pypi: ggplot | 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

10.7717/peerj.4278

Forecasting biodiversity in breeding birds using best practices
Cited by: 37
Author(s): David J. Harris, Shawn D. Taylor, Ethan P. White
Software Mentions: 21
Published: almost 7 years ago

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: over 11 years ago

10.1038/s41598-020-73413-5

The macroevolutionary landscape of short-necked plesiosaurians
Cited by: 13
Author(s): Valentin Fischer, Jamie A. MacLaren, Laura C. Soul, Rebecca Bennion, Patrick S. Druckenmiller, Roger Benson
Software Mentions: 19
Published: about 4 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: about 5 years ago

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.1038/s41598-020-75345-6

High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)
Cited by: 9
Author(s): Sara L. Martin, Leshawn Benedict, Wei Wei, Connie A. Sauder, Hugh J. Beckie, Linda M. Hall
Software Mentions: 17
Published: about 4 years ago

10.1038/s41598-021-81688-5

Fungal diversity and community structure from coastal and barrier island beaches in the United States Gulf of Mexico
Cited by: 14
Author(s): Allison K. Walker, Brent M. Robicheau
Software Mentions: 16
Published: almost 4 years ago

10.12688/f1000research.22139.2

scRepertoire: An R-based toolkit for single-cell immune receptor analysis
Cited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
Published: over 4 years ago

10.1093/jas/skaa402

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1
Cited by: 4
Author(s): Gota Morota, Hao Cheng, Dianne Cook, Emi Tanaka
Software Mentions: 15
Published: almost 4 years ago

10.1128/mSphere.01023-20

Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly
Cited by: 15
Author(s): Justinn Renelies‐Hamilton, Kristjan Germer, David Sillam‐Dussès, Kasun H. Bodawatta, Michael Poulsen
Software Mentions: 15
Published: over 3 years ago

10.1038/s41598-020-72571-w

Persistent fire foci in all biomes undermine the Paris Agreement in Brazil
Cited by: 51
Author(s): Carlos Antônio da Silva, Paulo Eduardo Teodoro, Rafael Coll Delgado, Larissa Pereira Ribeiro Teodoro, Mendelson Lima, Ariane de Andréa Pantaleão, Fábio Henrique Rojo Baio, Gileno Brito de Azevedo, Glauce Táıs de Oliveira Sousa Azevedo, Guilherme Fernando Capristo-Silva, Damien Arvor, Cassiele Uliana Facco
Software Mentions: 15
Published: about 4 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12888-020-02645-6

Depression, anxiety, and burnout among medical students and residents of a medical school in Nepal: a cross-sectional study
Cited by: 66
Author(s): Nishan Babu Pokhrel, Ramesh Khadayat, P Tulachan
Software Mentions: 14
Published: over 4 years ago

10.12688/f1000research.24956.2

gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler
Cited by: 274
Author(s): Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi Peterson
Software Mentions: 14
Published: about 4 years ago

10.3389/fimmu.2021.557994

Investigation of Genetic Determinants of Glioma Immune Phenotype by Integrative Immunogenomic Scale Analysis
Cited by: 10
Author(s): Binghao Zhao, Yuekun Wang, Yaning Wang, Congxin Dai
Software Mentions: 14
Published: over 3 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

10.1038/s41598-020-80165-9

Multi-level remodelling of chromatin underlying activation of human T cells
Cited by: 23
Author(s): Naiara G. Bediaga, Hannah D. Coughlan, Timothy M. Johanson, Alexandra L. Garnham, Gaetano Naselli, Jan Schröder, Liam G. Fearnley, Esther Bandala‐Sanchez, Rhys S. Allan, Gordon K. Smyth, Leonard C. Harrison
Software Mentions: 14
Published: almost 4 years ago

10.7554/eLife.62915

ImmunoCluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data
Cited by: 9
Author(s): James W. Opzoomer, Jessica A Timms, Kevin Blighe, Thanos P. Mourikis, Nicolas Chapuis, Richard Bekoe, Sedigeh Kareemaghay, Paola Nocerino, Benedetta Apollonio, Alan G. Ramsay, Mahvash Tavassoli, Claire Harrison, Francesca D. Ciccarelli, Peter J. Parker, Michaéla Fontenay, Paul R. Barber, James N. Arnold, Shahram Kordasti
Software Mentions: 13
Published: over 3 years ago

10.3389/fimmu.2020.620716

Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Cited by: 14
Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer‐Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Software Mentions: 13
Published: almost 4 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 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

10.1155/2021/6653247

A Risk Signature with Nine Stemness Index-Associated Genes for Predicting Survival of Patients with Uterine Corpus Endometrial Carcinoma
Cited by: 9
Author(s): Haoya Xu, Ruoyao Zou, Jiyu Liu, Li Zhu
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-021-02293-3

Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells
Cited by: 47
Author(s): Drew Neavin, Quan Nguyen, Maciej Daniszewski, Helena Liang, Han Sheng Chiu, Yong Kiat Wee, Anne Senabouth, Samuel W. Lukowski, Duncan E. Crombie, Grace E. Lidgerwood, Damián Hernández, James C. Vickers, Anthony Cook, Nathan J. Palpant, Alice Pébay, Alex W. Hewitt, Joseph E. Powell
Software Mentions: 12
Published: over 3 years ago

10.7717/peerj.10469

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: almost 4 years ago

10.1371/journal.pone.0238835

Analyzing the fine structure of distributions
Cited by: 35
Author(s): Michael C. Thrun, Tino Gehlert, Alfred Ultsch
Software Mentions: 12
Published: about 4 years ago

10.1002/ece3.8020

Functional groups in piscivorous fishes
Cited by: 8
Author(s): Michalis Mihalitsis, David R. Bellwood
Software Mentions: 12
Published: about 3 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

10.7717/peerj.11534

AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change
Cited by: 5
Author(s): Roeland Kindt
Software Mentions: 12
Published: over 3 years ago

10.1038/s41421-021-00321-x

Dynamics of TCR repertoire and T cell function in COVID-19 convalescent individuals
Cited by: 23
Author(s): Lingjie Luo, Wenhua Liang, Jianfeng Pang, Gang Xu, Yingying Chen, Xinrong Guo, Xin Wang, Yi Zhao, Yang-dian Lai, Yang Liu, Bin Li, Bing Su, Shuye Zhang, Michal Baniyash, Lei Shen, Lei Chen, Yun Ling, Ying Wang, Qiming Liang, Hongzhou Lu, Zheng Zhang, Feng Wang
Software Mentions: 12
Published: about 3 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

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: almost 6 years ago

10.3389/fgene.2021.706907

ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram
Cited by: 97
Author(s): Chunhui Gao, Guangchuang Yu, Peng Cai
Software Mentions: 12
Published: about 3 years ago

10.1038/s41416-019-0519-1

Stroma-normalised vessel density predicts benefit from adjuvant fluorouracil-based chemotherapy in patients with stage II/III colon cancer
Cited by: 5
Author(s): Artur Mezheyeuski, Ina Hrynchyk, Mercedes Herrera, Mia Karlberg, Erik Osterman, Peter Ragnhammar, David Edler, Anna Portyanko, Fredrik Pontén, Tobias Sjöblom, Bengt Glimelius, Arne Östman
Software Mentions: 12
Published: over 5 years ago

10.1186/s12885-021-08442-y

Genetic expression and mutational profile analysis in different pathologic stages of hepatocellular carcinoma patients
Cited by: 9
Author(s): Xingjie Gao, Chunyan Zhao, Nan Zhang, Xiaoteng Cui, Yuanyuan Ren, Chao Su, Shaoyuan Wu, Zhi Yao, Jie Yang
Software Mentions: 12
Published: over 3 years ago

10.1186/gb-2012-13-8-r77

ggbio: an R package for extending the grammar of graphics for genomic data
Cited by: 265
Author(s): Tao Yin, Dianne Cook, Michael C. Lawrence
Software Mentions: 11
Published: almost 13 years ago

10.3390/microorganisms8101619

Salt Marsh Elevation Drives Root Microbial Composition of the Native Invasive Grass Elytrigia atherica
Cited by: 6
Author(s): Edisa García Hernández, Elena Baraza, Christian Smit, Matty P. Berg, Joana Falcão Salles
Software Mentions: 11
Published: about 4 years ago

10.3389/fonc.2021.672928

Glioma-Associated Stromal Cells Stimulate Glioma Malignancy by Regulating the Tumor Immune Microenvironment
Cited by: 13
Author(s): Xiangming Cai, Feng Yuan, Junhao Zhu, Jin Yang, Chao Tang, Zixiang Cong, Chiyuan Ma
Software Mentions: 11
Published: over 3 years ago

10.1038/s41598-018-28356-3

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver
Cited by: 34
Author(s): Chris Duncan, Sara A. Grimm, Daniel L. Morgan, Pierre R. Bushel, Brian D. Bennett, John D. Roberts, Frederick L. Tyson, B. Alex Merrick, Paul A. Wade
Software Mentions: 11
Published: over 6 years ago

10.3389/fimmu.2018.03017

A Computational Approach Identifies Immunogenic Features of Prognosis in Human Cancers
Cited by: 8
Author(s): Malini Manoharan, Nitin Mandloi, Sushri Priyadarshini, Ashwini Patil, Rohit Gupta, Laxman Iyer, Ravi Gupta, Amitabha Chaudhuri
Software Mentions: 11
Published: almost 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: almost 5 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: over 3 years ago

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
Published: over 4 years ago

10.4178/epih.e2019006

Dose-response meta-analysis: application and practice using the R software
Cited by: 28
Author(s): Sung Ryul Shim, Jong Hoo Lee
Software Mentions: 11
Published: over 5 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 3 years ago

10.1002/hbm.25161

Longitudinal functional brain network reconfiguration in healthy aging
Cited by: 27
Author(s): Brigitta Malagurski, Franziskus Liem, Jessica Oschwald, Susan Mérillat, Lutz Jäncke
Software Mentions: 10
Published: about 4 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

10.1371/journal.pone.0209331

Rethomics: An R framework to analyse high-throughput behavioural data
Cited by: 66
Author(s): Quentin Geissmann, Luis García Rodríguez, Esteban J. Beckwith, Giorgio F. Gilestro
Software Mentions: 10
Published: almost 6 years ago

10.1186/s13059-020-02245-3

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts
Cited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 10
Published: almost 4 years ago

10.1186/s40168-019-0647-0

Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils
Cited by: 218
Author(s): Zhi Bo Zhao, Ji Zheng He, Stefan Geisen, Han Long, Jun Tao Wang, Ju-Pei Shen, Wen Jun Wei, Yun Fang, Pei Pei Li, Limei Zhang
Software Mentions: 10
Published: over 5 years ago

10.1186/s13059-014-0413-3

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators
Cited by: 19
Author(s): Laurence D. Hurst, Oxana Sachenkova, Carsten O. Daub, Alistair R.R. Forrest, Łukasz Huminiecki
Software Mentions: 10
Published: over 10 years ago

10.1111/eva.13209

Mixed‐stock analysis using Rapture genotyping to evaluate stock‐specific exploitation of a walleye population despite weak genetic structure
Cited by: 17
Author(s): Peter T. Euclide, Tom MacDougall, Jason M. Robinson, Matthew D. Faust, Chris C. Wilson, Kuan‐Yu Chen, Elizabeth A. Marschall, Wesley A. Larson, Stuart A. Ludsin
Software Mentions: 10
Published: over 3 years ago

10.1002/ece3.5064

North‐facing slopes and elevation shape asymmetric genetic structure in the range‐restricted salamander Plethodon shenandoah
Cited by: 10
Author(s): Kevin P. Mulder, Nandadevi Cortés-Rodríguez, Evan H. Campbell Grant, Adrianne B. Brand, Robert C. Fleischer
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0222603

Clinical correlates of workplace injury occurrence and recurrence in adults
Cited by: 1
Author(s): Zhaoyi Chen, Mattia Prosperi, Jiang Bian, Jae Min, Mo Wang, Chang Li
Software Mentions: 10
Published: about 5 years ago

10.1186/s12915-021-01029-w

Global population genetic structure and demographic trajectories of the black soldier fly, Hermetia illucens
Cited by: 36
Author(s): Cengiz Kaya, Tomas N Generalovic, Gunilla Ståhls, Martin Hauser, Ana Clariza Samayoa, Carlos Gustavo Nunes-Silva, Heather Roxburgh, Jens Wohlfahrt, Ebenezer Ato Ewusie, Marc Kenis, Yupa Hanboonsong, Jesús Orozco, Nancy Carrejo, Satoshi Nakamura, Laura Gasco, Santos Rojo, Chrysantus M. Tanga, Rudolf Meier, Clint Rhode, Christine Picard, Chris D. Jiggins, Florian Leiber, Jeffery K. Tomberlin, Martin Hasselmann, Wolf U. Blanckenhorn, Martin Kapun, Christoph Sandrock
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pcbi.1007803

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: over 4 years ago

10.1002/ece3.4550

Size does matter: Parallel evolution of adaptive thermal tolerance and body size facilitates adaptation to climate change in domestic cattle
Cited by: 20
Author(s): Muhammed Elayadeth-Meethal, Aravindakshan Thazhathu Veettil, Shane K. Maloney, N. J. Hawkins, Tom Misselbrook, Veerasamy Sejian, M. Jordana Rivero, Michael R. F. Lee
Software Mentions: 10
Published: about 6 years ago

10.3390/microorganisms8121887

A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
Cited by: 13
Author(s): Laurin Christopher Gierse, Alexander Meene, Daniel Schultz, Theresa Schwaiger, Claudia Karte, Charlotte Schröder, Haitao Wang, Christine Wünsche, Karen Methling, Bernd Kreikemeyer, Stephan Fuchs, Jörg Bernhardt, Dörte Becher, Michael Lalk, Tim Urich, Katharina Riedel
Software Mentions: 10
Published: almost 4 years ago

10.1186/s12859-021-04254-w

ORFik: a comprehensive R toolkit for the analysis of translation
Cited by: 13
Author(s): Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski, Eivind Valen
Software Mentions: 10
Published: over 3 years ago

10.1186/s12920-020-00754-5

Identification of potential crucial genes in atrial fibrillation: a bioinformatic analysis
Cited by: 15
Author(s): Junguo Zhang, Xin Huang, Xiaojie Wang, Yanhui Gao, Li Liu, Ziyi Li, Xuejiao Chen, Jie Zeng, Zebing Ye, Guowei Li
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.ppat.1007945

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype
Cited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: over 5 years ago

10.1038/s41437-018-0059-0

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Cited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: almost 7 years ago

10.12688/f1000research.7035.1

RNA-Seq workflow: gene-level exploratory analysis and differential expression
Cited by: 253
Author(s): Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber
Software Mentions: 9
Published: about 9 years ago

10.7717/peerj.3580

The influence of mortality and socioeconomic status on risk and delayed rewards: a replication with British participants
Cited by: 14
Author(s): Gillian Pepper, Deirdre Corby, Rachel Bamber, Holly Smith, Nicky Wong, Daniel Nettle
Software Mentions: 9
Published: over 7 years ago

10.3390/microorganisms9091814

Presence of Human Pathogens of the Borrelia burgdorferi sensu lato Complex Shifts the Sequence Read Abundances of Tick Microbiomes in Two German Locations
Cited by: 7
Author(s): Angeline Hoffmann, Thomas Müller, Volker Fingerle, Matthias Noll
Software Mentions: 9
Published: about 3 years ago

10.1111/eva.13296

Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA
Cited by: 8
Author(s): Eleanor A. Fairfield, David S. Richardson, Carly L. Daniels, Christopher L. Butler, Ewen Bell, Martin I. Taylor
Software Mentions: 9
Published: about 3 years ago

10.20900/immunometab20210022

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: over 3 years ago

10.1128/mSystems.00815-20

Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions
Cited by: 11
Author(s): Ashok Sharma, Klára J. Petrželková, Barbora Pafčo, Carolyn A. Jost Robinson, Terence Fuh, Brenda A. Wilson, Rebecca M. Stumpf, Manolito Torralba, Ran Blekhman, Bryan A. White, Karen E. Nelson, Steven R. Leigh, Andrés Gómez
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-020-74952-7

Characterising the effect of crop species and fertilisation treatment on root fungal communities
Cited by: 6
Author(s): Liina Soonvald, Kaire Loit, Eve Runno-Paurson, Alar Astover, Leho Tedersoo
Software Mentions: 9
Published: about 4 years ago

10.3389/fonc.2021.582040

The Effects of Autophagy-Related Genes and lncRNAs in Therapy and Prognosis of Colorectal Cancer
Cited by: 5
Author(s): Yang Yang, Mingyang Feng, Liangliang Bai, Mengxi Zhang, Kaiyu Zhou, Wei‐Ting Liao, Wenhua Lei, Nan Zhang, Jiaxing Huang, Li Qiu
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0129213

Association between Influenza A Virus Infection and Pigs Subpopulations in Endemically Infected Breeding Herds
Cited by: 35
Author(s): Andrés Díaz, Andrés Pérez, Srinand Sreevatsan, Peter Davies, Marie Culhane, Montserrat Torremorell
Software Mentions: 9
Published: over 9 years ago

10.3389/fgene.2020.564301

Identification of Specific Circular RNA Expression Patterns and MicroRNA Interaction Networks in Mesial Temporal Lobe Epilepsy
Cited by: 10
Author(s): Lachlan G. Gray, James D. Mills, Ashton Curry‐Hyde, Sasha Devore, Daniel Friedman, Maria Thom, Catherine Scott, Roland D. Thijs, Eleonora Aronica, Orrin Devinsky, Michael Janitz
Software Mentions: 9
Published: about 4 years ago

10.18632/aging.203290

Expression mode and prognostic value of FXYD family members in colon cancer
Cited by: 8
Author(s): Ming Jin, Hui Zhang, Jun Yang, Zheng Zhao, Kaitai Liu
Software Mentions: 9
Published: over 3 years ago

10.3389/fncel.2021.648570

Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers
Cited by: 5
Author(s): Rachel A. Keuls, Ronald J. Parchem
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.2-192.v2

Cyrface: An interface from Cytoscape to R that provides a user interface to R packages
Cited by: 3
Author(s): Emanuel Gonçalvès, Franz Mirlach, Julio Sáez-Rodríguez
Software Mentions: 8
Published: over 10 years ago

10.7717/peerj.10971

Trophic niche differentiation and utilisation of food resources in Collembola is altered by rainforest conversion to plantation systems
Cited by: 14
Author(s): Winda Ika Susanti, Rahayu Widyastuti, Stefan Scheu, Anton M. Potapov
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-020-02155-4

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Cited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: about 4 years ago

10.3389/fpls.2021.616975

Heterotic Patterns of Temperate and Tropical Maize by Ear Photometry
Cited by: 1
Author(s): Seth Tolley, Amritpal Singh, Mitchell R. Tuinstra
Software Mentions: 8
Published: over 3 years ago

10.3390/v12111240

TBEV Subtyping in Terms of Genetic Distance
Cited by: 19
Author(s): Andrei A. Deviatkin, Galina G. Karganova, Yulia A. Vakulenko
Software Mentions: 8
Published: about 4 years ago

10.1038/s41598-020-80881-2

Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq
Cited by: 24
Author(s): Bin Wang, Yingyi Zhang, Tao Qing, Kaichen Xing, Jie Li, Timing Zhen, Sibo Zhu, Xi Zhan
Software Mentions: 8
Published: almost 4 years ago

10.1002/1878-0261.12381

A pan‐cancer atlas of cancer hallmark‐associated candidate driver lnc <scp>RNA</scp> s
Cited by: 19
Author(s): Yulan Deng, Shangyi Luo, Xinxin Zhang, Chaoxia Zou, Huating Yuan, Gaoming Liao, Liwen Xu, Chunyu Deng, Yujia Lan, Tingting Zhao, Xu Gao, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 6 years ago

10.3390/toxins13080583

Metaproteomics Reveals Alteration of the Gut Microbiome in Weaned Piglets Due to the Ingestion of the Mycotoxins Deoxynivalenol and Zearalenone
Cited by: 6
Author(s): Johan S. Sáenz, Alina Kurz, Ursula Ruczizka, Moritz Bünger, Maximiliane Dippel, Veronika Nagl, Bertrand Grenier, Andrea Ladinig, Jana Seifert, Evelyne Selberherr
Software Mentions: 8
Published: over 3 years ago

10.1093/bioinformatics/btx738

PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
Cited by: 17
Author(s): Sergio Castillo-Lara, Josep F. Abril
Software Mentions: 8
Published: almost 7 years ago

10.3389/fonc.2021.625007

Comprehensive Analysis of the Functions and Prognostic Value of RNA-Binding Proteins in Thyroid Cancer
Cited by: 7
Author(s): Yue Ma, Shi Yin, Xiaofeng Liu, Jing Hu, Ning Cai, Xiao-bei Zhang, Fu Li, Xuchen Cao, Yue Yu
Software Mentions: 8
Published: over 3 years ago

10.3390/cancers13061212

Comparison of Structural and Short Variants Detected by Linked-Read and Whole-Exome Sequencing in Multiple Myeloma
Cited by: 3
Author(s): Ashwini Kumar, Sadiksha Adhikari, Matti Kankainen, Caroline A. Heckman
Software Mentions: 8
Published: over 3 years ago

10.3389/fneur.2021.615790

Retinal Thickness Analysis in Progressive Multiple Sclerosis Patients Treated With Epigallocatechin Gallate: Optical Coherence Tomography Results From the SUPREMES Study
Cited by: 7
Author(s): Katharina Klumbies, Rebekka Rust, Jan Dörr, Frank Konietschke, Friedemann Paul, Judith Bellmann‐Strobl, Alexander U. Brandt, Hanna Zimmermann
Software Mentions: 8
Published: over 3 years ago

10.3389/fmicb.2020.01987

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome
Cited by: 15
Author(s): Ryan McClure, Dan Naylor, Yuliya Farris, Michelle Davison, Sarah Fansler, Kirsten Hofmockel, Janet K. Jansson
Software Mentions: 8
Published: about 4 years ago

10.3389/fmolb.2021.657087

N6-Methyladenosine RNA Methylation Regulator-Related Alternative Splicing (AS) Gene Signature Predicts Non–Small Cell Lung Cancer Prognosis
Cited by: 16
Author(s): Zhenyu Zhao, Qidong Cai, Peng-Fei Zhang, Boxue He, Ping Xiong, Guangxu Tu, Weilin Peng, Li Wang, Fenglei Yu, Xiang Wang
Software Mentions: 8
Published: over 3 years ago

10.1128/mSphere.00488-17

Novel ITS1 Fungal Primers for Characterization of the Mycobiome
Cited by: 68
Author(s): Mykhaylo Usyk, Christine P. Zolnik, Hitesh D. Patel, Michael H. Levi, Robert D. Burk
Software Mentions: 8
Published: almost 7 years ago

10.1098/rspb.2020.1158

Parasite infection disrupts escape behaviours in fish shoals
Cited by: 3
Author(s): Nicolle Demandt, Marit Praetz, Ralf H. J. M. Kurvers, Jens Krause, Joachim Kurtz, Jörn P. Scharsack
Software Mentions: 8
Published: about 4 years ago

10.1186/s12859-021-04166-9

PTMViz: a tool for analyzing and visualizing histone post translational modification data
Cited by: 4
Author(s): Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson, Stephanie D. Byrum
Software Mentions: 8
Published: over 3 years ago

10.1002/pmic.201400377

Open source libraries and frameworks for biological data visualisation: A guide for developers
Cited by: 37
Author(s): Rui Wang, Yasset Perez‐Riverol, Henning Hermjakob, Juan Antonio Vizcaíno
Software Mentions: 8
Published: almost 10 years ago

10.1155/2021/8892849

Correlation Analysis between GDM and Gut Microbial Composition in Late Pregnancy
Cited by: 17
Author(s): Genxia Li, Pan Yin, Shuhui Chu, Wen Gao, Shihong Cui, Shuhua Guo, Yajuan Xu, Enwu Yuan, Texuan Zhu, Jie You, Junya Zhang, Manman Yang
Software Mentions: 8
Published: almost 4 years ago

10.3389/fgene.2020.568223

Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria
Cited by: 32
Author(s): Jaime Alcorta, Tomás Alarcón-Schumacher, Óscar Rivero Salgado, Beatriz Dı́ez
Software Mentions: 8
Published: about 4 years ago

10.1038/s41598-018-26332-5

Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority
Cited by: 47
Author(s): John K. Pearman, Matthieu Leray, Rodrigo Villalobos, Ryuji J. Machida, Michael L. Berumen, Nancy Knowlton, Susana Carvalho
Software Mentions: 8
Published: over 6 years ago

10.7717/peerj.3944

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
Cited by: 24
Author(s): Ara S. Winter, Jennifer J.M. Hathaway, Jason C. Kimble, Debbie C. Buecher, Ernest W. Valdez, Andrea Porras-Alfaro, Jesse M. Young, Kaitlyn J. H. Read, Diana E. Northup
Software Mentions: 7
Published: about 7 years ago

10.7717/peerj.5727

An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotyping
Cited by: 30
Author(s): Jeffrey C. Berry, Noah Fahlgren, Alexandria A Pokorny, Rebecca Bart, Kira M. Veley
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0257386

(DIGSS) Determination of Intervals using Georeferenced Survey Simulation: An R package for subsurface survey
Cited by: 0
Author(s): William J. Pestle, Cara Hubbell, Mark Hübbe
Software Mentions: 7
Published: about 3 years ago

10.12688/f1000research.16032.3

epiflows: an R package for risk assessment of travel-related spread of disease
Cited by: 3
Author(s): Paula Moraga, Ilaria Dorigatti, Zhian N. Kamvar, Paweł Piątkowski, Salla Toikkanen, VP Nagraj, Christl A. Donnelly, Thibaut Jombart
Software Mentions: 7
Published: about 5 years ago

10.1007/s00253-021-11475-9

Do initial concentration and activated sludge seasonality affect pharmaceutical biotransformation rate constants?
Cited by: 10
Author(s): Tamara J. H. M. van Bergen, Ana B. Rios‐Miguel, Tom M. Nolte, A.M.J. Ragas, Rosalie van Zelm, Martien H.F. Graumans, Paul T.J. Scheepers, Mike S. M. Jetten, A. Jan Hendriks, Cornelia U. Welte
Software Mentions: 7
Published: over 3 years ago

Projects: pypi: ggplot

Papers Mentioning ggplot 796