L. Weiner, Joshua E. Elias
Software Mentions: 11
Published: about 7 years ago

10.3390/jcm9082591

Risk of Adverse Drug Events Following the Virtual Addition of COVID-19 Repurposed Drugs to Drug Regimens of Frail Older Adults with Polypharmacy
Cited by: 14
Author(s): Sweilem B. Al Rihani, Matt K. Smith, Ravil Bikmetov, Malavika Deodhar, Pamela Dow, Jacques Turgeon, Véronique Michaud
Software Mentions: 11
Published: about 6 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: over 6 years ago

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: over 6 years ago

10.1242/bio.018713

3D for the people: multi-camera motion capture in the field with consumer-grade cameras and open source software
Cited by: 65
Author(s): Brandon E. Jackson, Dennis Evangelista, Dylan D. Ray, Tyson L. Hedrick
Software Mentions: 11
Published: about 10 years ago

10.3389/fmicb.2017.00682

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Cited by: 314
Author(s): David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, Philip Hugenholtz
Software Mentions: 11
Published: over 9 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: about 5 years ago

10.3389/fpubh.2021.649190

Shifting From Sectoral to Integrated Surveillance by Changing Collaborative Practices: Application to West Nile Virus Surveillance in a Small Island State of the Caribbean
Cited by: 2
Author(s): Mariana Geffroy, Nonito Pagès, David Chavernac, Alexis Dereeper, L. Aubert, Cécile Herrmann-Storck, Anubis Vega-Rúa, Sylvie Lecollinet, Jennifer Pradel
Software Mentions: 11
Published: over 5 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: over 6 years ago

10.1186/s41235-018-0133-4

App icon similarity and its impact on visual search efficiency on mobile touch devices
Cited by: 5
Author(s): Anna Trapp, Carolin Wienrich
Software Mentions: 11
Published: almost 8 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: over 5 years ago

10.1038/s41392-021-00753-7

Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patients
Cited by: 18
Author(s): Xiang-Na Zhao, Yue You, Xiaoming Cui, Han Gao, Guolin Wang, Shengbo Zhang, Lilin Ye, Lei Duan, Ka-Li Zhu, Yuling Wang, Li Li, Jianhua Lu, Haibin Wang, Jingfang Fan, Huanwei Zheng, Erfu Dai, Luyi Tian, Mai‐Juan Ma
Software Mentions: 11
Published: about 5 years ago

10.1016/j.cels.2018.09.003

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Cited by: 56
Author(s): Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber
Software Mentions: 11
Published: almost 8 years ago

10.1186/s40064-015-0795-z

Rapid publication-ready MS-Word tables for two-way ANOVA
Cited by: 56
Author(s): Houssein Assaad, Yongqing Hou, Lan Zhou, Raymond J. Carroll, Guoyao Wu
Software Mentions: 11
Published: over 11 years ago

10.3389/fphys.2020.00845

Dynamic Courtship Signals and Mate Preferences in Sepia plangon
Cited by: 5
Author(s): Alejandra López Galán, Wen-Sung Chung, N. Justin Marshall
Software Mentions: 11
Published: about 6 years ago

10.7554/eLife.11613

Epigenomic landscapes of retinal rods and cones
Cited by: 107
Author(s): Alisa Mo, Chongyuan Luo, Fred P. Davis, Eran A. Mukamel, Gilbert L. Henry, Joseph R. Nery, Mark A. Urich, Serge Picard, Ryan Lister, Sean R. Eddy, M Beer, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 11
Published: over 10 years ago

10.1371/journal.pone.0016432

An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-Seq
Cited by: 41
Author(s): Eloi Mercier, Arnaud Droit, Leping Li, Gordon Robertson, Xuekui Zhang, Raphaël Gottardo
Software Mentions: 11
Published: over 15 years ago

10.3389/fpsyg.2018.02251

Disabled or Cyborg? How Bionics Affect Stereotypes Toward People With Physical Disabilities
Cited by: 28
Author(s): Bertolt Meyer, Frank Asbrock
Software Mentions: 11
Published: almost 8 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: about 5 years ago

10.1038/s41598-017-02464-y

UROPA: a tool for Universal RObust Peak Annotation
Cited by: 38
Author(s): Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Software Mentions: 11
Published: over 9 years ago

10.3897/BDJ.6.e20760

spind: an R Package to Account for Spatial Autocorrelation in the Analysis of Lattice Data
Cited by: 7
Author(s): Gudrun Carl, Sam Levin, Ingolf Kühn
Software Mentions: 11
Published: over 8 years ago

10.1111/jcmm.15615

Gene regulation network analysis reveals core genes associated with survival in glioblastoma multiforme
Cited by: 15
Author(s): Lan Jiang, Min Zhong, Tianbing Chen, Xiaolong Zhu, Hui Yang, Kun Lv
Software Mentions: 11
Published: about 6 years ago

10.1136/bmjopen-2018-027834

Spatial epidemiology of gestational age and birth weight in Switzerland: census-based linkage study
Cited by: 8
Author(s): Veronika Skrivankova, Marcel Zwahlen, Mark Adams, Nicola Low, Claudia E. Kuehni, Matthias Egger
Software Mentions: 11
Published: almost 7 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: almost 20 years ago

10.3389/fmicb.2019.01770

Gut Microbiota as an Objective Measurement for Auxiliary Diagnosis of Insomnia Disorder
Cited by: 55
Author(s): Bingdong Liu, Win Lin, Shujie Chen, Ting Xiang, Yifan Yang, Yulong Yin, Guohuan Xu, Zhihong Liu, Li Liu, Jiyang Pan, Liwei Xie
Software Mentions: 11
Published: about 7 years ago

10.1038/s41598-020-58111-6

Projected distribution and climate refugia of endangered Kashmir musk deer Moschus cupreus in greater Himalaya, South Asia
Cited by: 19
Author(s): Paras B. Singh, Kumar P. Mainali, Zhigang Jiang, Arjun Thapa, Naresh Subedi, Muhammad Naeem Awan, Orus Ilyas, Himal Luitel, Zhixin Zhou, Huijian Hu
Software Mentions: 11
Published: over 6 years ago

10.15252/msb.20177697

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations
Cited by: 153
Author(s): Julia Jabs, Franziska Maria Zickgraf, Jeongbin Park, Sven Wagner, Xiaoqi Jiang, Katharina Jechow, Kortine Kleinheinz, Umut Toprak, Marc A. Schneider, Michael Meister, Saskia Spaich, Marc Sütterlin, Matthias Schlesner, Andreas Trumpp, Martin R. Sprick, Roland Eils, Christian Conrad
Software Mentions: 11
Published: almost 9 years ago

10.1038/s41598-021-93411-5

Epidemiological overview of multidimensional chromosomal and genome toxicity of cannabis exposure in congenital anomalies and cancer development
Cited by: 33
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 11
Published: about 5 years ago

10.1186/s12935-021-01795-1

Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinoma
Cited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: over 5 years ago

10.1186/s12859-018-2105-6

Building protein-protein interaction networks for Leishmania species through protein structural information
Cited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 8 years ago

10.1093/rheumatology/keaa615

Changes in the illness perceptions of patients with rheumatoid arthritis over the first year of methotrexate therapy
Cited by: 7
Author(s): James M Gwinnutt, Sam Norton, Kimme L Hyrich, Mark Lunt, Anne Barton, Lis Cordingley, Suzanne Verstappen, Rams co-investigators
Software Mentions: 11
Published: almost 6 years ago

10.3390/cancers12030692

Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles
Cited by: 29
Author(s): Geoffroy Walbrecq, Odile Lecha, Anthoula Gaigneaux, Miriam Rebecca Fougeras, Demetra Philippidou, Christiane Margue, Miléne Tetsi Nomigni, François Bernardin, Gunnar Dittmar, Iris Behrmann, Stephanie Kreis
Software Mentions: 11
Published: over 6 years ago

10.1093/bioinformatics/btz889

<i>CellBench</i>: <i>R/Bioconductor</i> software for comparing single-cell RNA-seq analysis methods
Cited by: 17
Author(s): Shian Su, Luyi Tian, Xueyi Dong, Peter Hickey, Saskia Freytag, Matthew E. Ritchie
Software Mentions: 11
Published: almost 7 years ago

10.1002/ece3.6044

Variation of chemical compounds in wild Heliconiini reveals ecological factors involved in the evolution of chemical defenses in mimetic butterflies
Cited by: 21
Author(s): Ombeline Sculfort, Érika Cristina Pinheiro de Castro, Krzysztof M. Kozak, Søren Bak, Marianne Élias, Bastien Nay, Violaine Llaurens
Software Mentions: 11
Published: over 6 years ago

10.3390/pharmaceutics13060868

Surfactant-Assisted Distal Pulmonary Distribution of Budesonide Revealed by Mass Spectrometry Imaging
Cited by: 0
Author(s): Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Barbara Pioselli, Valentina Mileo, Xabier Murgia, Fabrizio Salomone, Giuseppe Pieraccini, Haruo Usada, Augusto F. Schmidt, Noah H. Hillman, Matthew W. Kemp, Alan H. Jobe
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0256694

Factors contributing to farm-level productivity and household income generation in coastal Bangladesh’s rice-based farming systems
Cited by: 18
Author(s): Shah Al Emran, Timothy J. Krupnik, Sreejith Aravindakshan, Virender Kumar, Cameron M. Pittelkow
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0188079

Episodic future thinking reduces temporal discounting in healthy adolescents
Cited by: 35
Author(s): Uli Bromberg, Maria Lobatcheva, Jan Peters
Software Mentions: 11
Published: almost 9 years ago

10.3390/ijerph18041816

Academic Achievement in Spanish Secondary School Students: The Inter-Related Role of Executive Functions, Physical Activity and Gender
Cited by: 7
Author(s): Elena Escolano Pérez, Marta Bestué
Software Mentions: 11
Published: over 5 years ago

10.3390/diagnostics10030171

GRB10 and E2F3 as Diagnostic Markers of Osteoarthritis and Their Correlation with Immune Infiltration
Cited by: 56
Author(s): Yajun Deng, Enhui Ren, Wenhua Yuan, Guang-Zhi Zhang, Zhi-Xi Wu, Qiqi Xie
Software Mentions: 11
Published: over 6 years ago

10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: over 5 years ago

10.1186/1756-0500-3-10

A collection of bioconductor methods to visualize gene-list annotations
Cited by: 46
Author(s): Gang Feng, Pan Du, Nancy L. Krett, Michael A. Tessel, Steven T. Rosen, Warren A. Kibbe, Simon Lin
Software Mentions: 11
Published: over 16 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 14 years ago

10.3389/fmolb.2021.611508

CXCL10 is a Tumor Microenvironment and Immune Infiltration Related Prognostic Biomarker in Pancreatic Adenocarcinoma
Cited by: 17
Author(s): Huimin Huang, Wangxiao Zhou, Renpin Chen, Bingfeng Xiang, Shipeng Zhou, Linhua Lan
Software Mentions: 11
Published: over 5 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: over 5 years ago

10.1111/jcmm.16773

Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA‐Seq
Cited by: 3
Author(s): Qi Zhang, Manchao Kuang, Haiyin An, Yajing Zhang, Kai Zhang, Feng Li, Lei Zhang, Shujun Cheng
Software Mentions: 11
Published: about 5 years ago

10.1016/j.cell.2016.08.041

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds
Cited by: 359
Author(s): Alejandra Bruna, Oscar M. Rueda, Wendy Greenwood, Ankita Batra, Maurizio Callari, R N Batra, Katherine Pogrebniak, José Luís Sandoval, John W. Cassidy, Ana Tufegdžić Vidaković, Stephen‐John Sammut, Linda Jones, Elena Provenzano, Richard D. Baird, Peter Eirew, James Hadfield, Matthew Eldridge, Anne McLaren-Douglas, Andrew Barthorpe, Howard Lightfoot, Mark J. O’Connor, Joe W. Gray, Javier Cortés, José Baselga, Elisabetta Marangoni, Alana L. Welm, Samuel Aparicio, Violeta Serra, Mathew J. Garnett, Carlos Caldas
Software Mentions: 11
Published: about 10 years ago

10.1038/s41598-019-41601-7

Characteristics and homogeneity of N6-methylation in human genomes
Cited by: 13
Author(s): Clare Pacini, Charles R. Bradshaw, Nigel Garrett, Magdalena J. Koziol
Software Mentions: 11
Published: over 7 years ago

10.1111/tpj.14784

Segmental duplications are hot spots of copy number variants affecting barley gene content
Cited by: 4
Author(s): Gianluca Bretani, Laura Rossini, Chiara Ferrandi, Joanne Russell, Robbie Waugh, Benjamin Kilian, Paolo Bagnaresi, Luigi Cattivelli, Agostino Fricano
Software Mentions: 11
Published: over 6 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 5 years ago

10.1093/molbev/msab091

Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids
Cited by: 20
Author(s): Julia Maria Kloos, João Alves Gama, Joachim Hegstad, Ørjan Samuelsen, Pål Jarle Johnsen
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pcbi.1006207

Network supporting contextual fear learning after dorsal hippocampal damage has increased dependence on retrosplenial cortex
Cited by: 18
Author(s): Cesar A.O. Coelho, Tatiana Lima Ferreira, Juliana Carlota Kramer Soares, João Ricardo Sato, Maria Gabriela Menezes Oliveira
Software Mentions: 11
Published: about 8 years ago

10.1186/s12885-021-07924-3

A geospatiotemporal and causal inference epidemiological exploration of substance and cannabinoid exposure as drivers of rising US pediatric cancer rates
Cited by: 26
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 11
Published: over 5 years ago

10.1080/21623945.2019.1697563

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: over 7 years ago

10.3389/fmolb.2021.684050

Characterization of Hypoxia-Related Molecular Subtypes in Clear Cell Renal Cell Carcinoma to Aid Immunotherapy and Targeted Therapy via Multi-Omics Analysis
Cited by: 10
Author(s): Weimin Zhong, Hongbin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 11
Published: about 5 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 5 years ago

10.3389/fgene.2021.620705

Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma
Cited by: 6
Author(s): Dongjun Dai, Lanyu Xie, Yongjie Shui, Jinfan Li, Qichun Wei
Software Mentions: 11
Published: over 5 years ago

10.3389/fmicb.2019.02291

Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder
Cited by: 25
Author(s): Terri L. Roth, Alexandra D. Switzer, Miki Watanabe-Chailland, Elisabeth M. Bik, David A. Relman, Lindsey E. Romick-Rosendale, Nicholas J. Ollberding
Software Mentions: 11
Published: almost 7 years ago

10.1186/s40168-020-00805-0

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed
Cited by: 80
Author(s): Hyun Kim, Kiseok Keith Lee, Jongbum Jeon, William Harris, Yong-Hwan Lee
Software Mentions: 11
Published: over 6 years ago

10.1038/s41598-020-68780-y

Protecting endangered species in the USA requires both public and private land conservation
Cited by: 15
Author(s): Niall G. Clancy, John P. Draper, J. Marshall Wolf, Umarfarooq A. Abdulwahab, Maya Pendleton, Soren Brothers, Janice Brahney, Jennifer Weathered, Edd Hammill, Trisha B. Atwood
Software Mentions: 11
Published: about 6 years ago

10.3389/fbioe.2020.00101

The Integrated Transcriptome Bioinformatics Analysis Identifies Key Genes and Cellular Components for Spinal Cord Injury-Related Neuropathic Pain
Cited by: 8
Author(s): Runzhi Huang, Tong Meng, Rui Zhu, Lijuan Zhao, Dianwen Song, Huabin Yin, Zongqiang Huang, Liming Cheng, Jie Zhang
Software Mentions: 11
Published: over 6 years ago

10.3389/fonc.2014.00147

An Integrative Analysis of Meningioma Tumors Reveals the Determinant Genes and Pathways of Malignant Transformation
Cited by: 7
Author(s): José Carlos Iglesias Gómez, Adrián Mosquera Orgueira
Software Mentions: 11
Published: over 12 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: over 5 years ago

10.1016/j.csbj.2021.05.040

Robustness of differential gene expression analysis of RNA-seq
Cited by: 31
Author(s): Alexey Stupnikov, Caitríona E. McInerney, Kienan I. Savage, Stuart McIntosh, Frank Emmert‐Streib, Richard D. Kennedy, Manuel Salto-Tellez, Kevin M. Prise, Darragh G. McArt
Software Mentions: 11
Published: over 5 years ago

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: over 5 years ago

10.7717/peerj.10411

Data quantity is more important than its spatial bias for predictive species distribution modelling
Cited by: 10
Author(s): Willson Gaul, Dinara Sadykova, Hannah J. White, Lupe León‐Sánchez, Paul Caplat, Mark Emmerson, Jon Yearsley
Software Mentions: 11
Published: almost 6 years ago

10.3389/fonc.2021.626654

Identification of a Novel Four-Gene Signature Correlated With the Prognosis of Patients With Hepatocellular Carcinoma: A Comprehensive Analysis
Cited by: 7
Author(s): Weihua Zhu, Lixin Ru, Zhenchao Ma
Software Mentions: 11
Published: over 5 years ago

10.3390/ijms21218148

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: almost 6 years ago

10.1038/s41598-020-65015-y

Toffee – a highly efficient, lossless file format for DIA-MS
Cited by: 9
Author(s): Brett Tully
Software Mentions: 11
Published: over 6 years ago

10.12688/f1000research.18458.2

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Cited by: 15
Author(s): Bernhard C. Thiel, Irene K. Beckmann, Peter Kerpedjiev, Ivo L. Hofacker
Software Mentions: 11
Published: over 7 years ago

10.1186/1756-0500-3-81

Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays
Cited by: 17
Author(s): Colin S. Gillespie, Guiyuan Lei, Richard J. Boys, Amanda Greenall, Darren J. Wilkinson
Software Mentions: 11
Published: over 16 years ago

10.3389/fpls.2020.599228

Hormopriming to Mitigate Abiotic Stress Effects: A Case Study of N9-Substituted Cytokinin Derivatives With a Fluorinated Carbohydrate Moiety
Cited by: 17
Author(s): Magdaléna Bryksová, Andrea Hybenová, Alba E. Hernándiz, Ondřej Novák, Aleš Pěnčík, Lukáš Spíchal, Nuria De Diego, Karel Doležal
Software Mentions: 11
Published: almost 6 years ago

10.1186/s41044-019-0043-6

A substrate for modular, extensible data-visualization
Cited by: 6
Author(s): Jordan Matelsky, Joseph Downs, Hannah Cowley, Brock Wester, William Gray-Roncal
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pbio.3000595

A role for triglyceride lipase brummer in the regulation of sex differences in Drosophila fat storage and breakdown
Cited by: 69
Author(s): Lianna W Wat, Charlotte Chao, Rachael Bartlett, Justin Buchanan, Jason W Millington, Hui Ju Chih, Zahid Sadek Chowdhury, Puja Biswas, Vivian Huang, Leah J Shin, Lin Chuan Wang, Marie-Pierre Gauthier, Maria Cecilia Barone, Kristi L. Montooth, Michael A. Welte, Elizabeth J. Rideout
Software Mentions: 11
Published: over 6 years ago

10.1371/journal.pone.0256339

Sex-specific spatial use of the winter foraging areas by Magellanic penguins and assessment of potential conflicts with fisheries during winter dispersal
Cited by: 6
Author(s): Samanta Dodino, Nicolás A. Lois, Luciana Riccialdelli, Michael J. Polito, Klemens Pütz, Andrea Raya Rey
Software Mentions: 11
Published: about 5 years ago

10.1186/s12942-017-0098-4

GridSample: an R package to generate household survey primary sampling units (PSUs) from gridded population data
Cited by: 38
Author(s): Dana R. Thomson, Forrest R. Stevens, Nick W. Ruktanonchai, Andrew J. Tatem, Márcia C. Castro
Software Mentions: 11
Published: about 9 years ago

10.3897/BDJ.8.e56876

Environmental DNA revealed the fish community of Hokkaido Island, Japan, after invasion by rainbow trout
Cited by: 5
Author(s): Akio Imamura, Kana Hayami, Masato Sakata, Toshifumi Minamoto
Software Mentions: 11
Published: almost 6 years ago

10.3389/fphys.2021.714195

Development and Validation of a Prediction Model for Elevated Arterial Stiffness in Chinese Patients With Diabetes Using Machine Learning
Cited by: 5
Author(s): Qingqing Li, Wenhui Xie, Liping Li, Lijing Wang, Qinyi You, Lu Chen, Jing Li, Yilang Ke, Jun Fang, Libin Liu, Huashan Hong
Software Mentions: 11
Published: about 5 years ago

10.7554/eLife.58705

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants
Cited by: 23
Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Software Mentions: 11
Published: about 6 years ago

10.3390/jcm10184245

Machine-Learning Points at Endoscopic, Quality of Life, and Olfactory Parameters as Outcome Criteria for Endoscopic Paranasal Sinus Surgery in Chronic Rhinosinusitis
Cited by: 4
Author(s): Jörn Lötsch, Constantin A. Hintschich, Petros Petridis, Jürgen Pade, Thomas Hummel
Software Mentions: 11
Published: about 5 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: about 10 years ago

10.3389/fninf.2019.00012

A Serverless Tool for Platform Agnostic Computational Experiment Management
Cited by: 13
Author(s): Gregory Kiar, Shawn T. Brown, Tristan Glatard, Alan C. Evans
Software Mentions: 11
Published: over 7 years ago

10.1155/2021/2291899

Crosstalk between Heart Failure and Cognitive Impairment via hsa-miR-933/RELB/CCL21 Pathway
Cited by: 8
Author(s): Wenxiao Feng, Jie Yang, Wen‐Chao Song, Yi-Tao Xue
Software Mentions: 11
Published: about 5 years ago

10.1016/j.eclinm.2021.101118

Unraveling the concepts of distress, burnout, and depression in type 1 diabetes: A scoping review
Cited by: 9
Author(s): Dona A. Kiriella, Sumaiya Islam, Olutobi Oridota, Nancy Sohler, Coralie Dessenne, Carine de Beaufort, Guy Fagherazzi, Gloria Aguayo
Software Mentions: 11
Published: almost 5 years ago

10.3389/fonc.2020.584404

In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster
Cited by: 6
Author(s): Yuwei Zhang, Guofang Zhao, Fatma Ahmed, Tianfei Yi, Shiyun Hu, Ting Cai, Qi Liao
Software Mentions: 11
Published: almost 6 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: over 10 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 6 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: over 17 years ago

10.7717/peerj.10680

Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinoma
Cited by: 5
Author(s): Shaoyong Zheng, Lan Yao, Fasheng Li, Luyu Huang, Yunfang Yu, Zenan Lin, Hao Li, Xiance Jin, Michael Lanuti, Haiyu Zhou
Software Mentions: 11
Published: over 5 years ago

10.1186/1471-2105-15-S1-S11

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
Cited by: 19
Author(s): Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 11
Published: over 12 years ago

10.1002/ece3.6407

Occupancy‐derived thermal affinities reflect known physiological thermal limits of marine species
Cited by: 8
Author(s): Thomas J. Webb, Aaron Lines, Leigh Michael Howarth
Software Mentions: 11
Published: over 6 years ago