cran: gtools | Projects | Ecosyste.ms: Papers

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: over 10 years ago

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: about 5 years ago

10.1037/rev0000169

Simultaneous consonance in music perception and composition.
Cited by: 47
Author(s): Peter M. C. Harrison, Marcus T. Pearce
Software Mentions: 23
Published: over 4 years ago

10.1093/molbev/msaa288

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: almost 4 years ago

10.3390/cancers13092163

Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma
Cited by: 10
Author(s): Ariane L. Moore, Aashil A. Batavia, Jack Kuipers, Jochen Singer, Elodie Burcklen, Peter Schraml, Christian Beisel, Holger Moch, Niko Beerenwinkel
Software Mentions: 20
Published: over 3 years ago

10.1186/s12859-019-3152-3

flowEMMi: an automated model-based clustering tool for microbial cytometric data
Cited by: 16
Author(s): Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller
Software Mentions: 18
Published: almost 5 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: over 4 years ago

10.1016/j.cell.2015.01.006

Enhancer Evolution across 20 Mammalian Species
Cited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: over 9 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: over 3 years ago

10.1371/journal.pone.0136452

Estimating Limit Reference Points for Western Pacific Leatherback Turtles (Dermochelys coriacea) in the U.S. West Coast EEZ
Cited by: 14
Author(s): K. Alexandra Curtis, Jeffrey E. Moore, Scott R. Benson
Software Mentions: 16
Published: about 9 years ago

10.1038/srep30325

In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells
Cited by: 72
Author(s): Joke Robijns, Freya Molenberghs, Tom Sieprath, Tobias Corne, Marlies Verschuuren, Winnok H. De Vos
Software Mentions: 14
Published: about 8 years ago

10.7554/eLife.61980

Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues
Cited by: 43
Author(s): Andrew W. DeVilbiss, Zhiyu Zhao, Misty S. Martin-Sandoval, Jessalyn M. Ubellacker, Alpaslan Tasdogan, Michalis Agathocleous, Thomas P. Mathews, Sean J. Morrison
Software Mentions: 13
Published: over 3 years ago

10.1186/s12920-015-0121-1

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities
Cited by: 52
Author(s): Eduardo Castro-Nallar, Ying Shen, Robert J. Freishtat, Marcos Pérez‐Losada, Solaiappan Manimaran, Gang Lv, W. Evan Johnson, Keith A. Crandall
Software Mentions: 12
Published: about 9 years ago

10.7717/peerj.1140

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls
Cited by: 190
Author(s): Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez‐Losada, Sarven Sabuncyan, Emily G. Severance, Faith Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall
Software Mentions: 11
Published: about 9 years ago

10.1371/journal.pone.0041169

Global Transcriptome Analysis in Influenza-Infected Mouse Lungs Reveals the Kinetics of Innate and Adaptive Host Immune Responses
Cited by: 93
Author(s): Claudia Pommerenke, Esther Wilk, Barkha Srivastava, Annika Schulze, Natalia Novoselova, Robert Geffers, Klaus Schughart
Software Mentions: 11
Published: about 12 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: almost 18 years ago

10.1038/s41598-019-46850-0

Deep Learning using Convolutional LSTM estimates Biological Age from Physical Activity
Cited by: 56
Author(s): Syed Ashiqur Rahman, Donald A. Adjeroh
Software Mentions: 11
Published: about 5 years ago

10.1002/ece3.5412

<i>learnPopGen</i> : An R package for population genetic simulation and numerical analysis
Cited by: 6
Author(s): Liam J. Revell
Software Mentions: 10
Published: about 5 years ago

10.1038/s41598-017-05505-8

Machine Learning Algorithms for Risk Prediction of Severe Hand-Foot-Mouth Disease in Children
Cited by: 15
Author(s): Bin Zhang, Xiang Wan, Fu Ouyang, Yu Dong, Dehui Luo, Jing Liu, Long Liang, Wen Bo Chen, Xiao Luo, Xiao Mo, Lu Zhang, Wen Hui Huang, Shu Fang Pei, Bao Liang Guo, Chun Liang, Long Zhou, Shui Xing Zhang
Software Mentions: 10
Published: about 7 years ago

10.1186/1472-6785-10-12

The world's richest tadpole communities show functional redundancy and low functional diversity: ecological data on Madagascar's stream-dwelling amphibian larvae
Cited by: 54
Author(s): Axel Strauß, Erik Reeve, Roger-Daniel Randrianiaina, Miguel Vences, Julian Glos
Software Mentions: 10
Published: over 14 years ago

10.3389/fimmu.2018.02074

Epigenetic Enhancer Marks and Transcription Factor Binding Influence Vκ Gene Rearrangement in Pre-B Cells and Pro-B Cells
Cited by: 13
Author(s): Eden Kleiman, Salvatore Loguercio, Ann J. Feeney
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-017-09382-z

New approaches to high-resolution mapping of marine vertical structures
Cited by: 43
Author(s): Katleen Robert, Veerle A.I. Huvenne, Aggeliki Georgiopoulou, Daniel O. B. Jones, Leigh Marsh, Gareth Carter, Leo Chaumillon
Software Mentions: 9
Published: about 7 years ago

10.1038/s41598-021-93699-3

Analysing omics data sets with weighted nodes networks (WNNets)
Cited by: 1
Author(s): Gabriele Tosadori, Dario Di Silvestre, Fausto Spoto, Pierluigi Mauri, Carlo Laudanna, Giovanni Scardoni
Software Mentions: 9
Published: about 3 years ago

10.1002/ece3.5466

Broodmate aggression and life history variation in accipitrid birds of prey
Cited by: 9
Author(s): Tomás Redondo, J.M. Latre Romero, Ricardo Dı́az-Delgado, Jenö Nagy
Software Mentions: 8
Published: about 5 years ago

10.1186/s12859-020-3538-2

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments
Cited by: 39
Author(s): H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens, Ryan M. O’Connell
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pmed.1003413

Body mass index and risk of dying from a bloodstream infection: A Mendelian randomization study
Cited by: 14
Author(s): Tormod Rogne, Erik Solligård, Stephen Burgess, Ben Brumpton, Julie Paulsen, Hallie C. Prescott, Randi Marie Mohus, Lise Tuset Gustad, Arne Mehl, Bjørn Olav Åsvold, Andrew T. DeWan, Jan Kristian Damås
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pntd.0006862

Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus
Cited by: 89
Author(s): Leah C. Katzelnick, Ana Coello Escoto, Benjamin D. McElvany, Christian Chávez, Henrik Salje, Wensheng Luo, Isabel Rodríguez-Barraquer, Richard G. Jarman, Anna P. Durbin, Sean A. Diehl, Derek J. Smith, Stephen S. Whitehead, Derek A. T. Cummings
Software Mentions: 8
Published: almost 6 years ago

10.1098/rspb.2017.0905

The evolution of dual meat and milk cattle husbandry in Linearbandkeramik societies
Cited by: 43
Author(s): Rosalind Gillis, Lenka Kovačíková, Stéphanie Bréhard, Émilie Guthmann, Ivana Vostrovská, Hana Nohálová, Rose‐Marie Arbogast, László Domboróczki, Joachim Pechtl, Alexander Anders, Arkadiusz Marciniak, Anne Tresset, Jean‐Denis Vigne
Software Mentions: 8
Published: about 7 years ago

10.1038/s41396-020-0622-6

Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes
Cited by: 35
Author(s): Bettina Glasl, Steven J. Robbins, Pedro R. Frade, Emma Marangon, Patrick W. Laffy, David G. Bourne, Nicole S. Webster
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0093742

Nest Grouping Patterns of Bonobos (Pan paniscus) in Relation to Fruit Availability in a Forest-Savannah Mosaic
Cited by: 90
Author(s): Adeline Serckx, Marie‐Claude Huynen, Jean-François Bastin, Alain Hambuckers, Roseline Beudels-Jamar, Marie Vimond, Emilien Raynaud, Hjalmar S. Kühl
Software Mentions: 7
Published: over 10 years ago

10.3897/CompCytogen.11(2).11395

The Cerrado (Brazil) plant cytogenetics database
Cited by: 6
Author(s): Fernando Roa, Mariana Pires de Campos Telles
Software Mentions: 7
Published: over 7 years ago

10.1186/s40425-018-0326-x

Measuring multiple parameters of CD8+ tumor-infiltrating lymphocytes in human cancers by image analysis
Cited by: 67
Author(s): Keith Steele, Tze Heng Tan, R Korn, Karma Dacosta, Charles O. Brown, Michael Kuziora, Johannes Zimmermann, Brian Laffin, Moritz Widmaier, Lorenz Rognoni, Rubén Cárdenes, Katrin Schneider, Anmarie Boutrin, Philip Martin, Jiping Zha, Tobias Wiestler
Software Mentions: 7
Published: over 6 years ago

10.1002/cti2.1127

High‐dimensional analyses reveal a distinct role of T‐cell subsets in the immune microenvironment of gastric cancer
Cited by: 18
Author(s): Minyu Wang, Yen-Yu Huang, Joseph C Kong, Yu Sun, Daniela Tantalo, Han Xian Aw Yeang, Le Ying, Feng Yan, Dakang Xu, Heloise M. Halse, Natasha Di Costanzo, Ian Gordon, Catherine Mitchell, Laura K. Mackay, Rita A. Busuttil, Paul J. Neeson, Alex Boussioutas
Software Mentions: 7
Published: over 4 years ago

10.1016/j.cell.2011.11.058

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Cited by: 504
Author(s): Dominic Schmidt, Petra Schwalie, Michael D. Wilson, Benoît Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Software Mentions: 6
Published: over 12 years ago

10.1371/journal.pbio.3001114

The plant metabolome guides fitness-relevant foraging decisions of a specialist herbivore
Cited by: 13
Author(s): Ricardo A. R. Machado, Vanitha Theepan, Christelle Robert, Tobias Züst, Lingfei Hu, Qi Su, Bernardus C. J. Schimmel, Matthias Erb
Software Mentions: 6
Published: over 3 years ago

10.3389/fpsyg.2020.00905

From Abstract Symbols to Emotional (In-)Sights: An Eye Tracking Study on the Effects of Emotional Vignettes and Pictures
Cited by: 5
Author(s): Franziska Usée, Arthur Jacobs, Jana Lüdtke
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0157033

Pattern Recognition on Read Positioning in Next Generation Sequencing
Cited by: 0
Author(s): Boseon Byeon, Igor Kovalchuk
Software Mentions: 6
Published: over 8 years ago

10.3389/fmicb.2020.571983

Large Enrichment of Anthropogenic Organic Matter Degrading Bacteria in the Sea-Surface Microlayer at Coastal Livingston Island (Antarctica)
Cited by: 12
Author(s): Alícia Martinez-Varela, Gemma Casas, Benjamı́n Piña, Jordi Dachs, Maria Vila‐Costa
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0102079

Harnessing Gene Expression Networks to Prioritize Candidate Epileptic Encephalopathy Genes
Cited by: 25
Author(s): Karen Oliver, Vesna Lukić, Natalie Thorne, Samuel F. Berkovic, Ingrid E. Scheffer, Melanie Bahlo
Software Mentions: 6
Published: about 10 years ago

10.1038/s41598-020-67897-4

New methodology to process shifted excitation Raman difference spectroscopy data: a case study of pollen classification
Cited by: 15
Author(s): Florian Korinth, Abdullah Saif Mondol, Clara Stiebing, Iwan W. Schie, Christoph Krafft, Jürgen Popp
Software Mentions: 5
Published: about 4 years ago

10.1186/1752-0509-8-56

Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
Cited by: 0
Author(s): Rosario M. Piro, Stefan Wiesberg, Gunnar Schramm, Nico Rebel, Marcus Oswald, Roland Eils, Gerhard Reinelt, Rainer König
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0256918

Using climatic variables alone overestimate climate change impacts on predicting distribution of an endemic species
Cited by: 8
Author(s): Somayeh Zangiabadi, Hassan Zare‐Maivan, LIuis Brotons, Hossein Mostafavi, Hojjatollah Ranjbar
Software Mentions: 5
Published: about 3 years ago

10.1186/s13073-020-00783-w

The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Cited by: 50
Author(s): Florent Petitprez, Sacha Lévy, Chengming Sun, Maxime Meylan, Christophe Linhard, Étienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catheriné Sautès-Fridman, Aurélien de Reyniès
Software Mentions: 5
Published: almost 4 years ago

10.1080/19490976.2020.1752605

Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome
Cited by: 20
Author(s): Tanya Monaghan, Tim J. Sloan, Stephen R. Stockdale, Adam Blanchard, Richard D. Emes, Mark H. Wilcox, Rima Biswas, Rupam Nashine, Sonali Manke, Jinal Gandhi, Pratishtha Jain, Shrejal Bhotmange, Shrikant Ambalkar, Ashish Satav, Lorraine A. Draper, Colin Hill, Rajpal S. Kashyap
Software Mentions: 5
Published: over 4 years ago

10.1038/srep45477

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data
Cited by: 69
Author(s): Saveria Mazzara, Riccardo L. Rossi, Renata Grifantini, Simone Donizetti, Sergio Abrignani, Mauro Bombaci
Software Mentions: 4
Published: over 7 years ago

10.1038/s41388-019-1047-4

Targeting chemoresistant colorectal cancer via systemic administration of a BMP7 variant
Cited by: 23
Author(s): Veronica Veschi, Laura Rosa Mangiapane, Antonietta Nicotra, Simone Di Franco, Emanuela Scavo, Tiziana Apuzzo, Davide Stefano Sardina, Micol Eleonora Fiori, Antonina Benfante, Maria Luisa Colorito, Gianfranco Cocorullo, Felice Giuliante, Calogero Cipolla, Giuseppe Pistone, Maria Rita Bongiorno, Aroldo Rizzo, Courtney M. Tate, Xiaohua Wu, Scott W. Rowlinson, Louis F. Stancato, Matilde Todaro, Ruggero De Maria, Giorgio Stassi
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0068678

Are High-Impact Species Predictable? An Analysis of Naturalised Grasses in Northern Australia
Cited by: 17
Author(s): Rieks D. van Klinken, F. D. Panetta, Shaun R. Coutts
Software Mentions: 4
Published: about 11 years ago

10.1186/s12874-020-01135-3

A Bayesian natural cubic B-spline varying coefficient method for non-ignorable dropout
Cited by: 0
Author(s): Camille M. Moore, Samantha MaWhinney, Nichole E. Carlson, Sarah M. Kreidler
Software Mentions: 4
Published: almost 4 years ago

10.1186/s40168-020-00986-8

Acquisition of oral microbiota is driven by environment, not host genetics
Cited by: 31
Author(s): Chiranjit Mukherjee, Christina O. Moyer, Heidi M. Steinkamp, Shahr B. Hashmi, Clifford J. Beall, Xiaohan Guo, Ai Ni, Eugene J. Leys, Ann L. Griffen
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.6917

Application of dynamic expansion tree for finding large network motifs in biological networks
Cited by: 6
Author(s): Sabyasachi Patra, Anjali Mohapatra
Software Mentions: 3
Published: over 5 years ago

10.3390/ph14010041

Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients
Cited by: 4
Author(s): Hana Votavová, Zuzana Urbanová, David Kundrát, Michaela Dostálová Merkerová, Martin Vostrý, Monika Hruba, Jaroslav Čermák, Monika Beličková
Software Mentions: 3
Published: over 3 years ago

10.1038/s41419-019-1851-3

A mechanism for increased sensitivity of acute myeloid leukemia to mitotoxic drugs
Cited by: 28
Author(s): Svetlana Panina, Natalia Baran, Fábio Henrique Brasil da Costa, Marina Konopleva, Natalia V. Kirienko
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0070603

Identification and Validation of Reference Genes for Transcript Normalization in Strawberry (Fragaria × ananassa) Defense Responses
Cited by: 72
Author(s): Francisco Amil-Ruíz, José Garrido-Gala, Rosario Blanco‐Portales, Kevin M. Folta, Juan Muñoz‐Blanco, José L. Caballero
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0083041

Reference Genes Selection for Quantitative Real-Time PCR Using RankAggreg Method in Different Tissues of Capra hircus
Cited by: 33
Author(s): Mohammad Javad Najafpanah, Mostafa Sadeghi, Mohammad Reza Bakhtiarizadeh
Software Mentions: 2
Published: almost 11 years ago

10.1038/s42003-020-01487-y

Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci
Cited by: 13
Author(s): Lvwen Ning, Josephine Mun‐Yee Ko, V. Y. H. Yu, Hoi Yan Ng, Candy King-Chi Chan, Lihua Tao, Shiu-Yeung Lam, Merrin Man-Long Leong, Roger K.C. Ngan, Dora Lai-Wan Kwong, Anne W.M. Lee, Wai‐Tong Ng, Ashley Cheng, Stewart Y. Tung, Victor Lee, Ka-On Lam, Chung-Kong Kwan, Wing-Sum Li, Stephen S.-T. Yau, Jin‐Xin Bei, Maria Li Lung
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0098129

A MLVA Genotyping Scheme for Global Surveillance of the Citrus Pathogen Xanthomonas citri pv. citri Suggests a Worldwide Geographical Expansion of a Single Genetic Lineage
Cited by: 59
Author(s): Olivier Pruvost, Maxime Magne, Karine Boyer, Alice Leduc, Christophe Tourterel, Christine Drevet, Virginie Ravigné, Lionel Gagnevin, Fabien Guérin, Frédéric Chiroleu, Ralf Koebnik, Valérie Verdier, Christian Vernière
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0145443

Social Preference in Preschoolers: Effects of Morphological Self-Similarity and Familiarity
Cited by: 14
Author(s): Nadja Richter, Bernard Tiddeman, Daniel B. M. Haun
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.10256

Genomic characterization and phylogenetic analysis of <i>Salmonella enterica</i> serovar Javiana
Cited by: 3
Author(s): Lauren K. Hudson, Lisha Constantine-Renna, Linda S Thomas, Charles A. Moore, Xiaorong Qian, Katie Garman, John R. Dunn, Thomas G. Denes
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12936-016-1591-0

Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing
Cited by: 11
Author(s): Mushal Allam, Belinda L. Spillings, Hiba Abdalla, Darlington Mapiye, Lizette L. Koekemoer, Alan Christoffels
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0028328

Location of Zeros of Wiener and Distance Polynomials
Cited by: 17
Author(s): Matthias Dehmer, Aleksandar Ilić
Software Mentions: 1
Published: over 12 years ago

Projects: cran: gtools

Papers Mentioning gtools 60