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: bioconductor: qvalue
https://packages.ecosyste.ms/registries/bioconductor.org/packages/qvalue
Q-value estimation for false discovery rate control
2 versions
Latest release: 12 months ago
44 dependent packages
1,357,363 downloads total
Papers Mentioning qvalue 248
10.1371/journal.pone.0044280
Sperm mRNA Transcripts Are Indicators of Sub-Chronic Low Dose Testicular Injury in the Fischer 344 RatCited by: 25
Author(s): Sara Pacheco, Linda M. Anderson, Moses A. Sandrof, Marguerite M. Vantangoli, Susan J. Hall, Kim Boekelheide
Software Mentions: 1
Published: about 12 years ago
10.1371/journal.pone.0011657
Heritability in the Efficiency of Nonsense-Mediated mRNA Decay in HumansCited by: 20
Author(s): Cathal Seoighe, Chris Gehring
Software Mentions: 1
Published: about 14 years ago
10.1074/mcp.RA120.002171
Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal LipasesCited by: 6
Author(s): Matthias Schittmayer, Nemanja Vujić, Barbara Darnhofer, Melanie Korbelius, Sophie Honeder, Dagmar Kratky, Ruth Birner‐Gruenberger
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pcbi.1000692
Interpreting Metabolomic Profiles using Unbiased Pathway ModelsCited by: 53
Author(s): Rahul C. Deo, Luke Hunter, Gregory D. Lewis, Guillaume Paré, Ramachandran S. Vasan, Daniel I. Chasman, Thomas J. Wang, Robert E. Gerszten, Frederick P. Roth
Software Mentions: 1
Published: over 14 years ago
10.3390/ani11071934
Proteomic Analysis of Liver from Finishing Beef Cattle Supplemented with a Rumen-Protected B-Vitamin Blend and Hydroxy Trace MineralsCited by: 0
Author(s): M. M. Lopes, Thaís Ribeiro Brito, Josiane Fonseca Lage, Thaís Correia Costa, Marta Maria dos Santos, Nick V. L. Serão, Tiago Antônio de Oliveira Mendes, Ricardo Andrade Reis, Renata Veroneze, Fabyano F. Silva, Márcio de Souza Duarte
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0114888
Molecular and Cellular Characterization of a Zebrafish Optic Pathway Tumor Line Implicates Glia-Derived Progenitors in TumorigenesisCited by: 5
Author(s): Staci L. Solin, Ying Wang, Joshua P. Mauldin, Linda Schultz, Deborah E. Lincow, Pavel Brodskiy, Crystal A. Jones, Judith Syrkin-Nikolau, Jasmine M. Linn, Jeffrey J. Essner, Jesse M. Hostetter, Elizabeth M. Whitley, J. Douglas Cameron, Hui Hsien Chou, Andrew J. Severin, Donald S. Sakaguchi, Maura McGrail
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pgen.1003486
A Statistical Framework for Joint eQTL Analysis in Multiple TissuesCited by: 248
Author(s): Timothée Flutre, Xiaoquan Wen, Jonathan K. Pritchard, Matthew Stephens
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pgen.1000609
The Drosophila foraging Gene Mediates Adult Plasticity and Gene–Environment Interactions in Behaviour, Metabolites, and Gene Expression in Response to Food DeprivationCited by: 95
Author(s): Clement F. Kent, T. E. Daskalchuk, Lisa Cook, Marla B. Sokolowski, Ralph J. Greenspan
Software Mentions: 1
Published: about 15 years ago
10.1186/1471-2164-14-756
Genomic divergence between nine- and three-spined sticklebacksCited by: 42
Author(s): Baocheng Guo, Frédéric J. J. Chain, Erich Bornberg‐Bauer, Erica H. Leder, Juha Merilä
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pgen.1000467
Tor1/Sch9-Regulated Carbon Source Substitution Is as Effective as Calorie Restriction in Life Span ExtensionCited by: 177
Author(s): Min Wei, Paola Fabrizio, Federica Madia, Jia Hu, Huanying Ge, Lei M. Li, Valter D. Longo
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pgen.1000052
A Genome-Wide Gene Expression Signature of Environmental Geography in Leukocytes of Moroccan AmazighsCited by: 97
Author(s): Youssef Idaghdour, John D. Storey, Sami Jadallah, Greg Gibson
Software Mentions: 1
Published: over 16 years ago
10.1038/s41598-018-26700-1
Combining micro-RNA and protein sequencing to detect robust biomarkers for Graves’ disease and orbitopathyCited by: 30
Author(s): Lei Zhang, Giulia Masetti, Giuseppe Colucci, Mario Salvi, Danila Covelli, Anja Eckstein, Ulrike Kaiser, Mohd Shazli Draman, Ilaria Muller, Marian Ludgate, Luigi Lucini, Filippo Biscarini
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2148-12-7
Rates of evolution in stress-related genes are associated with habitat preference in two Cardamine lineagesCited by: 18
Author(s): Lino Ometto, Mingai Li, Luisa Bresadola, Claudio Varotto
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pbio.1000623
Association of Lipidome Remodeling in the Adipocyte Membrane with Acquired Obesity in HumansCited by: 211
Author(s): Kirsi H. Pietiläinen, Tomasz Róg, Tuulikki Seppänen‐Laakso, Sam Virtue, Peddinti Gopalacharyulu, Jing Tang, Sergio Rodríguez‐Cuenca, Arkadiusz Maciejewski, Jussi Naukkarinen, Anna-Liisa Ruskeepää, Perttu Niemelä, Laxman Yetukuri, Chong Yew Tan, Vidya Velagapudi, Sandra Castillo, Heli Nygrén, Tuulia Hyötyläinen, Aila Rissanen, Jaakko Kaprio, Hannele Yki‐Järvinen, Ilpo Vattulainen, António Vidal-Puig, Matej Orešič
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0014436
No Difference between the Sexes in Fine-Scale Spatial Genetic Structure of Roe DeerCited by: 29
Author(s): Nadège C. Bonnot, Jean‐Michel Gaillard, Aurélie Coulon, Maxime Galan, Jean‐François Cosson, Daniel Delorme, François Klein, A. J. Mark Hewison
Software Mentions: 1
Published: almost 14 years ago
10.1371/journal.pcbi.1000446
Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase InhibitorsCited by: 46
Author(s): Andrew J. Olaharski, Nina Gonzaludo, Hans Bitter, David Goldstein, Stephan Kirchner, Hirdesh Uppal, Kyle L. Kolaja
Software Mentions: 1
Published: about 15 years ago
10.1371/journal.pone.0004055
Comparative Developmental Expression Profiling of Two C. elegans IsolatesCited by: 31
Author(s): Emily J. Capra, Sonja M. Skrovanek, Leonid Kruglyak
Software Mentions: 1
Published: almost 16 years ago
10.1186/1479-5876-11-75
Gene expression profiling of whole blood in ipilimumab-treated patients for identification of potential biomarkers of immune-related gastrointestinal adverse eventsCited by: 134
Author(s): Vafa Shahabi, David M. Berman, Scott D. Chasalow, Lisu Wang, Zenta Tsuchihashi, Beihong Hu, Lisa Panting, Maria Jure-Kunkel, Rui-Ru Ji
Software Mentions: 1
Published: over 11 years ago
10.1186/1741-7007-7-79
Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfacesCited by: 226
Author(s): Imke Mulder, Bettina Schmidt, Christopher Stokes, Marie Lewis, Mick Bailey, Rustam Aminov, James I. Prosser, B. P. Gill, J.R. Pluske, Claus Mayer, Corran C. Musk, Denise Kelly
Software Mentions: 1
Published: almost 15 years ago
10.3389/fgene.2018.00325
Binge Ethanol Drinking Produces Sexually Divergent and Distinct Changes in Nucleus Accumbens Signaling Cascades and Pathways in Adult C57BL/6J MiceCited by: 24
Author(s): Deborah A. Finn, Joel G. Hashimoto, Debra K. Cozzoli, Melinda L. Helms, Michelle A. Nipper, Moriah N. Kaufman, Kristine M. Wiren, Marina Guizzetti
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.pgen.1006170
Sex-Specific Selection and Sex-Biased Gene Expression in Humans and FliesCited by: 105
Author(s): Changde Cheng, Mark Kirkpatrick
Software Mentions: 1
Published: about 8 years ago
10.3389/fimmu.2019.00060
Repurposing of Drugs as Novel Influenza Inhibitors From Clinical Gene Expression Infection SignaturesCited by: 41
Author(s): Andrés Pizzorno, Benjamin Terrier, Claire Nicolas de Lamballerie, Thomas Julien, Blandine Padey, Aurélien Traversier, Magali Roche, Marie‐Ève Hamelin, Chantal Rhéaume, Séverine Croze, Vanessa Escuret, Julien Poissy, Bruno Lina, Catherine Legras-Lachuer, Julien Textoris, Guy Boivin, Manuel Rosa‐Calatrava
Software Mentions: 1
Published: over 5 years ago
10.3389/fimmu.2015.00630
Weaning Markedly Affects Transcriptome Profiles and Peyer’s Patch Development in Piglet IleumCited by: 20
Author(s): Ryo Inoüe, Takamitsu Tsukahara, Masako Nakatani, Mie Okutani, Ryoichiro Nishibayashi, Shuntaro Ogawa, Tomoko Harayama, Takayuki Nagino, Hironori Hatanaka, Kikuto Fukuta, Gustavo A. Romero-Pérez, Kazunari Ushida, Denise Kelly
Software Mentions: 1
Published: almost 9 years ago
10.1186/1471-2164-12-488
Effects of elevated seawater p CO2 on gene expression patterns in the gills of the green crab, Carcinus maenasCited by: 44
Author(s): Sandra Fehsenfeld, Rainer Kiko, Yasmin Appelhans, David W. Towle, Martin Zimmer, Frank Melzner
Software Mentions: 1
Published: about 13 years ago
10.3389/fpls.2016.01540
Determining Phenological Patterns Associated with the Onset of Senescence in a Wheat MAGIC Mapping PopulationCited by: 31
Author(s): Anyela Camargo, Richard Mott, Keith A. Gardner, Ian Mackay, Fiona Corke, John H. Doonan, Jan T. Kim, Alison R. Bentley
Software Mentions: 1
Published: almost 8 years ago
10.3389/fpls.2018.00810
Signatures of Selection in the Genomes of Chinese Chestnut (Castanea mollissima Blume): The Roots of Nut Tree DomesticationCited by: 15
Author(s): Nicholas R. LaBonte, Peng Zhao, Keith Woeste
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2105-14-287
Statistical analysis of dendritic spine distributions in rat hippocampal culturesCited by: 26
Author(s): Aruna Jammalamadaka, Sourav Banerjee, B.S. Manjunath, Kenneth S. Kosik
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0035484
Network Analysis of Oyster Transcriptome Revealed a Cascade of Cellular Responses during Recovery after Heat ShockCited by: 25
Author(s): Lingling Zhang, Rui Hou, Hailin Su, Xiaoli Hu, Shi Wang, Zhenmin Bao
Software Mentions: 1
Published: over 12 years ago
10.1534/g3.115.024950
Accuracy of Genomic Prediction in Switchgrass (<i>Panicum virgatum</i> L.) Improved by Accounting for Linkage DisequilibriumCited by: 29
Author(s): Guillaume P. Ramstein, Joseph P. Evans, Shawn M. Kaeppler, Robert B. Mitchell, Kenneth P. Vogel, C. Robin Buell, Michael D. Casler
Software Mentions: 1
Published: over 8 years ago
10.3390/toxins7104035
HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomesCited by: 32
Author(s): M. Nguyen, Alex Ekstrom, Xueqiong Li, Yanbin Yin
Software Mentions: 1
Published: almost 9 years ago
10.3389/fgene.2018.00115
Empirical Bayes Estimation of Semi-parametric Hierarchical Mixture Models for Unbiased Characterization of Polygenic Disease ArchitecturesCited by: 9
Author(s): Junichi Nishino, Yuta Kochi, Daichi Shigemizu, Mamoru Kato, Katsunori Ikari, Hidenori Ochi, Hisashi Noma, Kazumi Matsui, Takashi Morizono, Keith A. Boroevich, Tatsuhiko Tsunoda, Shigeyuki Matsui
Software Mentions: 1
Published: over 6 years ago
10.1186/s12859-019-2595-x
Statistical significance approximation for local similarity analysis of dependent time series dataCited by: 3
Author(s): Fang Zhang, Fengzhu Sun, Yihui Luan
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2164-8-396
Inter- and intra-combinatorial regulation by transcription factors and microRNAsCited by: 109
Author(s): Yiming Zhou, John Ferguson, Joseph T. Chang, Yuval Kluger
Software Mentions: 1
Published: almost 17 years ago
10.1186/1471-2164-15-907
A genome wide association scan for (1,3;1,4)-β-glucan content in the grain of contemporary 2-row Spring and Winter barleysCited by: 52
Author(s): Kelly Houston, Joanne Russell, Miriam Schreiber, Claire Halpin, Helena Oakey, Jennifer Washington, Allan Booth, Neil J. Shirley, Rachel A. Burton, Geoffrey B. Fincher, Robbie Waugh
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.pone.0186142
Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profilesCited by: 25
Author(s): Erik Andersson, Daniel Bergemalm, Robert L. Kruse, Gunter Neumann, Mauro D’Amato, Dirk Repsilber, Jonas Halfvarson
Software Mentions: 1
Published: about 7 years ago
10.1186/1471-2105-9-404
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cellsCited by: 34
Author(s): Atsushi Niida, Andrew D. Smith, Seiya Imoto, Sadami Tsutsumi, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama
Software Mentions: 1
Published: about 16 years ago
10.3390/ani9100813
Behavioural Differences in Dogs with Atopic Dermatitis Suggest Stress Could Be a Significant Problem Associated with Chronic PruritusCited by: 15
Author(s): Naomi D. Harvey, Peter J. Craigon, Stephen Shaw, Sarah Blott
Software Mentions: 1
Published: almost 5 years ago
10.1186/gb-2008-9-7-r119
The IL-10 and IFN-γ pathways are essential to the potent immunosuppressive activity of cultured CD8+ NKT-like cellsCited by: 12
Author(s): Li Zhou, Hongjie Wang, Xing Zhong, Yulan Jin, Qing Sheng Mi, Ashok Sharma, Richard A. McIndoe, Nikhil Garge, Robert H. Podolsky, Jin‐Xiong She
Software Mentions: 1
Published: almost 17 years ago
10.1186/1471-2164-12-167
Stochastic variation of transcript abundance in C57BL/6J miceCited by: 23
Author(s): Peter T. Vedell, Karen L. Svenson, Gary A. Churchill
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2350-12-148
Heritability and genome-wide association analysis of renal sinus fat accumulation in the Framingham Heart StudyCited by: 11
Author(s): Meredith C. Foster, Qiong Yang, Shih‐Jen Hwang, Udo Hoffmann, Caroline S. Fox
Software Mentions: 1
Published: almost 13 years ago
10.1186/s12864-017-4227-z
Computational identification of harmful mutation regions to the activity of transposable elementsCited by: 2
Author(s): Lingling Jin, Ian McQuillan, Longhai Li
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pone.0169018
Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber CorkCited by: 17
Author(s): Vera Inácio, Pedro M. Barros, Alexandre Costa, Cristóvão Roussado, Elsa Gonçalves, Rita Costa, José Graça, M. Margarida Oliveira, Leonor Morais-Cecílio
Software Mentions: 1
Published: almost 8 years ago
10.1186/1471-2164-10-135
Comparative expression pathway analysis of human and canine mammary tumorsCited by: 145
Author(s): Paolo Uva, Luigi Aurisicchio, James Watters, Andrey Loboda, Amit Kulkarni, John C. Castle, Fabio Palombo, Valentina Viti, Giuseppe Mesiti, Valentina Zappulli, Laura Marconato, Francesca Abramo, Gennaro Ciliberto, Armin Lahm, Nicola La Monica, Emanuele de Rinaldis
Software Mentions: 1
Published: over 15 years ago
10.1186/1471-2164-8-219
Inference of transcription modification in long-live yeast strains from their expression profilesCited by: 34
Author(s): Chao Cheng, Paola Fabrizio, Huanying Ge, Valter D. Longo, Lei M. Li
Software Mentions: 1
Published: over 17 years ago
10.1186/1471-2105-15-193
Phenotype prediction based on genome-wide DNA methylation dataCited by: 21
Author(s): Thomas Wilhelm
Software Mentions: 1
Published: over 10 years ago
10.1186/1471-2350-10-43
Genome-wide association study identifies single-nucleotide polymorphism in KCNB1 associated with left ventricular mass in humans: The HyperGEN StudyCited by: 41
Author(s): Donna K. Arnett, Na Li, Weihong Tang, D. C. Rao, Richard B. Devereux, Steven A. Claas, Rachel Kraemer, Ulrich Broeckel
Software Mentions: 1
Published: over 15 years ago
10.1186/1471-2350-14-10
Reduced genetic influence on childhood obesity in small for gestational age childrenCited by: 10
Author(s): Dug Yeo Han, Rinki Murphy, Angharad R. Morgan, Wen Jiun Lam, John M. D. Thompson, Clare Wall, Karen E. Waldie, Edwin A. Mitchell, Lynnette R. Ferguson
Software Mentions: 1
Published: over 11 years ago