cran: RColorBrewer | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-52294-3

Oct4-mediated reprogramming induces embryonic-like microRNA expression signatures in human fibroblasts
Cited by: 16
Author(s): Lucie Pešková, Kateřina Černá, Jan Oppelt, Marek Mráz, Tomáš Bárta
Software Mentions: 7
Published: about 5 years ago

10.3390/biomedicines9050454

mRNA Profiles of Porcine Parathyroid Glands Following Variable Phosphorus Supplies throughout Fetal and Postnatal Life
Cited by: 8
Author(s): Michael Oster, Henry Reyer, Christian Gerlinger, Nares Trakooljul, Puntita Siengdee, Jonas Keiler, Siriluck Ponsuksili, Petra Wolf, Klaus Wimmers
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.12845

Two FGFRL-Wnt circuits organize the planarian anteroposterior axis
Cited by: 90
Author(s): M. Lucila Scimone, Lauren E. Cote, Travis Rogers, Peter W. Reddien
Software Mentions: 7
Published: over 8 years ago

10.7717/peerj.6902

Optimizing de novo genome assembly from PCR-amplified metagenomes
Cited by: 26
Author(s): Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent Northen, Matthew B. Sullivan, V. I. Rich, Rex R. Malmstrom, Emiley A. Eloe‐Fadrosh
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.7233

An artificial-vision- and statistical-learning-based method for studying the biodegradation of type I collagen scaffolds in bone regeneration systems
Cited by: 9
Author(s): Y. Robles-Bykbaev, Salvador Naya, Silvia Díaz‐Prado, D. Calle-Lopez, Vladimir Robles-Bykbaev, Luis Garzón, Clara Sanjurjo‐Rodríguez, Javier Tarrío-Saavedra
Software Mentions: 7
Published: over 5 years ago

10.7717/peerj.3622

Correlated evolution of sternal keel length and ilium length in birds
Cited by: 5
Author(s): Tao Zhao, Di Liu, Zhiheng Li
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pbio.1001555

The Geography of Recent Genetic Ancestry across Europe
Cited by: 318
Author(s): Peter L. Ralph, Graham Coop
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pone.0232682

A chronological model for the Late Paleolithic at Shuidonggou Locality 2, North China
Cited by: 10
Author(s): Fei Peng, Sam C. Lin, Ilaria Patania, Vladimir Levchenko, Jialong Guo, Huimin Wang, Xing Gao
Software Mentions: 7
Published: over 4 years ago

10.1128/mBio.00258-20

Critical Relevance of Stochastic Effects on Low-Bacterial-Biomass 16S rRNA Gene Analysis
Cited by: 27
Author(s): John R. Erb-Downward, Nicole R. Falkowski, Jennifer D’Souza, Lisa McCloskey, Roderick A. McDonald, Christopher Brown, Kerby Shedden, Robert P. Dickson, Christine M. Freeman, Kathleen A. Stringer, Betsy Foxman, Gary B. Huffnagle, Jeffrey L. Curtis, Sara D. Adar
Software Mentions: 7
Published: over 4 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: about 4 years ago

10.1371/journal.pone.0242987

A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more
Cited by: 24
Author(s): Magdalena Skarżyńska, Pimlapas Leekitcharoenphon, René S. Hendriksen, Frank Møller Aarestrup, Dariusz Wasyl
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0007225

MicroRNAs Show Mutually Exclusive Expression Patterns in the Brain of Adult Male Rats
Cited by: 94
Author(s): Line Olsen, Mikkel Klausen, Lone Helboe, Finn Cilius Nielsen, Thomas Werge
Software Mentions: 7
Published: about 15 years ago

10.1186/s13054-021-03503-x

Fluid proteomics of CSF and serum reveal important neuroinflammatory proteins in blood–brain barrier disruption and outcome prediction following severe traumatic brain injury: a prospective, observational study
Cited by: 26
Author(s): Caroline Lindblad, Elisa Pin, David R. Just, Faiez Al Nimer, Peter Nilsson, Bo‐Michael Bellander, Mikael Svensson, Fredrik Piehl, Eric Peter Thelin
Software Mentions: 7
Published: over 3 years ago

10.1016/j.dib.2021.107324

Data for modeling nitrogen dioxide concentration levels across Germany
Cited by: 2
Author(s): Markus Fritsch, Svenia Behm
Software Mentions: 7
Published: about 3 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 7 years ago

10.12688/f1000research.9005.3

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Cited by: 297
Author(s): Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Tian Li, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 7
Published: almost 6 years ago

10.1007/s11192-021-03962-7

Can tweets be used to detect problems early with scientific papers? A case study of three retracted COVID-19/SARS-CoV-2 papers
Cited by: 11
Author(s): Robin Haunschild, Lutz Bornmann
Software Mentions: 7
Published: over 3 years ago

10.3389/fgene.2019.00292

Identification of Long Non-coding and Messenger RNAs Differentially Expressed Between Primary and Metastatic Melanoma
Cited by: 16
Author(s): Lichang Sun, Zhiguang Guan, Shanshan Wei, Rui Tan, Pengfei Li, Yan Liu
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.732211

A Ferroptosis-Related Prognostic Signature Based on Antitumor Immunity and Tumor Protein p53 Mutation Exploration for Guiding Treatment in Patients With Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Xin Fan, YangShaobo Ou, Huijie Liu, Liangzhen Zhan, Xiaohui Zhu, Mingyang Cheng, Qun Li, Dongmei Yin, Lan Liao
Software Mentions: 7
Published: about 3 years ago

10.3389/fmicb.2020.536978

Repetitive Sampling and Control Threshold Improve 16S rRNA Gene Sequencing Results From Produced Waters Associated With Hydraulically Fractured Shale
Cited by: 2
Author(s): Jennifer L. Shelton, Elliott P. Barnhart, Leslie F. Ruppert, Aaron M. Jubb, Madalyn S. Blondes, Christina A. DeVera
Software Mentions: 7
Published: about 4 years ago

10.3389/fmicb.2018.02520

Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms
Cited by: 63
Author(s): Claire Bertelli, Sophie Courtois, Marta Rosikiewicz, P. Piriou, Sébastien Aeby, Robert Salais, Jean-François Loret, Gilbert Greub
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2017.02624

Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica
Cited by: 15
Author(s): Juan G. Abarca, Ibrahim Zuñiga, Gilmary Ortiz-Morales, Armando Lugo, Mariel Viquez-Cervilla, Natalia Rodríguez-Hernández, Frances Vázquez-Sánchez, Catalina Murillo‐Cruz, Ernesto A. Torres-Rivera, Adrián A. Pinto‐Tomás, Filipa Godoy-Vitorino
Software Mentions: 7
Published: almost 7 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 3 years ago

10.3389/fpls.2020.01085

Biomonitoring of Polycyclic Aromatic Hydrocarbon Deposition in Greenland Using Historical Moss Herbarium Specimens Shows a Decrease in Pollution During the 20th Century
Cited by: 12
Author(s): Karen Martinez-Swatson, Eszter Mihály, Christian Lange, Madeleine Ernst, Majbrit Dela Cruz, Michelle Price, Teis Nørgaard Mikkelsen, Jan H. Christensen, Nina Lundholm, Nina Rønsted
Software Mentions: 7
Published: over 4 years ago

10.1186/s12879-016-1475-5

DotMapper: an open source tool for creating interactive disease point maps
Cited by: 17
Author(s): Catherine M. Smith, Andrew Hayward
Software Mentions: 7
Published: over 8 years ago

10.3390/genes12010123

Satellite DNA in Neotropical Deer Species
Cited by: 6
Author(s): Miluše Vozdová, Svatava Kubı́čková, Natalia Martínková, David Javier Galindo, Agda Maria Bernegossi, Halina Černohorská, Dita Kadlčíková, Petra Musilová, José Maurício Barbanti Duarte, Jiřı́ Rubeš
Software Mentions: 7
Published: almost 4 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 9 years ago

10.3390/v13030454

Discovery of RSV-Induced BRD4 Protein Interactions Using Native Immunoprecipitation and Parallel Accumulation—Serial Fragmentation (PASEF) Mass Spectrometry
Cited by: 18
Author(s): Morgan Mann, David S. Roberts, Yanlong Zhu, Yi Li, Jia Zhou, Ying Ge, Allan R. Brasier
Software Mentions: 6
Published: over 3 years ago

10.15252/msb.20177974

Systematic characterization of pan‐cancer mutation clusters
Cited by: 31
Author(s): Marija Buljan, Peter Blattmann, Ruedi Aebersold, Michael Boutros
Software Mentions: 6
Published: over 6 years ago

10.1186/s12859-020-3404-2

IPCO: Inference of Pathways from Co-variance analysis
Cited by: 3
Author(s): Mrinmoy Das, Tarini Shankar Ghosh, Ian B. Jeffery
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-017-19059-2

Consensus Clustering of temporal profiles for the identification of metabolic markers of pre-diabetes in childhood (EarlyBird 73)
Cited by: 4
Author(s): Mario Lauria, Maria Persico, N. Ðorđević, Ornella Cominetti, Alice Matone, Joanne Hosking, Alison Jeffery, Jonathan Pinkney, Laeticia Da Silva, Corrado Priami, Ivan Montoliu, François‐Pierre J. Martin
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-021-87296-7

Genomic prediction for growth using a low-density SNP panel in dromedary camels
Cited by: 9
Author(s): Morteza Bitaraf Sani, Javad Zare Harofte, Mohammad Hossein Banabazi, Saeid Esmaeilkhanian, Ali Naderi, Nader Salim, Abbas Teimoori, Ahmad Bitaraf, Mohammad Zadehrahmani, Pamela Anna Burger, V. Landi, Mohammad Silawi, Afsaneh Taghipour Sheshdeh, Mohammad Ali Faghihi
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22116052

Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species
Cited by: 18
Author(s): Eugenia E. Montiel, Francisco Panzera, Teresa Palomeque, Pedro Lorite, Sebastián Pita
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.ppat.1006967

KSHV induces immunoglobulin rearrangements in mature B lymphocytes
Cited by: 28
Author(s): Jennifer Totonchy, Jessica M. Osborn, Amy Chadburn, Romina Nabiee, Lissenya B. Argueta, Geoffrey Mikita, Ethel Cesarman
Software Mentions: 6
Published: over 6 years ago

10.3390/genes11060599

Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran
Cited by: 5
Author(s): Morteza Bitaraf Sani, Javad Zare Harofte, Ahmad Bitaraf, Saeid Esmaeilkhanian, Mohammad Hossein Banabazi, Nader Salim, Abbas Teimoori, Ali Naderi, Mohammad Ali Faghihi, Pamela A. Burger, Mohammad Silawi, Afsaneh Taghipour Sheshdeh
Software Mentions: 6
Published: over 4 years ago

10.1186/s13229-020-00346-1

Identification of amygdala-expressed genes associated with autism spectrum disorder
Cited by: 19
Author(s): María Jesús Presentación Herrero, Dmitry Velmeshev, David Hernandez‐Pineda, Saarthak Sethi, Shawn F. Sorrells, Payal Banerjee, Catherine Sullivan, Abha R. Gupta, Arnold R. Kriegstein, Joshua G. Corbin
Software Mentions: 6
Published: over 4 years ago

10.1093/cid/ciaa1153

Investigating the Meat Pathway as a Source of Human Nontyphoidal Salmonella Bloodstream Infections and Diarrhea in East Africa
Cited by: 18
Author(s): John A. Crump, Kate M. Thomas, Jackie Benschop, Matthew A. Knox, David Wilkinson, Anne C. Midwinter, Peninah Munyua, John B. Ochieng, Godfrey Bigogo, Jennifer R. Verani, Marc‐Alain Widdowson, Gerard Prinsen, Sarah Cleaveland, Esron D. Karimuribo, Rudovick Kazwala, Blandina T. Mmbaga, Emanuel S. Swai, Nigel French, Ruth N. Zadoks
Software Mentions: 6
Published: over 4 years ago

10.1186/s40168-021-01006-z

Combined effects of composting and antibiotic administration on cattle manure–borne antibiotic resistance genes
Cited by: 26
Author(s): Ishi Keenum, Robert Williams, Partha Pratim Ray, Emily Garner, Katharine F. Knowlton, Amy Pruden
Software Mentions: 6
Published: over 3 years ago

10.1186/s40168-019-0689-3

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
Cited by: 184
Author(s): Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pbio.2003703

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
Cited by: 164
Author(s): Torsten Günther, Helena Malmström, Emma Svensson, Ayça Omrak, Federico Sánchez-Quinto, Gülşah Merve Kılınç, Maja Krzewińska, Gunilla Eriksson, Magdalena Fraser, Hanna Edlund, Arielle R. Munters, Alexandra Coutinho, Luciana G. Simões, Mário Vicente, Anders Sjölander, Berit J. Sellevold, Roger Jørgensen, Peter Claes, Mark D. Shriver, Cristina Valdiosera, Mihai G. Netea, Jan Apel, Kerstin Lidén, Birgitte Skår, Jan Storå, Anders Götherström, Mattias Jakobsson
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-021-07720-0

Comparative neurotranscriptomics reveal widespread species differences associated with bonding
Cited by: 5
Author(s): Joel A. Tripp, Alejandro Berrío, Lisa A. McGraw, Mikhail V. Matz, Jamie K. Davis, Kiyoshi Inoue, James W. Thomas, Larry J. Young, Steve Phelps
Software Mentions: 6
Published: over 3 years ago

10.3390/microorganisms9010002

Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori
Cited by: 15
Author(s): Tal Domanovich-Asor, Yair Motro, Boris Khalfin, Hillary A. Craddock, Avi Peretz, Jacob Moran-Gilad
Software Mentions: 6
Published: almost 4 years ago

10.3389/fphys.2018.01767

Fractal and Multifractal Properties of Electrographic Recordings of Human Brain Activity: Toward Its Use as a Signal Feature for Machine Learning in Clinical Applications
Cited by: 29
Author(s): Lucas Gabriel Souza França, José García Vivas Miranda, Marco Leite, Niraj Sharma, Matthew C. Walker, Louis Lemieux, Yujiang Wang
Software Mentions: 6
Published: almost 6 years ago

10.1111/tpj.14184

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes
Cited by: 91
Author(s): Genevieve M. Hoopes, John Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart, C. Robin Buell
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-87643-8

Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis
Cited by: 1
Author(s): Lea Seep, Zahra Razaghi-Moghadam, Zoran Nikoloski
Software Mentions: 6
Published: over 3 years ago

10.7717/peerj.4402

Comparative genomic analysis of a new tellurite-resistantPsychrobacterstrain isolated from the Antarctic Peninsula
Cited by: 19
Author(s): Claudia Muñoz-Villagrán, Katterinne N. Mendez, Fabián A. Cornejo, Maximiliano Figueroa, Agustina Undabarrena, Eduardo Morales, Mauricio Arenas-Salinas, Felipe Arenas, Eduardo Castro-Nallar, Claudio C. Vásquez
Software Mentions: 6
Published: almost 7 years ago

10.7717/peerj.3411

Taxonomic richness and abundance of cryptic peracarid crustaceans in the Puerto Morelos Reef National Park, Mexico
Cited by: 9
Author(s): Luz Verónica Monroy-Velázquez, Rosa E. Rodríguez-Martínez, Fernando Álvarez
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0223147

Gibberellic acid in Citrus spp. flowering and fruiting: A systematic review
Cited by: 22
Author(s): Alfonso Garmendia, Roberto Beltrán, Carlos Zornoza, Francisco J. García‐Breijo, José Luis Peset Reig, Hugo Merlé
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0184890

Effects of Eimeria tenella infection on chicken caecal microbiome diversity, exploring variation associated with severity of pathology
Cited by: 92
Author(s): Sarah E. Macdonald, Matthew J. Nolan, Kimberley Harman, Kay Boulton, David Hume, Fiona M. Tomley, Richard A. Stabler, Damer P. Blake
Software Mentions: 6
Published: about 7 years ago

10.1002/ece3.7904

Is the grass always greener? Land surface phenology reveals differences in peak and season‐long vegetation productivity responses to climate and management
Cited by: 6
Author(s): David J. A. Wood, Scott Powell, Paul C. Stoy, Lindsey L. Thurman, Erik A. Beever
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2164-15-353

Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Cited by: 49
Author(s): Richard Landstorfer, Svenja Simon, Steffen Schober, Daniel A. Keim, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 6
Published: over 10 years ago

10.7717/peerj.997

Deep sequencing of the viralphoHgene reveals temporal variation, depth-specific composition, and persistent dominance of the same viralphoHgenes in the Sargasso Sea
Cited by: 34
Author(s): Dawn B. Goldsmith, Rachel Parsons, Damitu Beyene, Peter Salamon, Mya Breitbart
Software Mentions: 6
Published: over 9 years ago

10.3390/antiox10040595

Antioxidants-Related Superoxide Dismutase (SOD), Catalase (CAT), Glutathione Peroxidase (GPX), Glutathione-S-Transferase (GST), and Nitric Oxide Synthase (NOS) Gene Variants Analysis in an Obese Population: A Preliminary Case-Control Study
Cited by: 28
Author(s): Amani M T Gusti, Safaa Qusti, Eida M. Alshammari, Eman A. Toraih, Manal S. Fawzy
Software Mentions: 6
Published: over 3 years ago

10.1038/s41426-018-0118-x

Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential
Cited by: 22
Author(s): Matthew Gemmell, Susan H. Berry, Indrani Mukhopadhya, Richard Hansen, Hans Linde Nielsen, Mona Bajaj-Elliott, Henrik Nielsen, Georgina L. Hold
Software Mentions: 6
Published: over 6 years ago

10.1210/en.2019-00165

Search for Early Pancreatic Cancer Blood Biomarkers in Five European Prospective Population Biobanks Using Metabolomics
Cited by: 18
Author(s): Jesse Fest, Lisanne S Vijfhuizen, Jelle J. Goeman, Olga Veth, Anni Joensuu, Markus Perola, Satu Männistö, Eivind Ness-Jensen, Kristian Hveem, Toomas Haller, Neeme Tõnisson, Kairit Mikkel, Andres Metspalu, Cornelia M. van Duijn, M. Arfan Ikram, Bruno H. Ch. Stricker, Rikje Ruiter, Casper H.J. van Eijck, Gert‐Jan B. van Ommen, Peter A.C. ’t Hoen
Software Mentions: 6
Published: over 5 years ago

10.1038/srep37387

The stable microbiome of inter and sub-tidal anemone species under increasing pCO2
Cited by: 13
Author(s): Erinn M. Muller, Maoz Fine, Kim B. Ritchie
Software Mentions: 6
Published: about 8 years ago

10.1038/s41598-020-65089-8

Immunorthodontics: in vivo gene expression of orthodontic tooth movement
Cited by: 28
Author(s): Yehuda Klein, Omer Fleissig, David Polak, Yechezkel Barenholz, Ofer Mandelboim, Stella Chaushu
Software Mentions: 6
Published: over 4 years ago

10.7717/peerj.11489

covid19.Explorer: a web application and R package to explore United States COVID-19 data
Cited by: 5
Author(s): Liam J. Revell
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2105-15-170

Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences
Cited by: 24
Author(s): Natalie S. Fox, Maud H.W. Starmans, Syed Haider, Philippe Lambin, Paul C. Boutros
Software Mentions: 6
Published: over 10 years ago

10.1007/s12275-020-9536-2

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
Cited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: almost 5 years ago

10.1038/s42003-020-01593-x

Coconut genome assembly enables evolutionary analysis of palms and highlights signaling pathways involved in salt tolerance
Cited by: 24
Author(s): Yaodong Yang, Stéphanie Bocs, Hang Fan, Alix Armero, Luc Baudouin, Pengwei Xu, Junyang Xu, Dominique This, Chantal Hamelin, Amjad Iqbal, Rashad Qadri, Lixia Zhou, Jing Li, Yi Wu, Zhiying Ma, Auguste Emmanuel Issali, Ronan Rivallan, Na Liu, Wei Xia, Ming Peng, Yong Xiao
Software Mentions: 6
Published: almost 4 years ago

10.1017/S0031182021000111

Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella
Cited by: 5
Author(s): Arnar K. S. Sandholt, Feifei Xu, Robert Söderlund, Anna Lundén, Karin Troell, Staffan G. Svärd, Eva Wattrang
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0173340

Prioritising surveillance for alien organisms transported as stowaways on ships travelling to South Africa
Cited by: 19
Author(s): Katelyn T. Faulkner, Mark P. Robertson, Mathieu Rouget, John R. Wilson
Software Mentions: 6
Published: over 7 years ago

10.1186/s12859-019-2778-5

eNetXplorer: an R package for the quantitative exploration of elastic net families for generalized linear models
Cited by: 26
Author(s): Julián Candia, John S. Tsang
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0227860

Fungal diversity in canopy soil of silver beech, Nothofagus menziesii (Nothofagaceae)
Cited by: 4
Author(s): Andy R. Nilsen, Suliana Teasdale, P. L. Guy, Tina C. Summerfield, David A. Orlovich
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0181109

Hypoxia tolerance and responses to hypoxic stress during heart and skeletal muscle inflammation in Atlantic salmon (Salmo salar)
Cited by: 33
Author(s): Morten Lund, Maria K. Dahle, Gerrit Timmerhaus, Marta Alarcón, Mark D. Powell, Vidar Aspehaug, Espen Rimstad, Sven Martin Jørgensen
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-021-81359-5

Aldehyde-specific responses of olfactory sensory neurons in the praying mantis
Cited by: 3
Author(s): Kota Ezaki, Takashi Yamashita, Thomas Carle, Hidehiro Watanabe, Fumio Yokohari, Yoshifumi Yamawaki
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1006667

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans
Cited by: 85
Author(s): Eve W. L. Chow, Shelly Applen Clancey, R. Blake Billmyre, Anna Floyd Averette, Joshua A. Granek, Piotr A. Mieczkowski, María E. Cárdenas, Joseph Heitman
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.9205

Human milk microbiota associated with early colonization of the neonatal gut in Mexican newborns
Cited by: 27
Author(s): Karina Corona-Cervantes, Igrid García-González, Loan Edel Villalobos-Flores, Fernando Hernández-Quiroz, Alberto Piña-Escobedo, Carlos Hoyo‐Vadillo, Martín Noé Rangel-Calvillo, Jaime García‐Mena
Software Mentions: 5
Published: over 4 years ago

10.1002/ece3.5580

Matrotrophic viviparity constrains microbiome acquisition during gestation in a live‐bearing cockroach, Diploptera punctata
Cited by: 6
Author(s): Emily C. Jennings, Matthew W. Korthauer, Trinity L. Hamilton, Joshua B. Benoit
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.55027.1

rmcorrShiny: A web and standalone application for repeated measures correlation
Cited by: 14
Author(s): Laura R. Marusich, Jonathan Z. Bakdash
Software Mentions: 5
Published: over 3 years ago

10.1186/s13071-020-04424-4

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)
Cited by: 3
Author(s): Maksim A. Nesterenko, Viktor V. Starunov, Sergei V. Shchenkov, Anna R. Maslova, Sofia Denisova, Andrey I. Granovich, Andrej A. Dobrovolskij, Konstantin Khalturin
Software Mentions: 5
Published: about 4 years ago

10.3389/fpubh.2021.619581

Disease Burden and Attributable Risk Factors of Ovarian Cancer From 1990 to 2017: Findings From the Global Burden of Disease Study 2017
Cited by: 18
Author(s): Zhangjian Zhou, Xuan Wang, Xueting Ren, Linghui Zhou, Nan Wang, Huafeng Kang
Software Mentions: 5
Published: about 3 years ago

10.1002/1878-0261.12779

TGF‐β‐induced IGFBP‐3 is a key paracrine factor from activated pericytes that promotes colorectal cancer cell migration and invasion
Cited by: 16
Author(s): Rocío Navarro, Antonio Tapia-Galisteo, Laura Martín-García, Carlos Tarin, Cesáreo Corbacho, Gonzalo Gómez‐López, Esther Sánchez‐Tirado, Susana Campuzano, Paloma Yánez‐Sedeño, Paloma Yánez‐Sedeño, Marta Compte, Luís Álvarez‐Vallina, Laura Sanz
Software Mentions: 5
Published: about 4 years ago

10.1186/s12874-016-0229-9

Health Equity Assessment Toolkit (HEAT): software for exploring and comparing health inequalities in countries
Cited by: 64
Author(s): Ahmad Reza Hosseinpoor, Devaki Nambiar, Anne Schlotheuber, Daniel D. Reidpath, Zev Ross
Software Mentions: 5
Published: about 8 years ago

10.1186/s13100-020-00224-w

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains
Cited by: 14
Author(s): Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi Imanishi, So Nakagawa
Software Mentions: 5
Published: about 4 years ago

10.3390/microorganisms8081115

Distribution and Control of Bacterial Community Composition in Marian Cove Surface Waters, King George Island, Antarctica during the Summer of 2018
Cited by: 8
Author(s): Soyeon Kim, Ju-Hyoung Kim, Jae-Hyun Lim, Jong-Gil Jeong, Jang-Mu Heo, Il-Nam Kim
Software Mentions: 5
Published: over 4 years ago

10.1021/acs.jcim.0c01382

Use of the Complementarity Principle in Docking Procedures: A New Approach for Evaluating the Correctness of Binding Poses
Cited by: 12
Author(s): Hrvoje Rimac, Maria Grishina, В. А. Потемкин
Software Mentions: 5
Published: over 3 years ago

10.3389/fimmu.2017.00308

Expression of Serum microRNAs is Altered During Acute Graft-versus-Host Disease
Cited by: 23
Author(s): Rachel E Crossland, Jean Norden, Mateja Kralj Juric, Kile Green, Kim Pearce, Clare Lendrem, Hildegard Greinix, AM Dickinson
Software Mentions: 5
Published: over 7 years ago

10.1186/s40168-018-0555-8

The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch
Cited by: 54
Author(s): Alice Michel, Lewis M. Ward, Shana K. Goffredi, Katherine S. Dawson, Daniel T. Baldassarre, Alec Brenner, Kiyoko M. Gotanda, John E. McCormack, Sean W. Mullin, Ariel O’Neill, Gabrielle S. Tender, J. Albert C. Uy, Kristie Yu, Victoria J. Orphan, Jaime A. Chaves
Software Mentions: 5
Published: about 6 years ago

10.1002/mbo3.1146

Deeper below the surface—transcriptional changes in selected genes of Clostridium beijerinckii in response to butanol shock
Cited by: 5
Author(s): Petra Patáková, Jan Kolek, Katerina Jureckova, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Ivo Provazník
Software Mentions: 5
Published: almost 4 years ago

10.1264/jsme2.ME17160

Chitin Increases Mycobacterium ulcerans Growth in Acidic Environments
Cited by: 6
Author(s): Daniel Sanhueza, Christine Chevillon, Nicolas Bouzinbi, Sylvain Godreuil, Jean‐François Guégan
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2019.01629

Sonic Hedgehog Is a Determinant of γδ T-Cell Differentiation in the Thymus
Cited by: 12
Author(s): Konstantinos Mengrelis, Ching‐In Lau, Jasmine Rowell, Anisha Solanki, S. Norris, Scott R. Ross, M. Ono, Susan V. Outram, Tessa Crompton
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2019.03023

Distinct Immunological Landscapes Characterize Inherited and Sporadic Mismatch Repair Deficient Endometrial Cancer
Cited by: 43
Author(s): Neal C Ramchander, Neil Ryan, Thomas D. J. Walker, Lauren J. Harries, James M. Bolton, Tjalling Bosse, D. Gareth Evans, Emma J. Crosbie
Software Mentions: 5
Published: almost 5 years ago

10.1155/2016/8409183

Azocasein Substrate for Determination of Proteolytic Activity: Reexamining a Traditional Method Using Bromelain Samples
Cited by: 60
Author(s): D. Coelho, Thais Peron Saturnino, Fernanda Freitas Fernandes, Priscila Gava Mazzola, Edgar Silveira, Elias Basile Tambourgi
Software Mentions: 5
Published: almost 9 years ago

10.3389/fmicb.2019.03153

Diversity of Bacterial Community in the Oxygen Minimum Zones of Arabian Sea and Bay of Bengal as Deduced by Illumina Sequencing
Cited by: 33
Author(s): Genevieve L. Fernandes, Belle Damodara Shenoy, Samir Damare
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12889-020-09791-2

Burden of prediabetes, undiagnosed, and poorly or potentially sub-controlled diabetes: Lolland-Falster health study
Cited by: 7
Author(s): Neda Esmailzadeh Bruun-Rasmussen, George Napolitano, Allan Kofoed‐Enevoldsen, Stig E. Bojesen, Christina Ellervik, Knud Rasmussen, Randi Jepsen
Software Mentions: 5
Published: about 4 years ago

10.1038/s41598-019-45368-9

Microbial communities in top- and subsoil of repacked soil columns respond differently to amendments but their diversity is negatively correlated with plant productivity
Cited by: 23
Author(s): Corinne Celestina, Jennifer L. Wood, James B. Manson, Xiaojuan Wang, P. W. G. Sale, Caixian Tang, Ashley E. Franks
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-021-90095-9

miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta
Cited by: 1
Author(s): Iram P. Rodríguez‐Sánchez, Daniel Rafael Saldaña-Torres, Olga Karina Villanueva-Segura, María Lourdes Garza‐Rodríguez, Mayra A. Gómez‐Govea, Ghongwei Liang, María de Lourdes Ramírez‐Ahuja, Margarita L. Martínez‐Fierro, Iván Delgado‐Enciso, Laura Elia Martínez-de-Villarreal, Yu Zhou, Adriana E. Flores-Suárez, Xi Chen, Diana Reséndez‐Pérez, Chenyu Zhang, Gustavo Ponce‐García
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2021.690251

Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs
Cited by: 16
Author(s): Marta Nierychlo, Caitlin M. Singleton, Francesca Petriglieri, Lisette Thomsen, Jette Fischer Petersen, Miriam Peces, Zivile Kondrotaite, Morten Simonsen Dueholm, Per Halkjær Nielsen
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-37679-0

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: almost 6 years ago

10.3389/fmicb.2017.00101

Freshwater Recirculating Aquaculture System Operations Drive Biofilter Bacterial Community Shifts around a Stable Nitrifying Consortium of Ammonia-Oxidizing Archaea and Comammox Nitrospira
Cited by: 163
Author(s): Ryan P. Bartelme, Sandra L. McLellan, Ryan J. Newton
Software Mentions: 5
Published: almost 8 years ago

10.1093/gbe/evab145

High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady ButterflyVanessa cardui
Cited by: 7
Author(s): Linlin Zhang, Rachel Steward, Christopher W. Wheat, Robert D. Reed
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-019-6179-y

Transcriptional variation and divergence of host-finding behaviour in Steinernema carpocapsae infective juveniles
Cited by: 5
Author(s): Neil D. Warnock, Deborah Cox, Ciaran J. McCoy, Robert Morris, Johnathan J. Dalzell
Software Mentions: 5
Published: about 5 years ago

10.1038/srep31587

Hepatic and serum lipid signatures specific to nonalcoholic steatohepatitis in murine models
Cited by: 33
Author(s): Franck Chiappini, Christophe Desterke, Justine Bertrand‐Michel, Catherine Guettier, François Le Naour
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-021-08015-0

Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use
Cited by: 11
Author(s): Mehtab Muhammad Aslam, Muhammad Waseem, Qian Zhang, Ke Wang, Jianhua Zhang, Weifeng Xu
Software Mentions: 5
Published: about 3 years ago

10.1093/gigascience/giy054

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments
Cited by: 82
Author(s): Alexandre Almeida, Alex L. Mitchell, Aleksandra Tarkowska, Alex Bateman
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-71864-4

Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing
Cited by: 25
Author(s): Katherine Chacón-Vargas, Julian Torres, Martha Gilés-Gómez, Adelfo Escalante, John G. Gibbons
Software Mentions: 5
Published: about 4 years ago

10.3389/fpls.2020.00545

Spatiotemporal Modulation of Flavonoid Metabolism in Blueberries
Cited by: 38
Author(s): Catrin S. Günther, Andrew P. Dare, Tony K. McGhie, Cecilia Deng, Declan J. Lafferty, Blue Plunkett, Ella Grierson, Janice L. Turner, Laura Jaakola, Nick W. Albert, Richard V. Espley
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2016.01225

TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity
Cited by: 29
Author(s): Niklas Schandry, Orlando de Lange, Philippe Prior, Thomas Lahaye
Software Mentions: 5
Published: over 8 years ago

Projects: cran: RColorBrewer

Papers Mentioning RColorBrewer 490