cran: viridis | Projects | Ecosyste.ms: Papers

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
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

10.7554/eLife.51254

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
Cited by: 102
Author(s): Christopher Jackson, Dayanne M. Castro, Giuseppe-Antonio Saldi, Richard Bonneau, David Gresham
Software Mentions: 20
Published: almost 5 years ago

10.1186/s12864-020-06832-3

Seamless integration of image and molecular analysis for spatial transcriptomics workflows
Cited by: 121
Author(s): Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg
Software Mentions: 20
Published: over 4 years ago

10.1186/s12866-021-02282-3

Associations between the gut microbiome and metabolome in early life
Cited by: 14
Author(s): Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal Pathmasiri, Susan McRitche, Susan Sumner, H. Robert Frost, Anne G. Hoen
Software Mentions: 19
Published: over 3 years ago

10.15252/emmm.202012640

Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor
Cited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: about 4 years ago

10.1016/j.molcel.2021.05.023

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago

10.1371/journal.pbio.3001296

Tapping into non-English-language science for the conservation of global biodiversity
Cited by: 79
Author(s): Tatsuya Amano, Violeta Berdejo‐Espinola, Alec P. Christie, Kate Willott, Munemitsu Akasaka, András Báldi, Anna Berthinussen, Sandro Bertolino, Andrew J. Bladon, Min Chen, Chang Yong Choi, Magda Bou Dagher Kharrat, Luís Guilherme de Oliveira, Perla Farhat, Marina Golivets, Nataly Hidalgo Aranzamendi, Kerstin Jantke, Joanna Kajzer‐Bonk, M. Çisel Kemahlı Aytekin, Igor Khorozyan, Kensuke Kito, Ko Konno, Da Li Lin, Nick A. Littlewood, Yang Liu, Yifan Liu, Matthias Claudio Loretto, Valentina Marconi, Philip A. Martin, William H. Morgan, Juan Pablo Narváez-Gómez, Pablo José Negret, Elham Nourani, José Manuel Ochoa Quintero, Nancy Ockendon, Rachel Rui Ying Oh, Silviu O. Petrovan, Ana Cláudia Piovezan-Borges, Ingrid L. Pollet, Danielle Leal Ramos, Ana L. Reboredo Segovia, A. Nayelli Rivera‐Villanueva, Ricardo Rocha, Marie Morgane Rouyer, Katherine A. Sainsbury, Richard Schuster, Dominik Schwab, Çaǧan H. Şekercioǧlu, Hae Min Seo, Gorm E. Shackelford, Yushin Shinoda, Rebecca K. Smith, Shan Dar Tao, Ming-shan Tsai, Elizabeth Tyler, Flóra Vajna, José O. Valdebenito, Svetlana Vozykova, Paweł Waryszak, Veronica Zamora‐Gutiérrez, Rafael Dudeque Zenni, Wenjun Zhou, William J. Sutherland
Software Mentions: 18
Published: about 3 years ago

10.1371/journal.pbio.3000673

“Frozen evolution” of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
Cited by: 15
Author(s): David Pascall, Kyriaki Nomikou, Emmanuel Bréard, Stéphan Zientara, Ana da Silva Filipe, Bernd Hoffmann, Maude Jacquot, Joshua B. Singer, Kris De Clercq, Anette Bøtner, Corinne Sailleau, Cyril Viarouge, Carrie Batten, Giantonella Puggioni, Ciriaco Ligios, Giovanni Savini, Piet A. van Rijn, Peter Mertens, Roman Biek, Massimo Palmarini
Software Mentions: 18
Published: over 4 years ago

10.1093/gigascience/giaa010

Interpretable and accurate prediction models for metagenomics data
Cited by: 29
Author(s): Edi Prifti, Yann Chevaleyre, Blaise Hanczar, Eugeni Belda, Antoine Danchin, Karine Clément, Jean-Daniel Zucker
Software Mentions: 18
Published: almost 5 years ago

10.1038/s41598-020-80340-y

Universal principles underlying segmental structures in parrot song and human speech
Cited by: 6
Author(s): Dan C. Mann, W. Tecumseh Fitch, Hsiao‐Wei Tu, Marisa Hoeschele
Software Mentions: 17
Published: almost 4 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: almost 4 years ago

10.3390/brainsci11081017

Facial Signals and Social Actions in Multimodal Face-to-Face Interaction
Cited by: 14
Author(s): Naomi Nota, James P. Trujillo, Judith Holler
Software Mentions: 17
Published: over 3 years ago

10.3389/fmicb.2019.00240

Changes in Trophic Groups of Protists With Conversion of Rainforest Into Rubber and Oil Palm Plantations
Cited by: 38
Author(s): Garvin Schulz, Dominik Schneider, Nicole Brinkmann, Nur Edy, Rolf Daniel, Andrea Polle, Stefan Scheu, Valentyna Krashevska
Software Mentions: 16
Published: almost 6 years ago

10.1371/journal.pone.0231982

Rapid processing of neutral and angry expressions within ongoing facial stimulus streams: Is it all about isolated facial features?
Cited by: 2
Author(s): Antonio Schettino, Emanuele Porcu, Christopher Gundlach, Christian Keitel, Matthias Müller
Software Mentions: 16
Published: over 4 years ago

10.7554/eLife.21883

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
Cited by: 72
Author(s): Lucas T. Gray, Zizhen Yao, Thuc Nghi Nguyen, Tae Kyung Kim, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 16
Published: almost 8 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: over 4 years ago

10.12688/f1000research.16198.2

scClustViz – Single-cell RNAseq cluster assessment and visualization
Cited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: almost 6 years ago

10.1128/mBio.00034-20

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes
Cited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: almost 5 years ago

10.1038/s41598-021-87843-2

Bodily ownership and agency sensations in a natural state
Cited by: 1
Author(s): Souta Hidaka, Kyoshiro Sasaki, Toshikazu Kawagoe, Nobuyuki Asai, Wataru Teramoto
Software Mentions: 15
Published: over 3 years ago

10.3389/fmicb.2020.580691

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
Cited by: 20
Author(s): Laura M. Carroll, Rachel A. Cheng, Jasna Kovač
Software Mentions: 15
Published: about 4 years ago

10.1038/s42003-021-01796-w

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Cited by: 73
Author(s): Rong Xu, Renfei Lu, Tao Zhang, Qian Wu, Wei Cai, Xudong Han, Zhenzhou Wan, Xia Jin, Zhigang Zhang, Chiyu Zhang
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: about 4 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 years ago

10.3389/fpls.2021.618028

Floral UV Features of Plant Species From a Neotropical Savanna
Cited by: 6
Author(s): Priscila Tunes, Maria Gabriela Gutierrez Camargo, Elza Guimarães
Software Mentions: 15
Published: over 3 years ago

10.1186/s13059-019-1783-3

AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
Cited by: 20
Author(s): Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard
Software Mentions: 14
Published: over 5 years ago

10.7554/eLife.53392

ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair
Cited by: 23
Author(s): Daniel Wells, Emmanuelle Bitoun, Daniela Moralli, Gang Zhang, Anjali Gupta Hinch, Julia Jankowska, Peter Donnelly, Catherine Green, Simon Myers
Software Mentions: 14
Published: over 4 years ago

10.1093/bioinformatics/btx657

heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Cited by: 334
Author(s): Tal Galili, Alan O’Callaghan, Jonathan Savage, Carson Sievert
Software Mentions: 14
Published: about 7 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

10.3390/microorganisms9061167

Diversity and Oil Degradation Potential of Culturable Microbes Isolated from Chronically Contaminated Soils in Trinidad
Cited by: 10
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 14
Published: over 3 years ago

10.3389/fpsyg.2020.564083

Correlates of Health-Protective Behavior During the Initial Days of the COVID-19 Outbreak in Norway
Cited by: 54
Author(s): Janis Zickfeld, Thomas W. Schubert, Anders Kuvaas Herting, Jon Grahe, Kate Faasse
Software Mentions: 14
Published: about 4 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pone.0253148

Enhancing monitoring of rewilding progress through wildlife tracking and remote sensing
Cited by: 1
Author(s): Julia Carolina Mata, Robert Buitenwerf, Jens‐Christian Svenning
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

10.1038/s41598-020-78747-8

Non-invasive assessment of skeletal muscle fibrosis in mice using nuclear magnetic resonance imaging and ultrasound shear wave elastography
Cited by: 6
Author(s): Aurea B. Martins-Bach, Damien Bachasson, E. Araujo, Lucas Soustelle, Paulo Loureiro de Sousa, Y. Fromes, Pierre Carlier
Software Mentions: 13
Published: almost 4 years ago

10.4269/ajtmh.20-0757

A Computational Modeling Study of COVID-19 in Bangladesh
Cited by: 7
Author(s): Irtesam Mahmud Khan, Ubydul Haque, Samiha Kaisar, Md. Saidur Rahman
Software Mentions: 12
Published: almost 4 years ago

10.7717/peerj.5661

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
Cited by: 17
Author(s): Camila Duarte Ritter, Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher J. Barnes, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 12
Published: about 6 years ago

10.3390/cells10051066

Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein’s Anomaly
Cited by: 5
Author(s): Masood Abu‐Halima, Viktoria Wagner, Lea Simone Becker, Basim Ayesh, Mohammed Abd El-Rahman, Ulrike Fischer, Eckart Meese, Hashim Abdul‐Khaliq
Software Mentions: 12
Published: over 3 years ago

10.3390/genes9120569

NeVOmics: An Enrichment Tool for Gene Ontology and Functional Network Analysis and Visualization of Data from OMICs Technologies
Cited by: 13
Author(s): Eduardo Zúñiga-León, Ulises Carrasco-Navarro, Francisco Fierro
Software Mentions: 12
Published: about 6 years ago

10.1186/s12974-021-02235-7

Sex differences and similarities in the neuroimmune response to central administration of poly I:C
Cited by: 14
Author(s): Caitlin K. Posillico, Rosa E. Garcia-Hernandez, Natalie C. Tronson
Software Mentions: 12
Published: over 3 years ago

10.1098/rsos.191333

Now or never: noticing occurs early in sustained inattentional blindness
Cited by: 4
Author(s): Katherine Wood, Daniel J. Simons
Software Mentions: 10
Published: about 5 years ago

10.3390/ijms21051754

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data
Cited by: 10
Author(s): Enrico Gaffo, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, Stefania Bortoluzzi
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pone.0238496

Lyme disease and relapsing fever in Mexico: An overview of human and wildlife infections
Cited by: 18
Author(s): Pablo Colunga‐Salas, Sokani Sánchez‐Montes, Patricia Volkow, Adriana Ruíz-Remigio, Ingeborg Becker
Software Mentions: 10
Published: over 4 years ago

10.1186/s11689-021-09360-7

Modeling familial predictors of proband outcomes in neurogenetic disorders: initial application in XYY syndrome
Cited by: 3
Author(s): Kathleen Wilson, Ari M. Fish, Catherine Mankiw, Anastasia Xenophontos, Allysa Warling, Ethan T. Whitman, Liv S. Clasen, Erin Torres, Jonathan D. Blumenthal, Armin Raznahan
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41598-020-62453-6

Patterns of Rift Valley fever virus seropositivity in domestic ruminants in central South Africa four years after a large outbreak
Cited by: 19
Author(s): Yusuf B. Ngoshe, Alida Avenant, Melinda K. Rostal, William B. Karesh, Janusz T. Pawęska, Whitney Bagge, Petrus Jansen van Vuren, Alan C. Kemp, Claudia Cordel, Veerle Msimang, Peter N. Thompson
Software Mentions: 10
Published: over 4 years ago

10.3390/metabo10030086

Local Phenomena Shape Backyard Soil Metabolite Composition
Cited by: 9
Author(s): Tra D Nguyen, Mahbobeh Lesani, Ines Forrest, Yunpeng Lan, Danya A. Dean, Quentin M. R. Gibaut, Yanting Guo, Ekram Hossain, Marcela Olvera, Hannah Panlilio, Adwaita R. Parab, Chao‐Yi Wu, Jean A. Bernatchez, Robert H. Cichewicz, Laura-Isobel McCall
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41598-018-30701-5

Electrophysiological correlates of the interplay between low-level visual features and emotional content during word reading
Cited by: 22
Author(s): Sebastian Schindler, Antonio Schettino, Gilles Pourtois
Software Mentions: 9
Published: over 6 years ago

10.3390/v11100910

Host Range of Bacteriophages Against a World-Wide Collection of Erwinia amylovora Determined Using a Quantitative PCR Assay
Cited by: 14
Author(s): Steven Gayder, Michael Parcey, Alan J. Castle, A. M. Svircev
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-020-74647-z

Passive acoustic listening stations (PALS) show rapid onset of ecological effects of harmful algal blooms in real time
Cited by: 9
Author(s): Athena M. Rycyk, Reny B. Tyson Moore, Randall S. Wells, Katherine McHugh, Elizabeth J. Berens McCabe, David A. Mann
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pone.0247790

Parasitism and host behavior in the context of a changing environment: The Holocene record of the commercially important bivalve Chamelea gallina, northern Italy
Cited by: 3
Author(s): John Warren Huntley, Daniele Scarponi
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.14966.1

iSEE: Interactive SummarizedExperiment Explorer
Cited by: 68
Author(s): Kévin Rue-Albrecht, Fédérico Marini, Charlotte Soneson, Aaron T. L. Lun
Software Mentions: 9
Published: over 6 years ago

10.1038/s41598-019-55984-0

Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype
Cited by: 16
Author(s): Matej Mihelčić, Tomislav Šmuc, Fran Supek
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-019-52241-2

Tradeoffs in the value of biodiversity feature and cost data in conservation prioritization
Cited by: 11
Author(s): Amanda D. Rodewald, Matthew Strimas‐Mackey, Richard Schuster, Peter Arcese
Software Mentions: 8
Published: about 5 years ago

10.3390/cells8080920

The Snapdragon LATE ELONGATED HYPOCOTYL Plays A Dual Role in Activating Floral Growth and Scent Emission
Cited by: 9
Author(s): Marta I. Terry, Fernando Pérez-Sánz, Pedro J. Navarro, Julia Weiß, Marcos Egea‐Cortines
Software Mentions: 8
Published: over 5 years ago

10.1128/mSphere.00916-19

Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal Cavities
Cited by: 15
Author(s): Charlotte De Rudder, Marta Calatayud, Sarah Lebeer, Tom Van de Wiele
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0199239

Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data
Cited by: 91
Author(s): Jamie Nuñez, Christopher R. Anderton, Ryan Renslow
Software Mentions: 8
Published: over 6 years ago

10.3390/s20236723

Wide Field Spectral Imaging with Shifted Excitation Raman Difference Spectroscopy Using the Nod and Shuffle Technique
Cited by: 7
Author(s): Florian Korinth, Elmar Schmälzlin, Clara Stiebing, T. Urrutia, Genoveva Micheva, C. Sandín, André Müller, Bernd Sumpf, Christoph Krafft, G. Tränkle, Martin Roth, Jürgen Popp
Software Mentions: 8
Published: about 4 years ago

10.1007/s12031-020-01787-2

Studying Autism Using Untargeted Metabolomics in Newborn Screening Samples
Cited by: 13
Author(s): Julie Courraud, Madeleine Ernst, Susan Svane Laursen, David M. Hougaard, Arieh Cohen
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pgen.1009385

Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive
Cited by: 19
Author(s): Georg Oberhofer, Tobin Ivy, Bruce A. Hay
Software Mentions: 7
Published: almost 4 years ago

10.3390/ijerph15020250

Using Twitter to Better Understand the Spatiotemporal Patterns of Public Sentiment: A Case Study in Massachusetts, USA
Cited by: 32
Author(s): Xiaodong Cao, Piers MacNaughton, Zhengyi Deng, Jie Yin, Xi Zhang, Joseph G. Allen
Software Mentions: 7
Published: almost 7 years ago

10.2196/19791

Investigating the Prevalence of Reactive Online Searching in the COVID-19 Pandemic: Infoveillance Study
Cited by: 27
Author(s): Rafael A Badell-Grau, Jordan P. Cuff, Brendan P. Kelly, Helen Waller-Evans, Emyr Lloyd-Evans
Software Mentions: 7
Published: about 4 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: over 3 years ago

10.1002/bit.27209

Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain
Cited by: 31
Author(s): Joseph Brady, Charles A. Whittaker, Melody C. Tan, D. Lee Kristensen, Duanduan Ma, Neil C. Dalvie, Kerry R. Love, J. Christopher Love
Software Mentions: 7
Published: about 5 years ago

10.5888/pcd17.190286

Visualizing 50 Years of Cancer Mortality Rates Across the US at Multiple Geographic Levels Using a Synchronized Map and Graph Animation
Cited by: 0
Author(s): Isaac H. Michaels, Sylvia Pirani, Alvaro Carrascal
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-019-43829-9

Tissue-specific genes as an underutilized resource in drug discovery
Cited by: 29
Author(s): Maria Ryaboshapkina, Mårten Hammar
Software Mentions: 7
Published: over 5 years ago

10.3390/v11030240

Bat Research Networks and Viral Surveillance: Gaps and Opportunities in Western Asia
Cited by: 26
Author(s): Kendra L. Phelps, Luke Hamel, Nisreen Al-Hmoud, Shahzad Ali, Raşi̇t Bi̇lgi̇n, Ketevan Sidamonidze, Lela Urushadze, William B. Karesh, Kevin J. Olival
Software Mentions: 7
Published: almost 6 years ago

10.1186/s41118-017-0018-2

Decomposition of regional convergence in population aging across Europe
Cited by: 16
Author(s): Ilya Kashnitsky, Joop de Beer, Leo van Wissen
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pntd.0008487

Non-invasive monitoring of drug action: A new live in vitro assay design for Chagas’ disease drug discovery
Cited by: 5
Author(s): Anna Fesser, Olivier Braissant, F.J. Olmo, John M. Kelly, Pascal Mäser, Marcel Kaiser
Software Mentions: 6
Published: over 4 years ago

10.2196/23369

Engagement With a Behavior Change App for Alcohol Reduction: Data Visualization for Longitudinal Observational Study
Cited by: 16
Author(s): Lauren N. Bell, Claire Garnett, Tianchen Qian, Olga Perski, Elizabeth Williamson, Henry W W Potts
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.9697

Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
Cited by: 2
Author(s): Karin Hirose, Yasuhiro Ishiga, Takashi Fujikawa
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2020.559035

Zika Virus Infection Results in Biochemical Changes Associated With RNA Editing, Inflammatory and Antiviral Responses in Aedes albopictus
Cited by: 6
Author(s): Maria G Onyango, Geoffrey M. Attardo, Erin Taylor Kelly, Sean M. Bialosuknia, Jessica Stout, Elyse Banker, Lili Kuo, Alexander T. Ciota, Laura D. Kramer
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0236200

Shelter use interactions of invasive lionfish with commercially and ecologically important native invertebrates on Caribbean coral reefs
Cited by: 6
Author(s): Christina L. Hunt, Dominic A. Andradi‐Brown, Callum J. Hudson, Joshua Bennett-Williams, Frankie Noades, Jocelyn Curtis-Quick, Owen T. Lewis, Dan A. Exton
Software Mentions: 6
Published: over 4 years ago

10.1186/s12885-020-07438-4

A 38-gene model comprised of key TET2-associated genes shows additive utility to high-risk prostate cancer cases in the prognostication of biochemical recurrence
Cited by: 1
Author(s): Shivani Kamdar, Neil Fleshner, Bharati Bapat
Software Mentions: 6
Published: about 4 years ago

10.1098/rstb.2020.0366

Phanerozoic parasitism and marine metazoan diversity: dilution versus amplification
Cited by: 16
Author(s): Kenneth De Baets, John Warren Huntley, Daniele Scarponi, Adiël A. Klompmaker, Aleksandra Skawina
Software Mentions: 6
Published: over 3 years ago

10.3390/cells8040343

The Petunia CHANEL Gene is a ZEITLUPE Ortholog Coordinating Growth and Scent Profiles
Cited by: 18
Author(s): Marta I. Terry, Fernando Pérez-Sánz, María Victoria Díaz-Galián, Felipe Pérez de los Cobos, Pedro J. Navarro, Marcos Egea‐Cortines, Julia Weiß
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers13040610

Comprehensive Epstein-Barr Virus Transcriptome by RNA-Sequencing in Angioimmunoblastic T Cell Lymphoma (AITL) and Other Lymphomas
Cited by: 17
Author(s): Nader Bayda, Valentin Tilloy, Alain Chaunavel, Racha Bahri, Mohamad Adnan Halabi, Jean Feuillard, Arnaud Jaccard, Sylvie Ranger-Rogez
Software Mentions: 5
Published: almost 4 years ago

10.1534/g3.119.400898

Interactively AUDIT Your Growth Curves with a Suite of R Packages
Cited by: 4
Author(s): Nicolas Coutin, Guri Giaever, Corey Nislow
Software Mentions: 5
Published: almost 5 years ago

10.1111/gcb.15548

Systemic effects of rising atmospheric vapor pressure deficit on plant physiology and productivity
Cited by: 74
Author(s): José R. López, Danielle A. Way, Walid Sadok
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-019-53975-9

Longitudinal study of the bacterial and fungal microbiota in the human sinuses reveals seasonal and annual changes in diversity
Cited by: 34
Author(s): Brett Wagner Mackenzie, Kevin Chang, Melissa Zoing, Ravi Jain, Michael Hoggard, Kristi Biswas, Richard Douglas, Michael W. Taylor
Software Mentions: 5
Published: about 5 years ago

10.1128/mBio.03551-20

The Termite Fungal Cultivar Termitomyces Combines Diverse Enzymes and Oxidative Reactions for Plant Biomass Conversion
Cited by: 13
Author(s): Felix Schalk, Cene Gostinčar, Nina B. Kreuzenbeck, Benjamin H. Conlon, Elisabeth Sommerwerk, Patrick Rabe, Immo Burkhardt, Thomas Krüger, Olaf Kniemeyer, Axel A. Brakhage, Nina Gunde‐Cimerman, Z. Wilhelm de Beer, Jeroen S. Dickschat, Michael Poulsen, Christine Beemelmanns
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.62529

Journal policies and editors’ opinions on peer review
Cited by: 24
Author(s): Daniel G Hamilton, Hannah Fraser, Rink Hoekstra, Fiona Fidler
Software Mentions: 5
Published: about 4 years ago

10.3390/microorganisms9071411

Enterocin Cross-Resistance Mediated by ABC Transport Systems
Cited by: 4
Author(s): Claudia Teso-Pérez, Manuel Martínez‐Bueno, Juan Manuel Peralta‐Sánchez, Eva Valdivia, Mercedes Maqueda, María Esther Fárez-Vidal, Antonio Manuel Martín-Platero
Software Mentions: 4
Published: over 3 years ago

10.1093/molbev/msaa328

Fast and Robust Identity-by-Descent Inference with the Templated Positional Burrows–Wheeler Transform
Cited by: 19
Author(s): William A. Freyman, Kimberly F. McManus, Suyash Shringarpure, Ethan M. Jewett, Katarzyna Bryc, Adam Auton
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13148-021-01153-y

Betamethasone administration during pregnancy is associated with placental epigenetic changes with implications for inflammation
Cited by: 9
Author(s): Darina Czamara, Linda Dieckmann, Simone Röh, Sarah Kraemer, Rebecca C. Rancourt, Sara Sammallahti, Eero Kajantie, Hannele Laivuori, Johan G. Eriksson, Katri Räikkönen, Wolfgang Henrich, Andreas Plagemann, Elisabeth B. Binder, Thorsten Braun, Sonja Entringer
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2020.00267

Metatranscriptomic Insights Into the Response of River Biofilm Communities to Ionic and Nano-Zinc Oxide Exposures
Cited by: 8
Author(s): Jordyn Bergsveinson, James W. Roy, Christine Maynard, Sylvie Sanschagrin, Claire N. Freeman, G. D. W. Swerhone, James J. Dynes, Julien Tremblay, Charles W. Greer, Darren R. Korber, John R. Lawrence
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2021.625400

Rumen Epithelial Communities Share a Core Bacterial Microbiota: A Meta-Analysis of 16S rRNA Gene Illumina MiSeq Sequencing Datasets
Cited by: 22
Author(s): Chiron J Anderson, Lucas R Koester, Stephan Schmitz‐Esser
Software Mentions: 4
Published: almost 4 years ago

10.1007/s00384-021-03944-4

Pilonidal sinus disease on the rise: a one-third incidence increase in inpatients in 13 years with substantial regional variation in Germany
Cited by: 17
Author(s): Christina Oetzmann von Sochaczewski, Jan Gödeke
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-019-2890-6

Detection and visualization of communities in mass spectrometry imaging data
Cited by: 16
Author(s): Karsten Wüllems, Jan Kölling, Hanna Bednarz, Karsten Niehaus, Volkmar Hans, Tim Wilhelm Nattkemper
Software Mentions: 3
Published: over 5 years ago

10.17691/stm2020.12.2.11

Correlation of Lipid Profile and Glycated Hemoglobin as a New Prognostic Criterion for Type 2 Diabetes Mellitus Development and Progression
Cited by: 1
Author(s): Е. А. Загребин, Е. А. Шевченко, E. Yu. Ivanchenko, V.I. Uspensky, S.R. Abasnia, А. В. Кочеткова, Olga Uspenskaya, A. R. Vaysberg
Software Mentions: 2
Published: over 4 years ago

10.1534/g3.118.200123

Loci That Control Nonlinear, Interdependent Responses to Combinations of Drought and Nitrogen Limitation
Cited by: 1
Author(s): Megan Chang, Danielle Allery Nail, Toni Kazic, Susan J. Simmons, Ann E. Stapleton
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.59954

Drift and termination of spiral waves in optogenetically modified cardiac tissue at sub-threshold illumination
Cited by: 30
Author(s): Sayedeh Hussaini, Vishalini Venkatesan, Valentina Biasci, José Miguel Romero Sepúlveda, Raul A Quiñonez Uribe, Leonardo Sacconi, Gil Bub, Claudia Richter, Valentin Krinski, Ulrich Parlitz, Rupamanjari Majumder, Stefan Luther
Software Mentions: 2
Published: almost 4 years ago

10.3390/cells10040840

NF-κB and TNF Affect the Astrocytic Differentiation from Neural Stem Cells
Cited by: 7
Author(s): Cindy Birck, Aurélien Ginolhac, Maria Angeliki S. Pavlou, Alessandro Michelucci, Paul Heuschling, Luc Grandbarbe
Software Mentions: 2
Published: over 3 years ago

Projects: cran: viridis

Papers Mentioning viridis 92