cran: ggplot2 | Projects | Ecosyste.ms: Papers

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 10 years ago

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 + T cell responses
Cited by: 133
Author(s): Benedikt Agerer, Maximilian Koblischke, Venugopal Gudipati, Luis Fernando Montaño-Gutierrez, Mark J. Smyth, Alexandra Popa, Jakob-Wendelin Genger, Lukas Endler, David M. Florian, Vanessa Mühlgrabner, Marianne Graninger, Stephan W. Aberle, Anna-Maria Husa, Lisa E. Shaw, Alexander Lercher, Pia Gattinger, Ricard Torralba-Gombau, Doris Trapin, Thomas Penz, Daniele Barreca, Ingrid Faé, S. Wenda, Marianna Traugott, Gernot Walder, Winfried F. Pickl, Volker Thiel, Franz Allerberger, Hannes Stockinger, Elisabeth Puchhammer‐Stöckl, Wolfgang Weninger, Gottfried Fischer, Wolfgang Hoepler, Erich Pawelka, Alexander Zoufaly, Rudolf Valenta, Christoph Bock, Wolfgang Paster, René Geyeregger, Matthias Farlik, Florian Halbritter, Johannes B. Huppa, Judith H. Aberle, Andréas Bergthaler
Software Mentions: 7
Published: over 5 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: almost 9 years ago

10.1186/s12284-019-0305-y

Deciphering Genetics Underlying Stable Anaerobic Germination in Rice: Phenotyping, QTL Identification, and Interaction Analysis
Cited by: 19
Author(s): S. Ghosal, Carlos Casal, Fergie Ann Quilloy, Endang M. Septiningsih, Merlyn S. Mendioro, Shalabh Dixit
Software Mentions: 7
Published: over 7 years ago

10.1186/s12931-020-01392-2

Characterisation of microbiota in saliva, bronchoalveolar lavage fluid, non-malignant, peritumoural and tumour tissue in non-small cell lung cancer patients: a cross-sectional clinical trial
Cited by: 27
Author(s): Rea Bingula, Edith Filaire, Ioana Molnar, Eve Delmas, Jean‐Yves Berthon, Marie‐Paule Vasson, Annick Bernalier-Donadille, Marc Filaire
Software Mentions: 7
Published: over 6 years ago

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: over 6 years ago

10.1093/bioinformatics/btu616

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
Cited by: 112
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 7
Published: about 12 years ago

10.1371/journal.pgen.1009201

Genomic and transcriptomic landscape of conjunctival melanoma
Cited by: 14
Author(s): Katarina Cisarova, Marc Folcher, Ikram El Zaoui, Rosanna Pescini Gobert, Virginie G. Peter, Béryl Royer‐Bertrand, Léonidas Zografos, Ann Schalenbourg, Michaël Nicolas, Donata Rimoldi, Serge Leyvraz, Nicolò Riggi, Alexandre Moulin, Carlo Rivolta
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pgen.1008265

Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Cited by: 23
Author(s): Aldrin B. Lugena, Ying Zhang, Jérôme S. Menet, Christine Merlin
Software Mentions: 7
Published: over 7 years ago

10.1098/rsos.200431

Make or break it: boundary conditions for integrating multiple elements in episodic memory
Cited by: 6
Author(s): Emma James, Gabrielle Ong, Lisa Henderson, Aidan J. Horner
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pgen.1008375

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
Cited by: 29
Author(s): Sheila Lutz, Christian Brion, Margaret Kliebhan, Frank W. Albert
Software Mentions: 7
Published: almost 7 years ago

10.1098/rsos.170051

Contradicting habitat type-extinction risk relationships between living and fossil amphibians
Cited by: 3
Author(s): Melanie Tietje, Mark‐Oliver Rödel
Software Mentions: 7
Published: over 9 years ago

10.1111/jcmm.15472

Transcriptomic landscape profiling of metformin‐treated healthy mice: Implication for potential hypertension risk when prophylactically used
Cited by: 4
Author(s): Yuhuan Meng, Rui Xiang, Han Yan, Yiran Zhou, Yuntao Hu, Jichun Yang, Yuan Zhou, Qinghua Cui
Software Mentions: 7
Published: over 6 years ago

10.1111/jcmm.15252

CA9 transcriptional expression determines prognosis and tumour grade in tongue squamous cell carcinoma patients
Cited by: 9
Author(s): Chenyu Guan, Dai-qiao Ouyang, Yongjie Qiao, Kan Li, Guanghui Zheng, Xiaomei Lao, Sien Zhang, Guiqing Liao, Yujie Liang
Software Mentions: 7
Published: over 6 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 6 years ago

10.7150/jca.50716

Detection of Pancreatic Ductal Adenocarcinoma by A qPCR-based Normalizer-free Circulating Extracellular Vesicles RNA Signature
Cited by: 6
Author(s): Dashan Qin, Yu Zhao, Qingdong Guo, Shoumin Zhu, Shutian Zhang, Li Min
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pntd.0005729

Dengue prediction by the web: Tweets are a useful tool for estimating and forecasting Dengue at country and city level
Cited by: 70
Author(s): Cecilia Marques-Toledo, Carolin Marlen Degener, Livia Vinhal, Giovanini Evelim Coelho, Wagner Meira, Cláudia Torres Codeço, Mauro Martins Teixeira
Software Mentions: 7
Published: over 9 years ago

10.1074/jbc.RA119.008853

Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity
Cited by: 4
Author(s): Suraj P. Bhat, Rajendra K. Gangalum, Dongjae Kim, Serghei Mangul, Raj K. Kashyap, Xinkai Zhou, David Elashoff
Software Mentions: 7
Published: about 7 years ago

10.1371/journal.pntd.0005050

Factors Associated with the Time of Admission among Notified Dengue Fever Cases in Region VIII Philippines from 2008 to 2014
Cited by: 5
Author(s): J Abello, Julita Gil Cuesta, Boyd Roderick Cerro, Debarati Guha-Sapir
Software Mentions: 7
Published: almost 10 years ago

10.1186/s40104-021-00601-2

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets
Cited by: 13
Author(s): Yan Hui, Paulina Tamez-Hidalgo, Tomasz Cieplak, Gizaw Dabessa Satessa, Witold Kot, Søren Kjærulff, Mette Olaf Nielsen, Dennis Sandris Nielsen, Łukasz Krych
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pntd.0006044

Exploratory metabolomics study of the experimental opisthorchiasis in a laboratory animal model (golden hamster, Mesocricetus auratus)
Cited by: 15
Author(s): Daria Kokova, Sarantos Kostidis, Judit Morello, Nataly Dementeva, Ekaterina A. Perina, V. V. Ivanov, Л. М. Огородова, А. Э. Сазонов, Irina V. Saltykova, Oleg A. Mayboroda
Software Mentions: 7
Published: almost 9 years ago

10.1172/jci.insight.138066

Effector Vγ9Vδ2 T cell response to congenital Toxoplasma gondii infection
Cited by: 3
Author(s): Lifang Ma, Maria V. Papadopoulou, Martin Taton, Francesca Genco, Arnaud Marchant, Valeria Meroni, David Vermijlen
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0222822

Range of motion and between-measurement variation of spinal kinematics in sound horses at trot on the straight line and on the lunge
Cited by: 8
Author(s): A. M. Hardeman, Anna Byström, L. Roepstorff, J. H. Swagemakers, P. R. van Weeren, F. M. Serra Bragança
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0147249

Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies
Cited by: 43
Author(s): Iddo Z. Ben‐Dov, Veronica M. Whalen, Béatrice Goilav, Klaas E.A. Max, Thomas Tuschl
Software Mentions: 7
Published: almost 11 years ago

10.1080/19490976.2021.1921927

Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro
Cited by: 7
Author(s): Dušan Radojević, Sergej Tomić, Dušan Mihajlović, Maja Tolinački, Bojan Pavlović, Dragana Vučević, Svetlana Bojić, Nataša Golić, Miodrag Čolić, Jelena Đokić
Software Mentions: 7
Published: almost 6 years ago

10.1080/19490976.2021.1921924

The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes
Cited by: 15
Author(s): Fergus W. J. Collins, Calum J. Walsh, Beatriz Gómez‐Sala, E. Guijarro-García, David J. Stokes, Klara B. Jakobsdóttir, Kristján Kristjánsson, Finlay Burns, Paul D. Cotter, Mary C. Rea, Colin Hill, R. Paul Ross
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0230945

Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River
Cited by: 3
Author(s): Jason T. Payne, Colin R. Jackson, Justin Millar, Clifford A. Ochs
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0208874

Assessing sound symbolism: Investigating phonetic forms, visual shapes and letter fonts in an implicit bouba-kiki experimental paradigm
Cited by: 5
Author(s): Léa De Carolis, Egidio Marsico, Vincent Arnaud, Christophe Coupé
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pone.0241777

Soil nematode functional diversity, successional patterns, and indicator taxa associated with vertebrate decomposition hotspots
Cited by: 7
Author(s): Lois S. Taylor, Gary L. Phillips, Ernest C. Bernard, Jennifer M. DeBruyn
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13073-019-0695-x

FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures
Cited by: 7
Author(s): Hyunbin Kim, Andy Jinseok Lee, Jongkeun Lee, Hyonho Chun, Young Seok Ju, Dong Ho Hong
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0254293

easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application
Cited by: 4
Author(s): Matteo Di Bernardo, Timothy A. Crombie, Daniel E. Cook, Erik C. Andersen
Software Mentions: 7
Published: about 5 years ago

10.3389/fpsyg.2019.00413

A Shared Food Source Is Not Necessary to Elicit Inequity Aversion in Dogs
Cited by: 5
Author(s): Jim McGetrick, Sabrina Ausserwöger, Ingrid Leidinger, Claudia Attar, Friederike Range
Software Mentions: 7
Published: over 7 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 8 years ago

10.3389/fpsyt.2021.668297

Estimating the Prevalence and Genetic Risk Mechanisms of ARFID in a Large Autism Cohort
Cited by: 26
Author(s): Tanner Koomar, Taylor Thomas, Natalie R. Pottschmidt, Michael Lutter, Jacob J. Michaelson
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0233899

Recapitulation of prostate tissue cell type-specific transcriptomes by an in vivo primary prostate tissue xenograft model
Cited by: 2
Author(s): Nelson T. Gross, Jianmin Wang, Michael V. Fiandalo, Eduardo Cortes Gomez, Anica Watts, Alejandro Godoy, Gary J. Smith, Yue Wu
Software Mentions: 7
Published: over 6 years ago

10.3389/fpls.2020.619404

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I
Cited by: 18
Author(s): Abdellah Barakate, Jamie Orr, Miriam Schreiber, Isabelle Colas, Dominika Lewandowska, Nicola McCallum, Malcolm Macaulay, Jenny Morris, Mikel Arrieta, Pete E. Hedley, Luke Ramsay, Robbie Waugh
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.14334

TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
Cited by: 104
Author(s): Raphaël Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, Benoît Aigouy, Guillaume Salbreux, Suzanne Eaton, Frank Jülicher
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pone.0106150

Towards Monitoring Biodiversity in Amazonian Forests: How Regular Samples Capture Meso-Scale Altitudinal Variation in 25 km2 Plots
Cited by: 9
Author(s): D. Ryan Norris, Marie‐Josée Fortin, William E. Magnusson
Software Mentions: 7
Published: about 12 years ago

10.3389/fpls.2020.589300

Intrafloral Color Modularity in a Bee-Pollinated Orchid
Cited by: 4
Author(s): João Marcelo Robazzi Bignelli Valente Aguiar, Artur A. Maciel, Pamela Cristina Santana, Francismeire Jane Telles, Pedro Joaquim Bergamo, Paulo Eugênio Oliveira, Vinícius Lourenço Garcia de Brito
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.55797

Dopaminergic and opioidergic regulation during anticipation and consumption of social and nonsocial rewards
Cited by: 32
Author(s): Sebastian Korb, Sebastian Jakob Götzendorfer, Claudia Massaccesi, Patrick Sezen, Irene Graf, Matthäus Willeit, Christoph Eisenegger, Giorgia Silani
Software Mentions: 7
Published: about 6 years ago

10.3389/fpls.2019.01645

Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply
Cited by: 15
Author(s): Paula Pongrac, Sina Fischer, Jacqueline Thompson, G. M. Wright, Philip J. White
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0245989

Effect of pre-operative bicarbonate infusion on maternal and perinatal outcomes among women with obstructed labour in Mbale hospital: A double blind randomized controlled trial
Cited by: 5
Author(s): Milton W. Musaba, Julius Wandabwa, Grace Ndeezi, Andrew Weeks, David Mukunya, Paul Waako, Victoria Nankabirwa, Kenneth Mugabe, Daniel Semakula, James K Tumwine, Justus K. Barageine
Software Mentions: 7
Published: over 5 years ago

10.3389/fpls.2020.602645

Bradyrhizobium as the Only Rhizobial Inhabitant of Mung Bean (Vigna radiata) Nodules in Tropical Soils: A Strategy Based on Microbiome for Improving Biological Nitrogen Fixation Using Bio-Products
Cited by: 11
Author(s): Vinício Oliosi Favero, Rita Hilário de Carvalho, Victória Monteiro da Motta, Ana Beatriz Carneiro Leite, Márcia Reed Rodrigues Coelho, Gustavo Ribeiro Xavier, Norma Gouvêa Rumjanek, Segundo Urquiaga
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0086986

Revealing Individual Signatures of Human T Cell CDR3 Sequence Repertoires with Kidera Factors
Cited by: 9
Author(s): Michael Epstein, Martino Barenco, Nigel Klein, Michael Hubank, Robin E. Callard
Software Mentions: 7
Published: over 12 years ago

10.7554/eLife.66788

An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma
Cited by: 11
Author(s): Rediet Zewdu, Elnaz Mirzaei Mehrabad, Kelley Ingram, Pengshu Fang, Katherine L Gillis, Soledad A. Camolotto, Grace Orstad, Alex Jones, Michelle C. Mendoza, Benjamin T. Spike, Eric L. Snyder
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0230767

The design and implementation of restraint devices for the injection of pathogenic microorganisms into Galleria mellonella
Cited by: 8
Author(s): Lance R. Fredericks, Mark D. Lee, Cooper R. Roslund, Angela Crabtree, Peter B. Allen, Paul A. Rowley
Software Mentions: 7
Published: about 6 years ago

10.3389/fonc.2020.608334

Nomogram for Predicting Lymph Node Involvement in Triple-Negative Breast Cancer
Cited by: 18
Author(s): Xiang Cui, Hongxia Zhu, Jiefu Huang
Software Mentions: 7
Published: almost 6 years ago

10.3389/fonc.2020.01444

Development and Validation of an m6A RNA Methylation Regulator-Based Signature for Prognostic Prediction in Cervical Squamous Cell Carcinoma
Cited by: 32
Author(s): Jianji Pan, Lichao Xu, Hongda Pan
Software Mentions: 7
Published: about 6 years ago

10.3389/fonc.2020.553399

CD8+ T Cell Co-Expressed Genes Correlate With Clinical Phenotype and Microenvironments of Urothelial Cancer
Cited by: 20
Author(s): Yutao Wang, Kexin Yan, Jiaxing Lin, Yang Liu, Jianfeng Wang, Xuejie Li, Xinxin Li, Zhixiong Hua, Zhenhua Zheng, Jianxiu Shi, Siqing Sun, Jianbin Bi
Software Mentions: 7
Published: almost 6 years ago

10.3389/fnins.2019.01042

Previous Musical Experience and Cortical Thickness Relate to the Beneficial Effect of Motor Synchronization on Auditory Function
Cited by: 3
Author(s): Natascha Merten, Johanna Kramme, Monique M.B. Breteler, Sibylle C. Herholz
Software Mentions: 7
Published: about 7 years ago

10.3389/fnins.2021.682247

Decreased MEF2A Expression Regulated by Its Enhancer Methylation Inhibits Autophagy and May Play an Important Role in the Progression of Alzheimer’s Disease
Cited by: 8
Author(s): Hui Li, Rui Wang, Xuqi Guo, Yugang Jiang
Software Mentions: 7
Published: over 5 years ago

10.3389/fneur.2019.01117

Normative Data and Minimally Detectable Change for Inner Retinal Layer Thicknesses Using a Semi-automated OCT Image Segmentation Pipeline
Cited by: 33
Author(s): Seyedamirhosein Motamedi, K. Gawlik, Noah Ayadi, Hanna Zimmermann, Susanna Asseyer, Charlotte Bereuter, Janine Mikolajczak, Friedemann Paul, Ella-Maria Kadas, Alexander U. Brandt
Software Mentions: 7
Published: almost 7 years ago

10.3389/fneur.2021.580440

Machine Learning Models on ADC Features to Assess Brain Changes of Children With Pierre Robin Sequence
Cited by: 0
Author(s): Ying Wang, Feng Yang, Meijiao Zhu, Ming Yang
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0216229

Effects of cropping, smoothing, triangle count, and mesh resolution on 6 dental topographic metrics
Cited by: 23
Author(s): Michael A. Berthaume, Julia M. Winchester, Kornelius Kupczik
Software Mentions: 7
Published: over 7 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 8 years ago

10.7554/eLife.60586

Task specialization across research careers
Cited by: 17
Author(s): Nicolás Robinson-García, Rodrigo Costas, Cassidy R. Sugimoto, Vincent Larivière, Gabriela F. Nane
Software Mentions: 7
Published: almost 6 years ago

10.3389/fnmol.2021.680280

Impaired SNF2L Chromatin Remodeling Prolongs Accessibility at Promoters Enriched for Fos/Jun Binding Sites and Delays Granule Neuron Differentiation
Cited by: 1
Author(s): Laura Rose Goodwin, Gerardo Zapata, Sara Timpano, Jacob Marenger, David J. Picketts
Software Mentions: 7
Published: over 5 years ago

10.3389/fnmol.2018.00225

NFIX Circular RNA Promotes Glioma Progression by Regulating miR-34a-5p via Notch Signaling Pathway
Cited by: 86
Author(s): Haidong Xu, Yu Zhang, Qi Ling, Lijuan Ding, Hong Jiang, Haojun Yu
Software Mentions: 7
Published: over 8 years ago

10.3389/fmolb.2021.624951

Metabolism-Relevant Molecular Classification Identifies Tumor Immune Microenvironment Characterization and Immunotherapeutic Effect in Cervical Cancer
Cited by: 4
Author(s): Luyi Li, Hui Gao, Danhan Wang, Hao Jiang, Hongzhu Wang, Jiajian Yu, Xin Jiang, Changjiang Huang
Software Mentions: 7
Published: over 5 years ago

10.3389/fmolb.2021.659168

Transcriptomic Profiling Identifies DCBLD2 as a Diagnostic and Prognostic Biomarker in Pancreatic Ductal Adenocarcinoma
Cited by: 9
Author(s): Zengyu Feng, Kexian Li, Yulian Wu, Chenghong Peng
Software Mentions: 7
Published: over 5 years ago

10.3390/cancers13092102

Integration of Urinary EN2 Protein & Cell-Free RNA Data in the Development of a Multivariable Risk Model for the Detection of Prostate Cancer Prior to Biopsy
Cited by: 4
Author(s): Shea P. Connell, Robert Mills, Hardev Pandha, Richard Morgan, Christopher S. Cooper, Jeremy Clark, Daniel Brewer
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.51529

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Cited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: almost 7 years ago

10.3389/fmicb.2020.577474

Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin
Cited by: 25
Author(s): Lisa Miclotte, Kim De Paepe, Leen Rymenans, Chris Callewaert, Jeroen Raes, Andreja Rajković, John Van Camp, Tom Van de Wiele
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmicb.2020.592189

From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies
Cited by: 6
Author(s): Robin-Tobias Jauss, Susanne Walden, Anna Maria Fiore‐Donno, Kenneth Dumack, Stefan Schaffer, Ronny Wolf, Martin Schlegel, Michael Bonkowski
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmicb.2021.685937

Metagenomic Survey of the Highly Polyphagous Anastrepha ludens Developing in Ancestral and Exotic Hosts Reveals the Lack of a Stable Microbiota in Larvae and the Strong Influence of Metamorphosis on Adult Gut Microbiota
Cited by: 10
Author(s): Martı́n Aluja, Jesús Alejandro Zamora‐Briseño, Vicente Pérez‐Brocal, Alma Altúzar-Molina, Larissa Guillén, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Enrique Ibarra-Laclette, Alexandro Alonso-Sánchez, Andrés Moya
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2018.01604

Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs
Cited by: 18
Author(s): Sara C. Bell, SM Garland, Ross A. Alford
Software Mentions: 7
Published: over 8 years ago

10.1038/s41419-021-03540-y

Metabolomic analyses of COVID-19 patients unravel stage-dependent and prognostic biomarkers
Cited by: 99
Author(s): François‐Xavier Danlos, Claudia Grajeda‐Iglesias, Sylvère Durand, Allan Sauvat, Mathilde Roumier, D. Cantin, Emeline Colomba, Julien Rohmer, Fanny Pommeret, Giulia Baciarello, Christophe Willekens, Marc Vasse, Franck Griscelli, Jean-Eudes Fahrner, Anne-Gaëlle Goubet, Agathe Dubuisson, Lisa Derosa, Nitharsshini Nirmalathasan, Delphine Bredel, Séverine Mouraud, Caroline Pradon, Annabelle Stoclin, Flore Rozenberg, Jérôme Duchemin, Georges Jourdi, Syrine Ellouze, Françoise Levavasseur, Laurence Albigès, Jean‐Charles Soria, Fabrice Barlési, Éric Solary, Fabrice André, Frédéric Pène, Félix Ackerman, Luc Mouthon, Laurence Zitvogel, Aurélien Marabelle, Jean‐Marie Michot, Michaëla Fontenay, Guido Kroemer
Software Mentions: 7
Published: over 5 years ago

10.1038/s41419-021-04067-y

Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4
Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2019.02037

Macroalga-Derived Alginate Oligosaccharide Alters Intestinal Bacteria of Atlantic Salmon
Cited by: 41
Author(s): S. R. Gupta, Jep Lokesh, Yousri Abdelhafiz, Prabhugouda Siriyappagouder, Ronan Pierre, Mette Sørensen, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 7
Published: about 7 years ago

10.7554/eLife.30952

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals
Cited by: 158
Author(s): Inge Kühl, María Miranda, Ilian Atanassov, Irina Kuznetsova, Yvonne Hinze, Arnaud Mourier, Aleksandra Filipovska, Nils‐Göran Larsson
Software Mentions: 7
Published: almost 9 years ago

10.3389/fgene.2020.577585

Development of an miRNA-Array-Based Diagnostic Signature for Periodontitis
Cited by: 11
Author(s): Sanli Jin, Jianguo Zhou, Xiaoyan Guan, Guohui Bai, Jianguo Liu, Liangwen Chen
Software Mentions: 7
Published: almost 6 years ago

10.3389/fgene.2021.737656

Integrated Analysis of the Expression Characteristics, Prognostic Value, and Immune Characteristics of PPARG in Breast Cancer
Cited by: 5
Author(s): Jianbin Wu, Mingmin Luo, Zhuangwei Chen, Lei Li, Xiaoxi Huang
Software Mentions: 7
Published: about 5 years ago

10.1534/g3.119.0011

Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis
Cited by: 31
Author(s): Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, André Pires-daSilva
Software Mentions: 7
Published: over 7 years ago

10.1016/j.lanepe.2021.100029

Adverse events of interest following influenza vaccination, a comparison of cell culture-based with egg-based alternatives: English sentinel network annual report paper 2019/20
Cited by: 6
Author(s): Simon de Lusignan, Ruby S M Tsang, Gayatri Amirthalingam, Oluwafunmi Akinyemi, Julian Sherlock, Manasa Tripathy, Alexandra Deeks, Filipa Ferreira, Gary Howsam, F D Richard Hobbs, Mark Joy
Software Mentions: 7
Published: over 5 years ago

10.18632/aging.102506

Reactive oxygen species metabolism-based prediction model and drug for patients with recurrent glioblastoma
Cited by: 7
Author(s): Nian Tan, Jianwei Liu, Ping Li, Zhaohao Sun, Jianming Pan, Wei Zhao
Software Mentions: 7
Published: almost 7 years ago

10.3390/ani11061835

An Investigation into the Influence of Different Types of Nesting Materials upon the Welfare of Captive Chimpanzees (Pan troglodytes)
Cited by: 2
Author(s): N. Anderson, Bala Amarasekaran, David Riba
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-018-1582-2

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis
Cited by: 77
Author(s): Anna R. Poetsch, Simon J. Boulton, Nicholas M. Luscombe
Software Mentions: 7
Published: almost 8 years ago

10.1186/s12859-019-2990-3

Analysis of networks of host proteins in the early time points following HIV transduction
Cited by: 8
Author(s): Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri, József Tözsér
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-020-71173-w

Standardized massage interventions as protocols for the induction of psychophysiological relaxation in the laboratory: a block randomized, controlled trial
Cited by: 10
Author(s): Maria Meier, Eva Unternäehrer, Stephanie J. Dimitroff, Annika Benz, Ulrike U. Bentele, Sabine M. Schorpp, Maya Wenzel, Jens C. Pruessner
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-020-03945-0

mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes
Cited by: 1
Author(s): Bing Song, August E. Woerner, John V. Planz
Software Mentions: 7
Published: almost 6 years ago

10.3389/fcell.2021.648279

Prognostic Value of a Novel Signature With Nine Hepatitis C Virus-Induced Genes in Hepatic Cancer by Mining GEO and TCGA Databases
Cited by: 5
Author(s): Jianming Wei, Bo Wang, Xibo Gao, Daqing Sun
Software Mentions: 7
Published: over 5 years ago

10.1186/s42523-021-00117-0

Gut microbiome is affected by gut region but robust to host physiological changes in captive active-season ground squirrels
Cited by: 3
Author(s): Kirsten Grond, Courtney C. Kurtz, Jasmine J. Hatton, Michelle M. Sonsalla, Khrystyne N. Duddleston
Software Mentions: 7
Published: about 5 years ago

10.3389/fcell.2021.688798

QSOX2 Is an E2F1 Target Gene and a Novel Serum Biomarker for Monitoring Tumor Growth and Predicting Survival in Advanced NSCLC
Cited by: 3
Author(s): Yaqi Li, Mei Liu, Zhuoxian Zhang, Libin Deng, Zhenyu Zhai, Hua Liu, Yiting Wang, Cheng Zhang, Jianping Xiong, Chao Shi
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-015-0831-x

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Cited by: 1,430
Author(s): Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Éric Viara, Chong Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, Emmanuel Barillot
Software Mentions: 7
Published: almost 11 years ago

10.18632/aging.101356

A hypothesis-driven approach identifies CDK4 and CDK6 inhibitors as candidate drugs for treatments of adrenocortical carcinomas
Cited by: 22
Author(s): Djihad Hadjadj, Su-Jung Kim, Thomas Denecker, Laura Ben Driss, Jean‐Charles Cadoret, Chrystelle Maric, Giuseppe Baldacci, Fabien Fauchereau
Software Mentions: 7
Published: almost 9 years ago

10.3390/nu12113444

Fructose-Induced Intestinal Microbiota Shift Following Two Types of Short-Term High-Fructose Dietary Phases
Cited by: 31
Author(s): Julia Beisner, Anita Gonzalez‐Granda, Maryam Basrai, Antje Damms-Machado, Stephan C. Bischoff
Software Mentions: 7
Published: almost 6 years ago

10.3390/nu12092569

Influence of Maternal Age and Gestational Age on Breast Milk Antioxidants During the First Month of Lactation
Cited by: 17
Author(s): Andrea Gila-Díaz, Gloria Herranz Carrillo, Silvia Cañas, Miguel Sáenz de Pipaón, José Martínez‐Orgado, Pilar Rodríguez-Rodríguez, Ángel L. López de Pablo, María Á. Martín-Cabrejas, David Ramiro-Cortijo, Silvia M. Arribas
Software Mentions: 7
Published: about 6 years ago

10.1186/s12859-021-04392-1

shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study
Cited by: 1
Author(s): Sonia Olaechea-Lázaro, Iraia García-Santisteban, José Ramón Pineda, Iker Badiola, Santos Alonso, José Ramón Bilbao, Nora Fernández-Jiménez
Software Mentions: 7
Published: about 5 years ago

10.3389/fcell.2019.00283

A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome
Cited by: 2
Author(s): Selma L van Esveld, Şirin Cansız-Arda, Fenna Hensen, Robin van der Lee, Martijn Huynen, Johannes N. Spelbrink
Software Mentions: 7
Published: almost 7 years ago

10.3390/nu12113269

Dietary Behaviors in the Post-Lockdown Period and Its Effects on Dietary Diversity: The Second Stage of a Nutrition Survey in a Longitudinal Chinese Study in the COVID-19 Era
Cited by: 54
Author(s): Jian Zhang, Aihua Zhao, Yalei Ke, Shanshan Huo, Yang Ma, Yumei Zhang, Zhiguo Ren, Zhongyu Li, Keyang Liu
Software Mentions: 7
Published: almost 6 years ago

10.2807/1560-7917.ES.2017.22.4.30452

Widespread activity of multiple lineages of Usutu virus, western Europe, 2016
Cited by: 105
Author(s): Dániel Cadar, Renke Lühken, Henk P. van der Jeugd, Mutien-Marie Garigliany, Ute Ziegler, Markus Keller, Jennifer Lahoreau, Lars Lachmann, Norbert Becker, Marja Kik, Bas B. Oude Munnink, Stefan Bosch, Egbert Tannich, Annick Lindén, Volker Schmidt, Marion Koopmans, Jolianne M. Rijks, Daniël Desmecht, Martin H. Groschup, Chantal Reusken, Jonas Schmidt‐Chanasit
Software Mentions: 7
Published: over 9 years ago

10.1155/2020/7658342

A Comprehensive Network Pharmacology-Based Strategy to Investigate Multiple Mechanisms of HeChan Tablet on Lung Cancer
Cited by: 6
Author(s): Zhenjie Zhuang, Qianying Chen, Cihui Huang, Junping Wen, Huayi Huang, Zhanhua Liu
Software Mentions: 7
Published: over 6 years ago

10.3390/nu13020303

Investigation of Iron and Zinc Concentrations in Human Milk in Correlation to Maternal Factors: An Observational Pilot Study in Poland
Cited by: 7
Author(s): Agnieszka Bzikowska‐Jura, Piotr Sobieraj, Magdalena Michalska-Kacymirow, Aleksandra Wesołowska
Software Mentions: 7
Published: almost 6 years ago

10.3390/pharmacy9010027

Sentiment Analysis of Online Reviews for Selective Serotonin Reuptake Inhibitors and Serotonin–Norepinephrine Reuptake Inhibitors
Cited by: 3
Author(s): Chad T. Compagner, Corey A. Lester, Michael P. Dorsch
Software Mentions: 7
Published: almost 6 years ago

10.3390/nu10091248

Effect of Whey Protein Supplementation on Physical Performance and Body Composition in Army Initial Entry Training Soldiers
Cited by: 15
Author(s): Jeremy McAdam, Kaitlin McGinnis, Darren T. Beck, Cody T. Haun, Matthew A. Romero, Petey W. Mumford, Paul A. Roberson, Kaelin C. Young, Keith R. Lohse, Lockwood Cm, Michael D. Roberts, Jo Ellen M. Sefton
Software Mentions: 7
Published: about 8 years ago

10.1002/gepi.22205

Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits
Cited by: 13
Author(s): Heather E. Wheeler, Sally Ploch, Alvaro N. Barbeira, Rodrigo Bonazzola, Angela Andaleon, Alireza Fotuhi Siahpirani, Ashis Saha, Alexis Battle, Sushmita Roy, Hae Kyung Im
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0240512

Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community
Cited by: 19
Author(s): Anne Eriksen, Tue Kjærgaard Nielsen, Henning Matthiesen, Christian Carøe, Lars Hestbjerg Hansen, David Gregory, Gordon Turner‐Walker, Matthew J. Collins, M. Thomas P. Gilbert
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pone.0256068

Parasitism to mutualism continuum for Joshua trees inoculated with different communities of arbuscular mycorrhizal fungi from a desert elevation gradient
Cited by: 5
Author(s): Jennifer Harrower, Gregory S. Gilbert
Software Mentions: 7
Published: about 5 years ago

10.1186/s13195-020-00709-z

TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages
Cited by: 25
Author(s): Hazel Hall‐Roberts, Devika Agarwal, Juliane Obst, Thomas B. Smith, Jimena Monzón‐Sandoval, Elena Di Daniel, Caleb Webber, William James, Emma Mead, John B. Davis, Sally A. Cowley
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12936-017-1738-7

Change in Anopheles richness and composition in response to artificial flooding during the creation of the Jirau hydroelectric dam in Porto Velho, Brazil
Cited by: 9
Author(s): Moreno S. Rodrigures, Elis P. A. Batista, Alexandre de Almeida e Silva, Fábio Medeiros da Costa, Verissimo A. S. Neto, Luiz Herman Soares Gil
Software Mentions: 7
Published: over 9 years ago

Projects: cran: ggplot2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning ggplot2 11,441