Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: grid
https://packages.ecosyste.ms/registries/pypi.org/packages/grid
Volumetric data module
28 versions
Latest release: over 10 years ago
426 downloads last month
Papers Mentioning grid 137
10.1371/journal.pone.0251194
A computational reproducibility study of PLOS ONE articles featuring longitudinal data analysesCited by: 15
Author(s): Heidi Seibold, Severin Czerny, Siona Decke, Roman Dieterle, Thomas Eder, Steffen Fohr, Nico Hahn, Rabea Hartmann, Christoph Heindl, Philipp Kopper, Dario Lepke, Verena Loidl, Maximilian Mandl, Sarah Musiol, Jessica Peter, Alexander Piehler, Elio Rojas, Stefanie Schmid, Hannah Schmidt, Melissa Schmoll, Lennart Schneider, Xiao-Yin To, Viêt Anh Tran, Antje Völker, Moritz Wagner, Joshua Wagner, Maria Waize, Hannah Wecker, Rui Yang, Simone Zellner, Malte Nalenz
Software Mentions: 46
Published: over 3 years ago
10.1038/s41598-020-76683-1
Revisiting potential associations between brain morphology, fear acquisition and extinction through new data and a literature reviewCited by: 7
Author(s): Mana R. Ehlers, Janne Nold, Manuel Kuhn, Maren Klingelhöfer-Jens, Tina B. Lonsdorf
Software Mentions: 44
Published: almost 4 years ago
10.1038/s41598-019-54004-5
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolatesCited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago
10.1016/j.cell.2019.07.038
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thalianaCited 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
10.3389/fvets.2020.547181
Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in QuébecCited by: 9
Author(s): Catherine Turcotte, Alexandre Thibodeau, Sylvain Quessy, Edward Topp, Guy Beauchamp, Philippe Fravalo, Marie Archambault, Marie-Lou Gaucher
Software Mentions: 23
Published: almost 4 years ago
10.1155/2021/8020879
Novel lncRNA Panel as for Prognosis in Esophageal Squamous Cell Carcinoma Based on ceRNA Network MechanismCited by: 10
Author(s): Jin Zhang, Fei Xiao, Guangliang Qiang, Zhenrong Zhang, Qianli Ma, Hao Yang, H. Rosie Xing, Chaoyang Liang
Software Mentions: 22
Published: about 3 years ago
10.3390/cells8091045
Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate UptakeCited by: 12
Author(s): Fabian Kern, Nicole Ludwig, Christina Backes, Esther Maldener, Tobias Fehlmann, Artur Suleymanov, Eckart Meese, Anne Hecksteden, Andreas Keller, Tim Meyer
Software Mentions: 21
Published: about 5 years ago
10.1038/s41598-019-55469-0
Minor compositional alterations in faecal microbiota after five weeks and five months storage at room temperature on filter papersCited by: 6
Author(s): Sebastian von Huth, Louise B. Thingholm, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 20
Published: almost 5 years ago
10.7717/peerj.2836
Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene ampliconsCited by: 273
Author(s): Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel
Software Mentions: 20
Published: almost 8 years ago
10.1155/2020/5418364
A Nomogram Based on Radiomics with Mammography Texture Analysis for the Prognostic Prediction in Patients with Triple-Negative Breast CancerCited by: 9
Author(s): Xian Jiang, Xiuhe Zou, Jing Sun, Aiping Zheng, Chao Su
Software Mentions: 20
Published: about 4 years ago
10.1371/journal.pntd.0005121
Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable ControlCited by: 20
Author(s): Christina Sunyoung Kim, Pierre Echaubard, Apiporn Suwannatrai, Sasithorn Kaewkes, Bruce A. Wilcox, Banchob Sripa
Software Mentions: 19
Published: almost 8 years ago
10.1093/gigascience/giaa010
Interpretable and accurate prediction models for metagenomics dataCited by: 29
Author(s): Edi Prifti, Yann Chevaleyre, Blaise Hanczar, Eugeni Belda, Antoine Danchin, Karine Clément, Jean-Daniel Zucker
Software Mentions: 18
Published: over 4 years ago
10.1371/journal.pone.0232822
SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populationsCited by: 5
Author(s): Paul M. Regular, Gregory J. Robertson, Keith P. Lewis, Jonathan Babyn, Brian Healey, Fran Mowbray
Software Mentions: 17
Published: over 4 years ago
10.1038/s41597-019-0171-x
A multi-omics digital research object for the genetics of sleep regulationCited by: 8
Author(s): Jan M, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios
Software Mentions: 17
Published: about 5 years ago
10.1038/s41419-021-03909-z
Diagnostic and prognostic potential of the proteomic profiling of serum-derived extracellular vesicles in prostate cancerCited by: 14
Author(s): Michele Signore, Romina Alfonsi, Giulia Federici, Simona Nanni, Antonio Addario, Lucia Bertuccini, Aurora Aiello, Anna Pace, Isabella Sperduti, Giovanni Muto, Alessandro Giacobbe, Devis Collura, Lidia Brunetto, Giuseppe Simone, Manuela Costantini, Lucio Crinò, Stefania Rossi, Claudio Tabolacci, Marco Diociaiuti, Tania Merlino, Michele Gallucci, Steno Sentinelli, Rocco Papalia, Ruggero De Maria, Dèsirèe Bonci
Software Mentions: 16
Published: over 3 years ago
10.1371/journal.pntd.0009232
Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-BissauCited by: 8
Author(s): Sebastian von Huth, Louise B. Thingholm, Poul Erik Kofoed, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 15
Published: over 3 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 adultsCited 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: over 3 years ago
10.3390/biom10081095
Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo SimulationsCited by: 26
Author(s): Joel Markgren, Mikael S. Hedenqvist, Faiza Rasheed, Marie Skepö, Eva Johansson
Software Mentions: 15
Published: over 4 years ago
10.3389/fimmu.2021.668391
A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade GliomaCited by: 21
Author(s): Yuhan Sun, Alexander James Sedgwick, Yaseelan Palarasah, Stefano Mangiola, Alexander D. Barrow
Software Mentions: 15
Published: about 3 years ago
10.3390/microorganisms9051050
Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianumCited by: 5
Author(s): Jing Zhu, Xiang Sun, Zhidong Zhang, Qi-Yong Tang, Minghong Gu, Lijuan Zhang, Min Hou, Amir Sharon, Hongli Yuan
Software Mentions: 15
Published: over 3 years ago
10.1038/s41598-019-46510-3
Differential prognostic impact of platelet-derived growth factor receptor expression in NSCLCCited by: 19
Author(s): Thomas K. Kilvaer, Mehrdad Rakaee, Turid Hellevik, Jørg Vik, Luigi De Petris, Tom Dønnem, Carina Strell, Arne Östman, Lill-Tove Busund, Iñigo Martínez-Zubiaurre
Software Mentions: 15
Published: over 5 years ago
10.3389/fonc.2020.573295
Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal CancerCited by: 11
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Zheng Liu, Qian Liu
Software Mentions: 14
Published: about 4 years ago
10.1371/journal.pgen.1008405
Causal relationships between obesity and the leading causes of death in women and menCited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: about 5 years ago
10.1099/mgen.0.000225
Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogenyCited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: over 5 years ago
10.1002/ece3.5968
Contrasting responses to climate change at Himalayan treelines revealed by population demographics of two dominant speciesCited by: 23
Author(s): Kumar P. Mainali, Bharat Babu Shrestha, Ravi Kumar Sharma, Arjun Adhikari, Eliezer Gurarie, Michael C. Singer, Camille Parmesan
Software Mentions: 13
Published: almost 5 years ago
10.1186/s12859-020-03922-7
annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusionsCited by: 3
Author(s): Krutika S. Gaonkar, Fédérico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam Resnick, Konstantin Strauch, Jaclyn N. Taroni, Jo Lynne Rokita
Software Mentions: 13
Published: almost 4 years ago
10.1371/journal.pone.0178783
Pharmacokinetics of caspofungin acetate to guide optimal dosing in catsCited by: 8
Author(s): Jana Leshinsky, Andrew J. McLachlan, David J. R. Foster, Ross Norris, Vanessa R. Barrs
Software Mentions: 13
Published: over 7 years ago
10.1186/s12864-020-07204-7
Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow troutCited by: 5
Author(s): Pratima Chapagain, Donald M. Walker, Timothy D. Leeds, Beth M. Cleveland, Mohamed Salem
Software Mentions: 13
Published: almost 4 years ago
10.1186/s12864-019-5700-7
RiboStreamR: a web application for quality control, analysis, and visualization of Ribo-seq dataCited by: 14
Author(s): Patrick Perkins, Serina Mazzoni-Putman, Anna N. Stepanova, José M. Alonso, Steffen Heber
Software Mentions: 13
Published: over 5 years ago
10.1186/s13567-021-00981-3
Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogensCited by: 8
Author(s): Christine Weiße, Denise Dittmar, Beata Jakóbczak, Volker Florian, Nicole Schütze, Gottfried Alber, Kristin Klose, Stephan Michalik, Peter Valentin‐Weigand, Uwe Völker, Christoph Georg Baums
Software Mentions: 12
Published: about 3 years ago
10.1038/s41598-021-89066-x
Lagged recovery of fish spatial distributions following a cold-water perturbationCited by: 3
Author(s): Masumi Robertson, Gao Jin, Paul M. Regular, M. J. Morgan, Fan Zhang
Software Mentions: 12
Published: over 3 years ago
10.3389/fgene.2021.689159
Analyzing Roles of NUSAP1 From Clinical, Molecular Mechanism and Immune Perspectives in Hepatocellular CarcinomaCited by: 3
Author(s): Wenjie Zhu, Jian Xu, Zehao Chen, Jianxin Jiang
Software Mentions: 12
Published: over 3 years ago
10.1093/gigascience/giz088
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mappingCited by: 5
Author(s): Luis Francisco Hernández Sánchez, Bram Burger, Carlos Horro, Antonio Fabregat, Stefan Johansson, Pål Rasmus Njølstad, Harald Barsnes, Henning Hermjakob, Marc Vaudel
Software Mentions: 12
Published: over 5 years ago
10.1371/journal.pone.0251323
The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databasesCited by: 2
Author(s): Weijun Shi, Xincan Li, Shuai Xu, Hexin Wen, Tianwen Chen, Huazhang Wu, Mulin Liu
Software Mentions: 12
Published: about 3 years ago
10.1371/journal.pone.0188079
Episodic future thinking reduces temporal discounting in healthy adolescentsCited by: 35
Author(s): Uli Bromberg, Maria Lobatcheva, Jan Peters
Software Mentions: 11
Published: almost 7 years ago
10.1371/journal.pone.0133625
Sub-Classification of Lateral Cervical Lymph Node Metastasis in Papillary Thyroid Carcinoma by Pathologic CriteriaCited by: 11
Author(s): Min Ji Jeon, Won Gu Kim, Eun Kyung Jang, Yun Mi Choi, Dong Eun Song, Tae‐Yon Sung, Jong Ho Yoon, Ki-Wook Chung, Suck Joon Hong, Jin‐Sook Ryu, Ji Min Han, Tae Yong Kim, Young Kee Shong
Software Mentions: 11
Published: over 9 years ago
10.1093/rheumatology/keaa615
Changes in the illness perceptions of patients with rheumatoid arthritis over the first year of methotrexate therapyCited by: 7
Author(s): James M Gwinnutt, Sam Norton, Kimme L Hyrich, Mark Lunt, Anne Barton, Lis Cordingley, Suzanne Verstappen, Rams co-investigators
Software Mentions: 11
Published: almost 4 years ago
10.3390/ijms19030742
Effect of Presence and Concentration of Plasticizers, Vegetable Oils, and Surfactants on the Properties of Sodium-Alginate-Based Edible CoatingsCited by: 48
Author(s): Tugce Sentürk Parreidt, Michael Schott, Markus Schmid, Kajetan Müller
Software Mentions: 11
Published: over 6 years ago
10.3389/fmicb.2018.02301
Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding ApproachCited by: 38
Author(s): Wen Chen, Graham Wilkes, Izhar U. H. Khan, Katarina Pintar, Joseph P. Thomas, C. André Lévesque, Julie T. Chapados, Edward Topp, David R. Lapen
Software Mentions: 11
Published: about 6 years ago
10.1016/j.eclinm.2021.101118
Unraveling the concepts of distress, burnout, and depression in type 1 diabetes: A scoping reviewCited by: 9
Author(s): Dona A. Kiriella, Sumaiya Islam, Olutobi Oridota, Nancy Sohler, Coralie Dessenne, Carine de Beaufort, Guy Fagherazzi, Gloria Aguayo
Software Mentions: 11
Published: about 3 years ago
10.1007/s11306-016-1090-x
Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysisCited by: 6
Author(s): Elisabete Carvalho, Pietro Franceschi, Antje Feller, Lorena Herrera, L. Palmieri, Panagiotis Arapitsas, Samantha Riccadonna, Stefan Martens
Software Mentions: 11
Published: over 8 years ago
10.7554/eLife.49064
Stepwise polarisation of developing bilayered epidermis is mediated by aPKC and E-cadherin in zebrafishCited by: 10
Author(s): Prateek Arora, Shivali Dongre, Renuka Raman, Mahendra Sonawane
Software Mentions: 11
Published: almost 5 years ago
10.7717/peerj.10680
Homologous recombination repair rathway and RAD54L in early-stage lung adenocarcinomaCited by: 5
Author(s): Shaoyong Zheng, Lan Yao, Fasheng Li, Luyu Huang, Yunfang Yu, Zenan Lin, Hao Li, Xiance Jin, Michael Lanuti, Haiyu Zhou
Software Mentions: 11
Published: over 3 years ago
10.3390/pharmaceutics13060868
Surfactant-Assisted Distal Pulmonary Distribution of Budesonide Revealed by Mass Spectrometry ImagingCited by: 0
Author(s): Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Barbara Pioselli, Valentina Mileo, Xabier Murgia, Fabrizio Salomone, Giuseppe Pieraccini, Haruo Usada, Augusto F. Schmidt, Noah H. Hillman, Matthew W. Kemp, Alan H. Jobe
Software Mentions: 11
Published: over 3 years ago
10.1371/journal.pbio.3000595
A role for triglyceride lipase brummer in the regulation of sex differences in Drosophila fat storage and breakdownCited by: 69
Author(s): Lianna W Wat, Charlotte Chao, Rachael Bartlett, Justin Buchanan, Jason W Millington, Hui Ju Chih, Zahid Sadek Chowdhury, Puja Biswas, Vivian Huang, Leah J Shin, Lin Chuan Wang, Marie-Pierre Gauthier, Maria Cecilia Barone, Kristi L. Montooth, Michael A. Welte, Elizabeth J. Rideout
Software Mentions: 11
Published: almost 5 years ago
10.1371/journal.pone.0220961
Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count dataCited by: 4
Author(s): Amanda H. Pendegraft, Boyi Guo, Nengjun Yi
Software Mentions: 11
Published: about 5 years ago
10.1371/journal.pone.0235283
Targeting the oral plaque microbiome with immobilized anti-biofilm peptides at tooth-restoration interfacesCited by: 18
Author(s): Dina G. Moussa, Conrado Aparicio
Software Mentions: 11
Published: over 4 years ago
10.1371/journal.pone.0256694
Factors contributing to farm-level productivity and household income generation in coastal Bangladesh’s rice-based farming systemsCited by: 18
Author(s): Shah Al Emran, Timothy J. Krupnik, Sreejith Aravindakshan, Virender Kumar, Cameron M. Pittelkow
Software Mentions: 11
Published: about 3 years ago
10.1093/aje/kwaa127
Conditional Cash Transfer Program and Leprosy Incidence: Analysis of 12.9 Million Families From the 100 Million Brazilian CohortCited by: 15
Author(s): Júlia Moreira Pescarini, Elizabeth Williamson, Maria Yury Ichihara, Rosemeire Leovigildo Fiaccone, Laura Forastiere, Anna Ramond, Joilda Silva Nery, Maria Lúcia Fernandes Penna, Agostino Strina, Sandra Reis, Liam Smeeth, Laura C. Rodrigues, Elizabeth B Brickley, Gerson Oliveira Penna, Marcos Barreto
Software Mentions: 10
Published: over 4 years ago
10.1186/s12918-015-0169-8
Increased robustness of early embryogenesis through collective decision-making by key transcription factorsCited by: 8
Author(s): Ali Sharifi-Zarchi, Mehdi Totonchi, Keynoush Khaloughi, Razieh Karamzadeh, Marcos J. Araúzo-Bravo, Hossein Baharvand, Ruzbeh Tusserkani, Hamid Pezeshk, Hamidreza Chitsaz, Mehdi Sadeghi
Software Mentions: 10
Published: over 9 years ago
10.1186/s40168-019-0647-0
Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soilsCited by: 218
Author(s): Zhi Bo Zhao, Ji Zheng He, Stefan Geisen, Han Long, Jun Tao Wang, Ju-Pei Shen, Wen Jun Wei, Yun Fang, Pei Pei Li, Limei Zhang
Software Mentions: 10
Published: over 5 years ago
10.7717/peerj.10421
Loss of HOXB3 correlates with the development of hormone receptor negative breast cancerCited by: 6
Author(s): Lizhe Zhu, Shibo Yu, Siyuan Jiang, Ge Gao, Yan Yu, Yong Jin Zhou, Ligang Niu, Jing He, Yu Ren, Bin Wang
Software Mentions: 10
Published: almost 4 years ago
10.1371/journal.pone.0114749
FindFoci: A Focus Detection Algorithm with Automated Parameter Training That Closely Matches Human Assignments, Reduces Human Inconsistencies and Increases Speed of AnalysisCited by: 88
Author(s): Alex Herbert, Antony Carr, Eva R. Hoffmann
Software Mentions: 10
Published: almost 10 years ago
10.1007/s00228-020-03052-2
Potentially inappropriate prescribing in older hospitalized Dutch patients according to the STOPP/START criteria v2: a longitudinal studyCited by: 9
Author(s): Birgit A. Damoiseaux-Volman, Stephanie Medlock, Kimmy Raven, Danielle Sent, Johannes A. Romijn, Nathalie van der Velde, Ameen Abu‐Hanna
Software Mentions: 10
Published: almost 4 years ago
10.3389/fimmu.2016.00372
SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell TranscriptsCited by: 52
Author(s): Chaim A. Schramm, Zizhang Sheng, Zhenhai Zhang, John R. Mascola, Peter D. Kwong, Lawrence Shapiro
Software Mentions: 10
Published: about 8 years ago
10.3389/fmicb.2021.642543
Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking ParasitesCited by: 6
Author(s): Jorge Doña, Stephany Virrueta Herrera, Tommi Nyman, Mervi Kunnasranta, Kevin P. Johnson
Software Mentions: 10
Published: over 3 years ago
10.3389/fmicb.2020.00037
FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome AssembliesCited by: 164
Author(s): Arkadiy I. Garber, Kenneth H. Nealson, Akimitsu Okamoto, Sean M. McAllister, Clara S. Chan, Roman A. Barco, Nancy Merino
Software Mentions: 10
Published: almost 5 years ago
10.3389/fmicb.2020.01190
Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in MilkCited by: 14
Author(s): Christopher Maier, Christopher Huptas, Mario von Neubeck, Stephen W. Scherer, Mareike Wenning, Genia Lücking
Software Mentions: 10
Published: over 4 years ago
10.1038/s41598-021-84545-7
Quantitative molecular detection of larval Atlantic herring (Clupea harengus) in stomach contents of Atlantic mackerel (Scomber scombrus) marks regions of predation pressureCited by: 11
Author(s): Bridie J. M. Allan, Jessica L. Ray, Maik Tiedemann, Valeriya Komyakova, Frode Vikebø, Katrine Sandnes Skaar, Martina Stiasny, Arild Folkvord, Richard Nash, Erling Kåre Stenevik, Olav Sigurd Kjesbu
Software Mentions: 10
Published: over 3 years ago
10.3390/ijerph17103383
Bivariate Spatial Pattern between Smoking Prevalence and Lung Cancer Screening in US CountiesCited by: 9
Author(s): Bian Liu, Jeremy Sze, Lihua Li, Katherine Ornstein, Emanuela Taioli
Software Mentions: 10
Published: over 4 years ago
10.1073/pnas.2100542118
Self-mediated positive selection of T cells sets an obstacle to the recognition of nonselfCited by: 9
Author(s): Balázs Koncz, Gergő Mihály Balogh, Benjamin Tamás Papp, Leó Asztalos, Lajos Kemény, Máté Manczinger
Software Mentions: 9
Published: about 3 years ago
10.1371/journal.ppat.1009577
Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCFCited by: 11
Author(s): Xiaogang Cheng, Ancy Joseph, Victor Castro, Alice Chen-Liaw, Zachary L. Skidmore, Takaharu Ueno, Jun–ichi Fujisawa, Daniel A. Rauch, Grant A. Challen, Michael P. Martinez, Patrick Green, Malachi Griffith, Jacqueline E. Payton, John Edwards, Lee Ratner
Software Mentions: 9
Published: over 3 years ago
10.1371/journal.pone.0192157
Tissue analyses reveal a potential immune-adjuvant function of FAP-1 positive fibroblasts in non-small cell lung cancerCited by: 30
Author(s): Thomas K. Kilvaer, Mehrdad Rakaee, Turid Hellevik, Arne Östman, Carina Strell, Roy M. Bremnes, Lill-Tove Busund, Tom Dønnem, Iñigo Martínez-Zubiaurre
Software Mentions: 9
Published: almost 7 years ago
10.1371/journal.pmed.1002362
Childhood adiposity and risk of type 1 diabetes: A Mendelian randomization studyCited by: 86
Author(s): Jenny C Censin, Christoph Nowak, Nicholas Cooper, Peter Bergsten, John A. Todd, Tove Fall
Software Mentions: 9
Published: over 7 years ago
10.1128/mSphere.00097-18
Influential Parameters for the Analysis of Intracellular Parasite MetabolomicsCited by: 11
Author(s): Maureen A. Carey, Vincent Covelli, Audrey C. Brown, Gregory L. Medlock, Mareike Haaren, Jessica G. Cooper, Jason A. Papin, Jennifer L. Guler
Software Mentions: 9
Published: over 6 years ago
10.1186/s12967-021-02770-0
Hypermethylation of heparanase 2 promotes colorectal cancer proliferation and is associated with poor prognosisCited by: 9
Author(s): Hui Zhang, Chang Xu, Shi Chen, Junying Zhang, Ting Qian, Zhuo Wang, Rong Ma, Jianzhong Wu, Feng Jiang, Jifeng Feng
Software Mentions: 9
Published: over 3 years ago
10.1186/s12859-017-1651-7
Zipper plot: visualizing transcriptional activity of genomic regionsCited by: 5
Author(s): Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter, Pieter Mestdagh
Software Mentions: 9
Published: over 7 years ago
10.1177/1179546820951793
Carotid Plaque Morphology is Similar in Patients with Reduced and Normal Renal FunctionCited by: 1
Author(s): Caroline Heijl, Fredrik Kahn, Andreas Edsfeldt, Christoffer Tengryd, Jan Nilsson, Isabel Gonçalves
Software Mentions: 9
Published: almost 5 years ago
10.1038/srep08508
No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controlsCited by: 64
Author(s): Aldona Dlugosz, Björn Winckler, E. Lundin, Katherina Zakikhany, Gunnar Sandström, Weimin Ye, Lars Engstrand, Greger Lindberg
Software Mentions: 9
Published: over 9 years ago
10.1371/journal.pone.0203346
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arraysCited by: 3
Author(s): Vinu José, Debora Fumagalli, Françoise Rothé, Samira Majjaj, Sherene Loi, Stefan Michiels, Christos Sotiriou
Software Mentions: 8
Published: about 6 years ago
10.7717/peerj.7816
CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosisCited by: 11
Author(s): Xuefeng Gu, Hongbo Li, Ling Sha, Man Yuan, Chao Shi, Wei Zhao
Software Mentions: 8
Published: about 5 years ago
10.1186/s13058-015-0550-y
Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune responseCited by: 223
Author(s): Pascal Jézéquel, Delphine Loussouarn, Catherine Guérin‐Charbonnel, Loı̈c Campion, Antoine Vanier, Wilfried Gouraud, Hamza Lasla, Catherine Guette, Isabelle Valo, Véronique Verrièle, Mario Campone
Software Mentions: 8
Published: over 9 years ago
10.3389/fonc.2021.625007
Comprehensive Analysis of the Functions and Prognostic Value of RNA-Binding Proteins in Thyroid CancerCited by: 7
Author(s): Yue Ma, Shi Yin, Xiaofeng Liu, Jing Hu, Ning Cai, Xiao-bei Zhang, Fu Li, Xuchen Cao, Yue Yu
Software Mentions: 8
Published: over 3 years ago
10.1080/16549716.2018.1440783
Health Equity Assessment Toolkit Plus (HEAT Plus): software for exploring and comparing health inequalities using uploaded datasetsCited by: 42
Author(s): Ahmad Reza Hosseinpoor, Anne Schlotheuber, Devaki Nambiar, Zev Ross
Software Mentions: 8
Published: over 6 years ago
10.1007/s00300-021-02823-6
Seasonal dynamics of meroplankton in a sub-Antarctic fjord (Southern Patagonia, Chile)Cited by: 1
Author(s): Santiago E A Pineda-Metz, Américo Montiel
Software Mentions: 8
Published: over 3 years ago
10.1093/rheumatology/keab060
Do people with rheumatoid arthritis maintain their physical activity level at treatment onset over the first year of methotrexate therapy?Cited by: 4
Author(s): James M Gwinnutt, Husain Alsafar, Kimme L Hyrich, Mark Lunt, Anne Barton, Suzanne Verstappen, Rams co-investigators
Software Mentions: 8
Published: over 3 years ago
10.1038/s41598-017-15742-6
Emergence of tick-borne diseases at northern latitudes in Europe: a comparative approachCited by: 43
Author(s): Atle Mysterud, Solveig Jore, Olav Østerås, Hildegunn Viljugrein
Software Mentions: 8
Published: almost 7 years ago
10.1038/s41598-019-44597-2
NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single moleculeCited by: 3
Author(s): Francisco Requena, Helena G Asenjo, Guillermo Barturen, Jordi Martorell-Marugán, Pedro Carmona-Sáez, David Landeira
Software Mentions: 8
Published: over 5 years ago
10.1186/s12863-020-00936-1
Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysisCited by: 7
Author(s): Heng Lin Yeap, Siu Fai Lee, Freya Robinson, Roslyn Mourant, J. A. Sved, Michael Frommer, Alexie Papanicolaou, Owain Edwards, John G. Oakeshott
Software Mentions: 8
Published: almost 4 years ago
10.1111/jcmm.15252
CA9 transcriptional expression determines prognosis and tumour grade in tongue squamous cell carcinoma patientsCited 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 4 years ago
10.1371/journal.pone.0216229
Effects of cropping, smoothing, triangle count, and mesh resolution on 6 dental topographic metricsCited by: 23
Author(s): Michael A. Berthaume, Julia M. Winchester, Kornelius Kupczik
Software Mentions: 7
Published: over 5 years ago
10.3390/jcm8081128
NEWS2 is Superior to qSOFA in Detecting Sepsis with Organ Dysfunction in the Emergency DepartmentCited by: 60
Author(s): Lisa Mellhammar, Adam Linder, Jonas Tverring, Bértil Christensson, John H. Boyd, Parham Sendi, Per Åkesson, Fredrik Kahn
Software Mentions: 7
Published: over 5 years ago
10.1186/1471-2334-14-539
The distribution of incubation and relapse times in experimental human infections with the malaria parasite Plasmodium vivaxCited by: 12
Author(s): Andrew A. Lover, Xiahong Zhao, Gengfeng Zheng, Richard Coker, Alex R. Cook
Software Mentions: 7
Published: about 10 years ago
10.3389/fonc.2020.01591
An Ultrasound Radiomics Nomogram for Preoperative Prediction of Central Neck Lymph Node Metastasis in Papillary Thyroid CarcinomaCited by: 38
Author(s): Shichong Zhou, Tong‐Tong Liu, Jin Zhou, Yao Qi Huang, Yi Guo, Jinhua Yu, Yuan‐Yuan Wang, Cai Chang
Software Mentions: 7
Published: about 4 years ago
10.1038/s41598-021-88944-8
Association between ACE2 and TMPRSS2 nasopharyngeal expression and COVID-19 respiratory distressCited by: 29
Author(s): Átila Duque Rossi, João Locke Ferreira de Araújo, Tailah Bernardo de Almeida, Marcelo Ribeiro-Alves, Camila de Almeida Velozo, Jéssica Maciel de Almeida, Isabela de Carvalho Leitão, Sâmila Natiane Ferreira, Jéssica da Silva Oliveira, Hugo José Alves, Helena Toledo Scheid, Débora S. Faffe, Rafael Mello Galliez, Renata Eliane de Ávila, Gustavo Gomes Resende, Mauro Martins Teixeira, Alice Laschuk Herlinger, Aliny dos Santos Carvalho, André F. Santos, Anna Carla Pinto Castiñeiras, Bianca Isabelle Barreto Teixeira, Bianca Ortiz da Silva, Bruno Clarkson, Bruno Eduardo Dematté, Camila Nacif, Camille Victória Leal Correia de Silva, Carolina M. Voloch, Caroline Macedo Nascimento, Carolyne Lalucha Alves L. da Graça, Cássia Cristina Alves Gonçalves, Cíntia Policarpo, Diana Mariani, Ekaterini Simões Goudouri, Elaine Sobral da Costa, Elisangela Costa da Silva, Enrico Bruno Riscarolli, Érica Ramos dos Santos Nascimento, Fabio Hecht Castro Medeiros, Fábio L. Monteiro, Fernanda Nunes Santos, Fernando Luz de Castro, Filipe Romero Rebello Moreira, Francine Bittencourt Schiffler, Gabriela Bergiante Kraychete, Gabriele Silveira da Cunha, Gisely Novaes Borges da Cunha, Guilherme Sant’Anna de Lira, Gustavo Peixoto Duarte da Silva, Harrison James Westgarth, Helena D.’Anunciação de Oliveira, Helena Keito Toma, Huang Fang, Inês Corrêa Gonçalves, Ingrid Camelo da Silva, Isabela Labarba Carvalho de Almeida, Joissy Aprigio de Oliveira, Juliana Cazarin de Menezes, Juliana T.S. Fortuna, Karyne Ferreira Monteiro, Kíssyla Harley Della Pascôa França, Laura Zalcberg Renault, Lendel Correia da Costa, Leticia Averbug Correa, Liane de Jesus Ribeiro, Lídia Theodoro Boullosa, Liliane Tavares de Faria Cavalcante, Luana dos Santos Costa, Lucas Matos Millioni, Luciana Jesus da Costa, Luiza M. Higa, Marcela dos Santos Durães, Marcelo Amaral de Souza, Marcelo Calado de Paula Tôrres, Mariana Freire Campos, Mariana Quinto, Mariane Talon de Menezes, Marisa Souza Correia, Mateus Rodrigues de Queiroz, Matheus Augusto Calvano Cosentino, Mayla Gabryele Miranda de Melo, Mirela D’arc Ferreira da Costa, Pedro Paz, Raíssa Mirella dos Santos Cunha da Costa, Raquel Fernandes Coelho, Richard Araujo Maia, Rodrigo de Moraes Brindeiro, Romina Carvalho Ferreira, Sérgio Machado Lisboa, Thamiris dos Santos Miranda, Victor Akira Ota, Victoria Cortes Bastos, Viviane Guimarães Gomes, Orlando da Costa Ferreira Júnior, Terezinha Marta Pereira Pinto Castiñeiras, Renan Pedra de Souza, Amílcar Tanuri, Renato Santana Aguiar, Shana Priscila Coutinho Barroso, Cynthia Chester Cardoso
Software Mentions: 7
Published: over 3 years ago
10.1186/s13059-015-0831-x
HiC-Pro: an optimized and flexible pipeline for Hi-C data processingCited 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
10.7717/peerj.5727
An automated, high-throughput method for standardizing image color profiles to improve image-based plant phenotypingCited by: 30
Author(s): Jeffrey C. Berry, Noah Fahlgren, Alexandria A Pokorny, Rebecca Bart, Kira M. Veley
Software Mentions: 7
Published: about 6 years ago
10.3390/foods8060203
The Development of a Uniform Alginate-Based Coating for Cantaloupe and Strawberries and the Characterization of Water Barrier PropertiesCited by: 29
Author(s): Tugce Sentürk Parreidt, Martina Lindner, Isabell Rothkopf, Markus Schmid, Kajetan Müller
Software Mentions: 7
Published: over 5 years ago
10.3390/biomedicines9020206
Zoom in on Antibody Aggregates: A Potential Pitfall in the Search of Rare EV PopulationsCited by: 1
Author(s): Rikke Wehner Rasmussen, Jaco Botha, Frederik Prip, Mathilde Sanden, Mads Nielsen, Aase Handberg
Software Mentions: 6
Published: over 3 years ago
10.1186/s13567-016-0374-5
Identification of epitopes recognised by mucosal CD4+ T-cell populations from cattle experimentally colonised with Escherichia coli O157:H7Cited by: 7
Author(s): Alexander Corbishley, Timothy Connelley, E Wolfson, Keith T. Ballingall, Amy Elizabeth Beckett, David L. Gally, Tom N. McNeilly
Software Mentions: 6
Published: about 8 years ago
10.1080/19490976.2021.1900995
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatmentCited by: 21
Author(s): Kang Kang, Lejla Imamovic, Maria-Anna Misiakou, Maria Bornakke Sørensen, Yoshitaro Heshiki, Yueqiong Ni, Tingting Zheng, Jun Li, Mostafa Mostafa Hashim Ellabaan, Marta Colomer-Lluch, Anne A Rode, Peter Bytzer, Gianni Panagiotou, Morten Otto Alexander Sommer
Software Mentions: 6
Published: almost 4 years ago
10.3389/fmicb.2018.02681
Ice Nucleation Activity and Aeolian Dispersal Success in Airborne and Aquatic MicroalgaeCited by: 36
Author(s): Sylvie V. M. Tesson, Tina Šantl-Temkiv
Software Mentions: 6
Published: almost 6 years ago
10.1186/s12920-019-0571-y
Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in gliomaCited by: 4
Author(s): Yuan Yin, Bo Li, Ke‐Jie Mou, Muhammad Tahir Khan, Aman Chandra Kaushik, Dong‐Qing Wei, Yujuan Zhang
Software Mentions: 6
Published: about 5 years ago
10.3390/biomedicines9020124
Conventional, High-Resolution and Imaging Flow Cytometry: Benchmarking Performance in Characterisation of Extracellular VesiclesCited by: 18
Author(s): Jaco Botha, Haley R. Pugsley, Aase Handberg
Software Mentions: 6
Published: almost 4 years ago
10.7717/peerj.2452
Canopy position has a profound effect on soybean seed compositionCited by: 27
Author(s): Steven C. Huber, Kunzhi Li, Randall L. Nelson, Alexander Ulanov, Catherine M. DeMuro, Ivan Baxter
Software Mentions: 6
Published: about 8 years ago
10.1371/journal.pone.0192834
Thermal physiology of Amazonian lizards (Reptilia: Squamata)Cited by: 27
Author(s): Luisa Maria Diele‐Viegas, Laurie J. Vitt, Barry Sinervo, Guarino Rinaldi Colli, Fernanda P. Werneck, Donald B. Miles, William E. Magnusson, Juan Carlos Santos, Carla M. Sette, Gabriel Henrique de Oliveira Caetano, Emerson Guedes Pontes, Teresa Cristina Sauer Ávila-Pires
Software Mentions: 6
Published: over 6 years ago
10.1038/s41598-020-70206-8
Remote, autonomous real-time monitoring of environmental DNA from commercial fishCited by: 28
Author(s): Brian Klitgaard Hansen, Marianne Jacobsen, Anne Lise Middelboe, Christina M. Preston, Roman Marin, Dorte Bekkevold, Steen Wilhelm Knudsen, Peter Rask Møller, Einar Eg Nielsen
Software Mentions: 5
Published: over 4 years ago
10.1186/s12885-020-07689-1
Prognostic implications of alcohol dehydrogenases in hepatocellular carcinomaCited by: 25
Author(s): Xiangye Liu, Tingting Li, Delong Kong, Hua You, Fanyun Kong, Renxian Tang
Software Mentions: 5
Published: almost 4 years ago
10.1002/acn3.50873
Agreement of amyloid PET and CSF biomarkers for Alzheimer's disease on LumipulseCited by: 89
Author(s): Daniel Alcolea, Jordi Malé i Pegueroles, Laia Muñoz, Valle Camacho, Diego Alfonso López-Mora, Alejandro Fernández-León, Nathalie Le Bastard, Els Huyck, Alícia Nadal, Verónica Olmedo, Frederic Sampedro, Víctor Montal, Eduard Vilaplana, Jordi Clarimón, Rafael Blesa, Juan Fortea, Alberto Lleó
Software Mentions: 5
Published: about 5 years ago
10.1186/s12874-016-0229-9
Health Equity Assessment Toolkit (HEAT): software for exploring and comparing health inequalities in countriesCited by: 64
Author(s): Ahmad Reza Hosseinpoor, Devaki Nambiar, Anne Schlotheuber, Daniel D. Reidpath, Zev Ross
Software Mentions: 5
Published: about 8 years ago