bioconductor: qvalue | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago

10.1111/eva.13202

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation
Cited by: 15
Author(s): Felix Vaux, Sandra Bohn, John R. Hyde, Kathleen G. O’Malley
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pgen.1009291

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci
Cited by: 30
Author(s): Marisa E. Miller, Eric S. Nazareno, Susan M. Rottschaefer, Jakob Riddle, Daniel A. Pereira, Feng Li, Hoa Nguyen-Phuc, Eva C Henningsen, Antoine Persoons, Diane G. O. Saunders, Eva H. Stukenbrock, Peter N. Dodds, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 13
Published: almost 4 years ago

10.1186/s13059-020-02001-7

Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing
Cited by: 7
Author(s): Jinyan Huang, Lijun Bai, Bowen Cui, Liang Wu, Liwen Wang, Zhiyin An, Shulin Ruan, Yue Yu, Xianyang Zhang, Jun Chen
Software Mentions: 13
Published: over 4 years ago

10.1186/1751-0473-5-3

MADAM - An open source meta-analysis toolbox for R and Bioconductor
Cited by: 20
Author(s): Karl G. Kugler, Laurin A. J. Mueller, Armin Graber
Software Mentions: 10
Published: almost 15 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: almost 5 years ago

10.1371/journal.pone.0224750

Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease
Cited by: 3
Author(s): Lavida R. K. Rogers, Madison Verlinde, George I. Mias
Software Mentions: 10
Published: about 5 years ago

10.1186/1471-2105-14-254

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Cited by: 49
Author(s): Mikel Esnaola, Pedro Puig, David Herrera González, Robert Castelo, Juan R. González
Software Mentions: 9
Published: over 11 years ago

10.1186/s13073-015-0225-4

Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers
Cited by: 104
Author(s): Sarah Voisin, Markus Sällman Almén, Galina Yurevna Zheleznyakova, Lina Lundberg, Sanaz Zarei, Sandra Castillo, Fia Ence Eriksson, Emil Nilsson, Matthias Blüher, Yvonne Böttcher, Peter Kovacs, Jānis Kloviņš, Mathias Rask‐Andersen, Helgi B. Schiöth
Software Mentions: 9
Published: about 9 years ago

10.1002/ece3.5734

Predicting the success of an invader: Niche shift versus niche conservatism
Cited by: 21
Author(s): Stéphanie Sherpa, Maya Guéguen, Julien Renaud, Michaël G. B. Blum, Thierry Gaude, Frédéric Laporte, Mustafa Akiner, Bülent Alten, Carles Aranda, Hélène Barre‐Cardi, Romeo Bellini, Mikel Bengoa Paulis, Xiaoguang Chen, Roger Eritja, Eleonora Flacio, Cipriano Foxi, Intan H. Ishak, Katja Kalan, Shinji Kasai, Fabrizio Montarsi, I. Pajović, Dušan Petrić, Rosa Termine, Nataša Turić, Gonzalo M. Vazquez‐Prokopec, Enkelejda Velo, Goran Vignjević, Xiaohong Zhou, Laurence Després
Software Mentions: 8
Published: about 5 years ago

10.1186/1471-2105-11-450

Filtering, FDR and power
Cited by: 43
Author(s): Maarten van Iterson, Judith M. Boer, Renée X. de Menezes
Software Mentions: 8
Published: over 14 years ago

10.1038/s41598-017-13731-3

The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation
Cited by: 16
Author(s): Mahdi Golkaram, Jaeshin Jang, Stefan Hellander, Kenneth S. Kosik, Linda R. Petzold
Software Mentions: 8
Published: about 7 years ago

10.1038/s41396-020-0621-7

Spatiotemporal dynamics of the archaeal community in coastal sediments: assembly process and co-occurrence relationship
Cited by: 120
Author(s): Jiwen Liu, Shangqing Zhu, Xiaoyue Liu, Peng Yao, Tiantian Ge, Xiao‐Hua Zhang
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12859-018-2069-6

A gene profiling deconvolution approach to estimating immune cell composition from complex tissues
Cited by: 12
Author(s): Shu Hwa Chen, Wen Yu Kuo, Sheng Su, Wei Chun Chung, Jen Ming Ho, Henry Horng Shing Lu, Chung Yen Lin
Software Mentions: 8
Published: over 6 years ago

10.1186/s12863-020-00921-8

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations
Cited by: 5
Author(s): Eva Jansson, François Besnier, Ketil Malde, Carl André, Geir Dahle, Kevin A. Glover
Software Mentions: 8
Published: about 4 years ago

10.1186/s40168-021-01140-8

Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria
Cited by: 18
Author(s): Olga María Pérez-Carrascal, Nicolas Tromas, Yves Terrat, Elisa Moreno, Alessandra Giani, Laísa Corrêa Braga Marques, Nathalie Fortin, Ben Shapiro
Software Mentions: 8
Published: about 3 years ago

10.1186/1471-2105-12-467

Empirical comparison of cross-platform normalization methods for gene expression data
Cited by: 88
Author(s): Jason R. Rudy, Faramarz Valafar
Software Mentions: 8
Published: about 13 years ago

10.1534/genetics.118.301595

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations
Cited by: 295
Author(s): Karl W. Broman, Daniel M. Gatti, Petr Šimeček, Nicholas A. Furlotte, Pjotr Prins, Śaunak Sen, Brian S. Yandell, Gary A. Churchill
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12915-017-0379-1

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
Cited by: 55
Author(s): Édouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, T. S. Yunusov, Kévin Floch, Sebastián Schornack
Software Mentions: 8
Published: over 7 years ago

10.1038/tp.2016.275

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score
Cited by: 28
Author(s): Diana‐Maria Ciuculete, Adrian Boström, Sarah Voisin, H. Philipps, Olga E. Titova, Marcus Bandstein, Lamia Nikontovic, Michael J. Williams, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 8
Published: almost 8 years ago

10.1002/gepi.22205

Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits
Cited by: 13
Author(s): Heather E. Wheeler, Sally Ploch, Alvaro N. Barbeira, Rodrigo Bonazzola, Angela Andaleon, Alireza Fotuhi Siahpirani, Ashis Saha, Alexis Battle, Sushmita Roy, Hae Kyung Im
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1002704

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Cited by: 45
Author(s): Leopold Parts, Åsa K. Hedman, Sarah Keildson, Andrew Knights, Cei Abreu‐Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartoniček, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C. Nica, Michael A. Quail, Kerrin S. Small, Daniel Glass, Anton J. Enright, John Winn, Panos Deloukas, Emmanouil T. Dermitzakis, Mark I. McCarthy, Timothy D. Spector, Richard Durbin, Cecilia M. Lindgren
Software Mentions: 7
Published: over 12 years ago

10.1002/1878-0261.12911

LncRNA NKX2‐1‐AS1 promotes tumor progression and angiogenesis via upregulation of SERPINE1 expression and activation of the VEGFR‐2 signaling pathway in gastric cancer
Cited by: 39
Author(s): Fei Teng, Ju‐Xiang Zhang, Yi Chen, Xiaodong Shen, Chang Su, Yanjiao Guo, Pu‐Hua Wang, Chencheng Shi, Ming Lei, Yiou Cao, Shao‐Qun Liu
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pgen.1006402

Gene co-expression network connectivity is an important determinant of selective constraint
Cited by: 96
Author(s): Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K. Ingvarsson, Nathaniel R. Street, Torgeir R. Hvidsten
Software Mentions: 7
Published: over 7 years ago

10.1186/s13059-019-1768-2

Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes
Cited by: 60
Author(s): Geoffrey M. Attardo, Adly M. M. Abd-Alla, Álvaro Acosta-Serrano, James Allen, Rosemary Bateta, Joshua B. Benoit, Kostas Bourtzis, Jo Caers, Guy Caljon, Mikkel Christensen, David W. Farrow, Markus Friedrich, Aurélie Hua-Van, Emily C. Jennings, Denis M. Larkin, Daniel Lawson, Michael J. Lehane, Vasileios Panagiotis Lenis, Ernesto Lowy-Gallego, Rosaline W. Macharia, Anna R. Malacrida, Heather G. Marco, Daniel Masiga, G. Maslen, Irina Matetovici, Richard P Meisel, Irene K. Meki, Veronika Michalková, Wolfgang J. Miller, Patrick Minx, Paul O. Mireji, Lino Ometto, Andrew G. Parker, Rita V. M. Rio, Clair Rose, Andrew J. Rosendale, Omar Rota‐Stabelli, Grazia Savini, Liliane Schoofs, Francesca Scolari, Martin Swain, Peter Takáč, Chad Tomlinson, George Tsiamis, Jan Van Den Abbeele, Aurélien Vigneron, Jingwen Wang, Wesley C. Warren, Robert M. Waterhouse, Matthew T. Weirauch, Brian L. Weiss, Richard K. Wilson, Xin Zhao, Serap Aksoy
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pmed.1002699

Deep-learning-assisted diagnosis for knee magnetic resonance imaging: Development and retrospective validation of MRNet
Cited by: 385
Author(s): Nicholas Bien, Pranav Rajpurkar, Robyn L. Ball, Jeremy Irvin, Allison Park, Erik Jones, Michael Bereket, Bhavik N. Patel, Kristen W. Yeom, Katie Shpanskaya, Safwan Halabi, Evan J. Zucker, Gary S. Fanton, Derek F. Amanatullah, Christopher F. Beaulieu, Geoffrey M. Riley, Russell J. Stewart, Francis G. Blankenberg, David B. Larson, Ricky Jones, Curtis P. Langlotz, Andrew Y. Ng, Matthew P. Lungren
Software Mentions: 7
Published: about 6 years ago

10.1038/s42003-020-01175-x

Genetic alterations in the 3q26.31-32 locus confer an aggressive prostate cancer phenotype
Cited by: 3
Author(s): Benjamin S. Simpson, Niedzica Camacho, Hayley J. Luxton, Hayley Pye, Ron Finn, Susan Heavey, Jason J. Pitt, Caroline M. Moore, Hayley C. Whitaker
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-017-1286-z

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Cited by: 68
Author(s): Matthias Heinig, Michiel E. Adriaens, Sebastian Schäfer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, András Varró, Nanette H. Bishopric, Alfred L. George, Cristobal dos Remedios, Aida Moreno‐Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J.R. Barton, Stuart A. Cook, Yigal M. Pinto, Connie R. Bezzina, Norbert Hübner
Software Mentions: 7
Published: over 7 years ago

10.1186/s13059-020-02098-w

Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Cited by: 11
Author(s): Maxime Rotival, Katherine J. Siddle, Martin Silvert, Julien Pothlichet, Hélène Quach, Lluı́s Quintana-Murci
Software Mentions: 7
Published: over 4 years ago

10.7554/eLife.62669

Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross
Cited by: 14
Author(s): Kaushik Renganaath, Rocky Cheung, Laura Day, Sriram Kosuri, Leonid Kruglyak, Frank W. Albert
Software Mentions: 7
Published: about 4 years ago

10.1016/j.cell.2016.10.026

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Cited by: 527
Author(s): Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Yan Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice Mann, José Marı́a Fernández, Sophia Rowlston, Steven P. Wilder, Samantha Farrow, Xiaojian Shao, John Lambourne, Adriana Redensek, Cornelis A. Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren A. Cheung, Olivier Delaneau, Emmanouil T. Dermitzakis, Heather Elding, Irina Colgiu, Frederik Otzen Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva M. Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T. Maurano, John A. Morris, Véra Pancaldi, Farzin Pourfarzad, Karola Rehnström, Augusto Rendon, Thomas S. Risch, Nilofar Sharifi, Simon Maguire, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E. Antonarakis, Laura Clarke, Marie–Laure Yaspo, Stephan Beck, Roderic Guigó, Daniel Rico, Joost H.A. Martens, Willem H. Ouwehand, Taco W. Kuijpers, Dirk S. Paul, Hendrik G. Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Software Mentions: 7
Published: about 8 years ago

10.1186/1471-2164-10-439

Relative power and sample size analysis on gene expression profiling data
Cited by: 64
Author(s): Maarten van Iterson, Peter A C ‘t Hoen, Paola Pedotti, Guido Hooiveld, Johan T. den Dunnen, Gjb van Ommen, JM Boer, R.M. Menezes
Software Mentions: 6
Published: over 15 years ago

10.1186/s12885-015-1993-3

TGFβ isoforms and receptors mRNA expression in breast tumours: prognostic value and clinical implications
Cited by: 23
Author(s): Chenfeng Chen, Kong‐Nan Zhao, Paul P. Masci, Sunil R. Lakhani, Annika Antonsson, Peter T. Simpson, Luis Vitetta
Software Mentions: 6
Published: about 9 years ago

10.3390/nu13030807

Transient Effect of Infant Formula Supplementation on the Intestinal Microbiota
Cited by: 6
Author(s): Ning Chin, Gema Méndez-Lagares, Diana H. Taft, Victoria Laleau, Hung T. Kieu, Narayan Nicole, Susan B. Roberts, David A. Mills, Dennis J. Hartigan-O’Connor, Valerie J. Flaherman
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-020-1942-6

A framework for transcriptome-wide association studies in breast cancer in diverse study populations
Cited by: 60
Author(s): Arjun Bhattacharya, Montserrat García‐Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love
Software Mentions: 6
Published: almost 5 years ago

10.7717/peerj.6103

The gut microbiome correlates with conspecific aggression in a small population of rescued dogs(Canis familiaris)
Cited by: 43
Author(s): Nicole Kirchoff, Monique A. R. Udell, Thomas J. Sharpton
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0219507

Discovery of potential urine-accessible metabolite biomarkers associated with muscle disease and corticosteroid response in the mdx mouse model for Duchenne
Cited by: 5
Author(s): Mathula Thangarajh, Aiping Zhang, Kirandeep Gill, Habtom W. Ressom, Zhenzhi Li, Rency S. Varghese, Eric P. Hoffman, Kanneboyina Nagaraju, Yetrib Hathout, Simina M. Boca
Software Mentions: 6
Published: over 5 years ago

10.3389/fcimb.2021.643968

Gut Microbiome Alterations in Patients With Thyroid Nodules
Cited by: 15
Author(s): Ang Li, Tiantian Li, Xinxin Gao, Hang Yan, Jingfeng Chen, Mingjie Huang, Lin Wang, Dengke Yin, Hongqiang Li, Runsheng Ma, Qiang Zeng, Shuzhe Ding
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0025279

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Cited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: about 13 years ago

10.1186/s13068-018-1215-8

The primary transcriptome of the fast-growing cyanobacterium Synechococcus elongatus UTEX 2973
Cited by: 42
Author(s): Xiaoming Tan, Songjun Hou, Kuo Song, Jens Georg, Stephan Klähn, Xuefeng Lü, Wolfgang R. Hess
Software Mentions: 5
Published: over 6 years ago

10.1016/j.bbrep.2021.101126

Cell-to-cell interaction analysis of prognostic ligand-receptor pairs in human pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Sayaka Suzuki, Akihiro Kuno, Haruka Ozaki
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0106298

Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines
Cited by: 56
Author(s): Montiago X. LaBute, Xiaohua Zhang, Jason Lenderman, Brian J. Bennion, Sergio E. Wong, Felice C. Lightstone
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2105-9-303

A unified approach to false discovery rate estimation
Cited by: 343
Author(s): Korbinian Strimmer
Software Mentions: 5
Published: over 16 years ago

10.1186/1756-0500-5-596

MetabR: an R script for linear model analysis of quantitative metabolomic data
Cited by: 30
Author(s): Ben Ernest, Jessica Gooding, Shawn R. Campagna, Arnold M. Saxton, Brynn H. Voy
Software Mentions: 5
Published: about 12 years ago

10.1186/s13059-015-0597-1

Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis
Cited by: 127
Author(s): Julieta L. Mateos, Pedro Madrigal, Kazuhiko Tsuda, Vimal Rawat, René Richter, Maida Romera-Branchat, Fabio Fornara, Korbinian Schneeberger, Paweł Krajewski, George Coupland
Software Mentions: 5
Published: almost 10 years ago

10.7554/eLife.35471

Genetics of trans-regulatory variation in gene expression
Cited by: 133
Author(s): Frank W. Albert, Joshua S. Bloom, Jake J. Siegel, Laura Day, Leonid Kruglyak
Software Mentions: 5
Published: over 6 years ago

10.1128/mSphere.00521-18

Marginal Zinc Deficiency and Environmentally Relevant Concentrations of Arsenic Elicit Combined Effects on the Gut Microbiome
Cited by: 32
Author(s): Christopher A. Gaulke, John Rolshoven, Carmen P. Wong, Laurie G. Hudson, Emily Ho, Thomas J. Sharpton
Software Mentions: 5
Published: almost 6 years ago

10.1128/mSystems.00061-20

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance
Cited by: 35
Author(s): Claudia Barelli, Davide Albanese, Rebecca M. Stumpf, Abigail E. Asangba, Claudio Donati, Francesco Rovero, Heidi C. Hauffe
Software Mentions: 5
Published: over 4 years ago

10.1038/srep46203

Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection
Cited by: 25
Author(s): Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Jason R. Grant, R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan, Paul Stothard, Graham Plastow
Software Mentions: 5
Published: over 7 years ago

10.3389/fmicb.2018.01128

Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas
Cited by: 23
Author(s): Yanlu Qiao, Jiwen Liu, Meixun Zhao, Xiaohua Zhang
Software Mentions: 5
Published: over 6 years ago

10.1186/1751-0473-8-8

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies
Cited by: 5
Author(s): Mehdi Pirooznia, Fayaz Seifuddin, Fernando S. Goes, Jeffrey T. Leek, Peter P. Zandi
Software Mentions: 5
Published: almost 12 years ago

10.1186/1471-2105-14-165

Separate-channel analysis of two-channel microarrays: recovering inter-spot information
Cited by: 28
Author(s): Gordon K. Smyth, Naomi Altman
Software Mentions: 5
Published: over 11 years ago

10.1534/g3.113.007849

Opposing Activities of DRM and MES-4 Tune Gene Expression and X-Chromosome Repression inCaenorhabditis elegansGerm Cells
Cited by: 8
Author(s): Tomoko M. Tabuchi, Andreas Rechtsteiner, Susan Strome, Kirsten Hagstrom
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pcbi.1005274

Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs
Cited by: 61
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-98614-4

Screening bioactive food compounds in honey bees suggests curcumin blocks alcohol-induced damage to longevity and DNA methylation
Cited by: 5
Author(s): Erik M. K. Rasmussen, Kristine L. Seier, Ingrid Kjelsberg Pedersen, Claus D. Kreibich, Gro V. Amdam, Daniel Münch, John Arne Dahl
Software Mentions: 5
Published: about 3 years ago

10.1186/1471-2105-12-209

Multiple testing for gene sets from microarray experiments
Cited by: 6
Author(s): Insuk Sohn, Kouros Owzar, Jong-Tae Lim, Stephen L. George, Stephanie M. Cushman, Sin‐Ho Jung
Software Mentions: 5
Published: over 13 years ago

10.1128/mBio.03186-19

Fecal Metabolomic Signatures in Colorectal Adenoma Patients Are Associated with Gut Microbiota and Early Events of Colorectal Cancer Pathogenesis
Cited by: 86
Author(s): Minsuk Kim, Emily Vogtmann, David A. Ahlquist, Mary E. Devens, John B. Kisiel, William R. Taylor, Bryan A. White, Vanessa L. Hale, Jaeyun Sung, Nicholas Chia, Rashmi Sinha, Jun Chen
Software Mentions: 5
Published: almost 5 years ago

10.1038/tp.2017.177

Genome-wide expression and response to exposure-based psychological therapy for anxiety disorders
Cited by: 15
Author(s): Stephen K. Roberts, Chloe Wong, Gerome Breen, Jonathan R. I. Coleman, Simone de Jong, Peter Jöhren, Robert Keers, Charles Curtis, Sang Hyuck Lee, Jürgen Margraf, Silvia Schneider, Tobias Teismann, André Wannemüller, Kathryn J. Lester, Thalia C. Eley
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0245824

MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction
Cited by: 51
Author(s): Otília Menyhárt, Boglárka Weltz, Balázs Győrffy
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-29687-x

Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization
Cited by: 68
Author(s): Jacobo de la Cuesta-Zuluaga, Vanessa Corrales-Agudelo, Eliana P. Velásquez-Mejía, Jenny Andrea Carmona, José M. Abad, Juan S. Escobar
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-10-11

Filtering for increased power for microarray data analysis
Cited by: 218
Author(s): Amber J. Hackstadt, Ann Hess
Software Mentions: 5
Published: almost 16 years ago

10.1186/s12936-021-03918-5

Transcriptome-based analysis of blood samples reveals elevation of DNA damage response, neutrophil degranulation, cancer and neurodegenerative pathways in Plasmodium falciparum patients
Cited by: 1
Author(s): Akua A. Karikari, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: about 3 years ago

10.1093/biostatistics/kxw041

False discovery rates: a new deal
Cited by: 474
Author(s): Matthew Stephens
Software Mentions: 4
Published: about 8 years ago

10.3390/biom11091286

Lipocalin 2 Deficiency Restrains Aging-Related Reshaping of Gut Microbiota Structure and Metabolism
Cited by: 2
Author(s): Xing‐Biao Qiu, Chi Chen, Xiaoli Chen
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-018-4526-z

Global study of holistic morphological effectors in the budding yeast Saccharomyces cerevisiae
Cited by: 19
Author(s): Godai Suzuki, Yang Wang, Kosuke Kubo, Eri Hirata, Shinsuke Ohnuki, Yoshikazu Ohya
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0008745

Lactobacillus casei Abundance Is Associated with Profound Shifts in the Infant Gut Microbiome
Cited by: 112
Author(s): Michael J. Cox, Yvonne J. Huang, Kei E. Fujimura, Jane T. Liu, Michelle McKean, Homer A. Boushey, Mark R. Segal, Eoin L. Brodie, Michael D. Cabana, Susan V. Lynch
Software Mentions: 4
Published: almost 15 years ago

10.1186/1752-0509-5-127

Exploring pathway interactions in insulin resistant mouse liver
Cited by: 16
Author(s): Thomas Kelder, Lars Eijssen, Robert Kleemann, Marjan van Erk, Teake Kooistra, Chris T. Evelo
Software Mentions: 4
Published: almost 14 years ago

10.1186/1471-213X-13-13

miRNA regulated pathways in late stage murine lung development
Cited by: 47
Author(s): Sana Mujahid, Tanya Logvinenko, MaryAnn V. Volpe, Heber C. Nielsen
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2105-11-465

Parallel multiplicity and error discovery rate (EDR) in microarray experiments
Cited by: 4
Author(s): Wayne Xu, Clay J. Carter
Software Mentions: 4
Published: over 14 years ago

10.1186/s12861-015-0085-6

Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species
Cited by: 6
Author(s): Christian Larney, Timothy L. Bailey, Peter Koopman
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.70055

Tissue environment, not ontogeny, defines murine intestinal intraepithelial T lymphocytes
Cited by: 11
Author(s): Alejandro Brenes, Maud Vandereyken, Olivia J. James, Harriet Watt, Jens Hukelmann, Laura Spinelli, Dina Dikovskaya, Angus I. Lamond, Mahima Swamy
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1005619

Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection
Cited by: 18
Author(s): Musa A. Hassan, Kirk D. C. Jensen, Vincent Butty, Kenneth H. Hu, Erwan Boedec, Pjotr Prins, Jeroen P. J. Saeij
Software Mentions: 4
Published: about 9 years ago

10.1186/s12859-018-2081-x

Control procedures and estimators of the false discovery rate and their application in low-dimensional settings: an empirical investigation
Cited by: 18
Author(s): Regina Brinster, Anna Köttgen, Bamidele O. Tayo, Martin Schumacher, Peggy Sekula
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0111637

miR-27 Negatively Regulates Pluripotency-Associated Genes in Human Embryonal Carcinoma Cells
Cited by: 14
Author(s): Heiko Fuchs, Matthias Theuser, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: about 10 years ago

10.1002/2211-5463.12982

Metabolomic analysis of fibrotic mice combined with public RNA‐Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis
Cited by: 8
Author(s): Yosui Nojima, Yoshito Takeda, Yohei Maeda, Takeshi Bamba, Eiichiro Fukusaki, Mari Itoh, Kenji Mizuguchi, Atsushi Kumanogoh
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1005627

A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation
Cited by: 7
Author(s): W. T. Anderson, Danielle DeCicco, James S. Schwaber, Rajanikanth Vadigepalli
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pbio.2005130

High-dimensional single-cell phenotyping reveals extensive haploinsufficiency
Cited by: 25
Author(s): Shinsuke Ohnuki, Yoshikazu Ohya
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0223692

Elevated serum alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality
Cited by: 12
Author(s): Scott C. Ritchie, Johannes Kettunen, Marta Brożyńska, Artika P. Nath, Aki S. Havulinna, Satu Männistö, Markus Perola, Veikko Salomaa, Mika Ala‐Korpela, Gad Abraham, Peter Würtz, Michael Inouye
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-43881-5

Comprehensive and Systematic Analysis of Gene Expression Patterns Associated with Body Mass Index
Cited by: 13
Author(s): Paule V. Joseph, Rosario B. Jaime-Lara, Yupeng Wang, Lichen Xiang, Wendy A. Henderson
Software Mentions: 4
Published: over 5 years ago

10.3390/jof7090769

Defining Functions of Mannoproteins in Saccharomyces cerevisiae by High-Dimensional Morphological Phenotyping
Cited by: 2
Author(s): Farzan Ghanegolmohammadi, Hiroki Okada, Yaxuan Liu, Kaori Itto-Nakama, Shinsuke Ohnuki, A. S. Savchenko, Erfei Bi, Satoshi Yoshida, Yoshikazu Ohya
Software Mentions: 4
Published: over 3 years ago

10.1016/j.celrep.2021.109032

Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome
Cited by: 17
Author(s): Alejandro Brenes, Harunori Yoshikawa, Dalila Bensaddek, Bogdan Mirauta, Daniel D Seaton, Jens Hukelmann, Hao Jiang, Oliver Stegle, Angus I. Lamond
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.527

Metabolic fingerprinting of gilthead seabream (Sparus aurata) liver to track interactions between dietary factors and seasonal temperature variations
Cited by: 28
Author(s): Tomé S. Silva, Ana M. Rosa da Costa, Luı́s E.C. Conceição, Jorge Dias, Pedro M. Rodrigues, Nadège Richard
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-017-05724-z

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development
Cited by: 14
Author(s): Wei Liu, Maoshan Chen, Lijun Bai, Zhenhua Zhuang, Chao Fan, Jiang Nong-hui, Junsheng Zhao, Shuaipeng Ma, Xiang Xu
Software Mentions: 4
Published: over 7 years ago

10.12688/wellcomeopenres.16584.2

A type I IFN, prothrombotic hyperinflammatory neutrophil signature is distinct for COVID-19 ARDS
Cited by: 31
Author(s): Leila Reyes, Manuel A. Sanchez-Garcia, Tyler Morrison, Andy J. M. Howden, Emily R. Watts, Simone Arienti, Pranvera Sadiku, Patricia Coelho, Ananda S. Mirchandani, Ailiang Zhang, David Hope, Sarah Clark, Jo Singleton, Shonna Johnston, Robert Grecian, Azin Poon, Sarah McNamara, Ian Harper, Max Head Fourman, Alejandro Brenes, Shalini Pathak, Adam Lloyd, Giovanny Rodriguez Blanco, Alex von Kriegsheim, Bart Ghesquière, Wesley Vermaelen, Camila Takeno Cologna, Kevin Dhaliwal, Nik Hirani, David H. Dockrell, Moira K. B. Whyte, David Griffith, Doreen A. Cantrell, Sarah R. Walmsley
Software Mentions: 4
Published: over 3 years ago

10.1186/2045-3701-2-26

Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
Cited by: 43
Author(s): Zhide Fang, Jeffrey A. Martin, Zhong Wang
Software Mentions: 4
Published: almost 13 years ago

10.1038/s41597-020-00642-8

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
Cited by: 65
Author(s): Solveig K. Sieberts, Thanneer M. Perumal, Minerva M. Carrasquillo, Mariet Allen, Joseph S. Reddy, Gabriel E. Hoffman, Kristen K. Dang, John N. Calley, Philip J. Ebert, James A. Eddy, X Wang, Anna K. Greenwood, Sara Mostafavi, Schahram Akbarian, Jaroslav Bendl, Michael S. Breen, Kristen J. Brennand, Leanne Brown, Andrew Browne, Joseph D. Buxbaum, Alex Charney, Andrew Chess, Lizette Couto, Greg Crawford, Olivia Devillers, Bernie Devlin, Amanda Dobbyn, Enrico Domenici, Michele Filosi, Elie Flatow, Nancy Francoeur, John F. Fullard, Sergio Espeso-Gil, Kiran Girdhar, Attila Gulyás-Kovács, Ruben C. Gur, Chang Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Laura Huckins, Rivka Jacobov, Yonghua Jiang, Jessica Johnson, Bibi Kassim, Y Kim, Lambertus Klei, Robin Kramer, Mario Lauria, Thomas Lehner, David A. Lewis, Barbara K. Lipska, Kelsey S. Montgomery, Royce Park, Chaggai Rosenbluh, Panos Roussos, Douglas M. Ruderfer, Geetha Senthil, Hardik Shah, Laura Sloofman, Song Li, Eli Stahl, Patrick F. Sullivan, Roberto Visintainer, J Wang, Y C Wang, Jennifer Wiseman, Eva Xia, W Zhang, Elizabeth Zharovsky, Laura Addis, Sadiya N. Addo, David Airey, Matthias Arnold, David A. Bennett, Ying Bi, Knut Biber, Colette Blach, E Bradhsaw, Patrick McKinley Brennan, R Canet-Aviles, Shaolong Cao, A Cavalla, Yooree Chae, W W Chen, Joyce Cheng, David A. Collier, Jeffrey L. Dage, Eric B. Dammer, J Davis, J Davis, Derek Drake, Duc Duong, Brian J. Eastwood, Michelle E. Ehrlich, Benjamin M. Ellingson, Brett W. Engelmann, Sahar Esmaeeli-Nieh, Daniel Felsky, Cory C. Funk, Chris Gaiteri
Software Mentions: 4
Published: about 4 years ago

10.1186/s13073-016-0262-7

Signatures of early frailty in the gut microbiota
Cited by: 267
Author(s): Matthew A. Jackson, Ian B. Jeffery, Michelle Beaumont, Jordana T. Bell, Andrew G. Clark, Ruth E. Ley, Paul W. O’Toole, Tim D. Spector, Claire J. Steves
Software Mentions: 4
Published: almost 9 years ago

10.1093/molbev/msz048

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection
Cited by: 26
Author(s): Iakov I. Davydov, Nicolas Salamin, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 6 years ago

10.1002/hep.26414

Proteome‐wide analyses of human hepatocytes during differentiation and dedifferentiation
Cited by: 108
Author(s): Cliff Rowe, Dave T. Gerrard, Roz Jenkins, Andrew Berry, Kesta Durkin, Lars Sundström, Chris Goldring, B. Kevin Park, Neil R. Kitteringham, Karen Piper Hanley, Neil A. Hanley
Software Mentions: 4
Published: over 11 years ago

10.1186/s13059-021-02438-4

CoCoA-diff: counterfactual inference for single-cell gene expression analysis
Cited by: 6
Author(s): Yongjin Park, M Kellis
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-019-0722-6

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease
Cited by: 28
Author(s): Samuel S. Minot, Amy Willis
Software Mentions: 4
Published: over 5 years ago

10.1111/jcmm.16222

The pioneer and differentiation factor FOXA2 is a key driver of yolk‐sac tumour formation and a new biomarker for paediatric and adult yolk‐sac tumours
Cited by: 13
Author(s): Wasco Wruck, Felix Bremmer, Mara Kotthoff, Alexander Fichtner, Margaretha A. Skowron, Stefan Schönberger, Gabriele Calaminus, Christian Vokuhl, David Pfister, Axel Heidenreich, Peter Albers, James Adjaye, Daniel Nettersheim
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2105-6-199

Cited by: 84
Author(s): Per Broberg
Software Mentions: 3
Published: almost 20 years ago

10.1242/bio.054189

A stem cell based in vitro model of NAFLD enables the analysis of patient specific individual metabolic adaptations in response to a high fat diet and AdipoRon interference
Cited by: 6
Author(s): Nina Graffmann, Audrey Ncube, Soraia Martins, Aurelian Robert Fiszl, Philipp Reuther, Martina Bohndorf, Wasco Wruck, Mathias Beller, Constantin Czekelius, James Adjaye
Software Mentions: 3
Published: almost 5 years ago

10.1186/1752-0509-2-95

Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome
Cited by: 152
Author(s): Angela P. Presson, Eric M. Sobel, Jeanette C. Papp, Charlyn Suarez, Toni Whistler, Mangalathu S. Rajeevan, Suzanne D. Vernon, Steve Horvath
Software Mentions: 3
Published: about 16 years ago

10.1186/s40359-021-00571-0

Exploring presentation differences in multi-cultural youth seeking assistance for mental health problems
Cited by: 0
Author(s): Stephane M. Shepherd, Cieran Harries, Benjamin Spivak, Anne-Sophie Pichler, Rosemary Purcell
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2007-8-10-r210

Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia
Cited by: 38
Author(s): Jack Cohen, Linda J. Van Marter, Yanfang Sun, Elizabeth N. Allred, Alan Leviton, Isaac S. Kohane
Software Mentions: 3
Published: almost 18 years ago

10.1186/s13059-016-0954-8

DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements
Cited by: 13
Author(s): Jun Wang, Yeisoo Yu, Tao Feng, Jian Wei Zhang, Dario Copetti, Dave Kudrna, Jayson Talag, Seung‐Hee Lee, Rod A. Wing, Chuanzhu Fan
Software Mentions: 3
Published: over 8 years ago

10.1016/j.ajhg.2016.07.001

Adiposity-Dependent Regulatory Effects on Multi-tissue Transcriptomes
Cited by: 24
Author(s): Craig A. Glastonbury, Ana Viñuela, Alfonso Buil, Gisli H. Halldorsson, Guðmar Þorleifsson, Hannes Helgason, Unnur Þorsteinsdóttir, Kāri Stefánsson, Emmanouil T. Dermitzakis, Tim D. Spector, Kerrin S. Small
Software Mentions: 3
Published: over 8 years ago

Projects: bioconductor: qvalue

Papers Mentioning qvalue 248