bioconductor: multtest | Projects

10.3390/ijms22063251

Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes
Cited by: 11
Author(s): Kristian Peters, Gerd Ulrich Balcke, Niklas Kleinenkuhnen, Hendrik Treutler, Steffen Neumann
Software Mentions: 31
Published: over 3 years ago

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: over 13 years ago

10.1371/journal.pone.0061217

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
Cited by: 11,386
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 19
Published: over 11 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 10 years ago

10.1038/sdata.2018.179

Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 13
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 17
Published: almost 6 years ago

10.1002/ece3.4361

Seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 28
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 16
Published: almost 6 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: about 14 years ago

10.3390/metabo9100222

Chemical Diversity and Classification of Secondary Metabolites in Nine Bryophyte Species
Cited by: 29
Author(s): Kristian Peters, Hendrik Treutler, Stefanie Döll, Alida Kindt, Thomas Hankemeier, Steffen Neumann
Software Mentions: 15
Published: almost 5 years ago

10.1186/s12859-015-0719-5

mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics
Cited by: 3
Author(s): Αλέξανδρος Σακελλαρίου, George M. Spyrou
Software Mentions: 15
Published: almost 9 years ago

10.1371/journal.pcbi.1003000

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: over 11 years ago

10.7554/eLife.07836

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: almost 9 years ago

10.3389/fimmu.2016.00339

IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
Cited by: 38
Author(s): Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie‐Paule Lefranc
Software Mentions: 11
Published: almost 8 years ago

10.1111/pbi.13299

Learning from methylomes: epigenomic correlates of<i>Populus balsamifera</i>traits based on deep learning models of natural DNA methylation
Cited by: 9
Author(s): Marc J. Champigny, Faride Unda, Oleksandr Skyba, Raju Soolanayakanahally, Shawn D. Mansfield, Malcolm M. Campbell
Software Mentions: 10
Published: over 4 years ago

10.1186/gb-2004-5-10-r80

Cited by: 10,848
Author(s): Robert Gentleman, Vincent J. Carey, Douglas M. Bates, Benjamin M. Bolstad, Marcel Dettling, Sandrine Dudoit, Byron Ellis, Laurent Gautier, Yongchao Ge, Jeff Gentry, Kurt Hornik, Torsten Hothorn, Wolfgang Huber, Stefano Maria Iacus, Rafael A. Irizarry, Friedrich Leisch, Cheng Li, Martin Maechler, Anthony Rossini, Günther Sawitzki, Colin A. Smith, Gordon K. Smyth, Luke Tierney, Jean Yee Hwa Yang, Jianhua Zhang
Software Mentions: 10
Published: over 20 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: almost 14 years ago

10.1038/s41598-020-80840-x

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil
Cited by: 7
Author(s): Luciana de Sousa Lopes, Lucas William Mendes, Jadson Emanuel Lopes Antunes, Louise Melo de Souza Oliveira, Vânia Maria Maciel Melo, Arthur Prudêncio de Araújo Pereira, Antônio Félix da Costa, José de Paula Oliveira, Cosme Rafael Martínez, Márcia do Vale Barreto Figueiredo, Ademir Sérgio Ferreira de Araújo
Software Mentions: 8
Published: over 3 years ago

10.4056/sigs.3377516

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.
Cited by: 8
Author(s): Kristen M. DeAngelis, Patrik D’haeseleer, Dylan Chivian, Blake A. Simmons, Adam P. Arkin, Konstantinos Mavromatis, Stephanie Malfatti, Susannah G. Tringe, Terry C. Hazen
Software Mentions: 7
Published: over 11 years ago

10.1371/journal.pone.0250496

Optimizing the P balance: How do modern maize hybrids react to different starter fertilizers?
Cited by: 7
Author(s): Thea Mi Weiß, Willmar L. Leiser, Alice-Jacqueline Reineke, Dongdong Li, Wenxin Liu, Volker Hahn, Tobias Würschum
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-13-270

Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data
Cited by: 11
Author(s): Αλέξανδρος Σακελλαρίου, Despina Sanoudou, George M. Spyrou
Software Mentions: 7
Published: almost 12 years ago

10.1186/1471-2105-9-46

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system
Cited by: 16
Author(s): Yuerong Zhu, Yuelin J. Zhu, Wei Xu
Software Mentions: 7
Published: over 16 years ago

10.1371/journal.pone.0258069

Does algae β-glucan affect the fecal bacteriome in dairy calves?
Cited by: 6
Author(s): G.F. Virgínio, Maria Eduarda Reis, Ana Paula da Silva, Ariany Faria de Toledo, Amanda Moelemberg Cezar, Lucas William Mendes, L.F. Greco, Horácio Montenegro, Luiz Lehmann Coutinho, Carla Maris Machado Bittar
Software Mentions: 6
Published: almost 3 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: almost 15 years ago

10.1186/1471-2105-9-86

The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Cited by: 75
Author(s): Frédéric Chalmel, Michael Primig
Software Mentions: 6
Published: over 16 years ago

10.1371/journal.pone.0099926

Insights from Computational Modeling in Inflammation and Acute Rejection in Limb Transplantation
Cited by: 23
Author(s): Dolores Wolfram, Ravi Starzl, Hubert Hackl, Derek Barclay, Theresa Hautz, Bettina Zelger, Gerald Brandacher, W. P. Andrew Lee, Nadine Eberhart, Yoram Vodovotz, Johann Pratschke, Gerhard Pierer, Stefan Schneeberger
Software Mentions: 6
Published: about 10 years ago

10.1186/1477-5956-8-66

A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis data
Cited by: 7
Author(s): Jeffrey C. Miecznikowski, Srinivasan Damodaran, Kimberly F. Sellers, Richard A. Rabin
Software Mentions: 6
Published: over 14 years ago

10.1186/s12859-019-2840-3

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network
Cited by: 30
Author(s): Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 6
Published: about 5 years ago

10.1186/s12896-019-0540-8

Enhancement of using combined packing materials on the removal of mixed sulfur compounds in a biotrickling filter and analysis of microbial communities
Cited by: 12
Author(s): Xiang Tu, Meiying Xu, Jianjun Li, Enze Li, Rongfang Feng, Gang Zhao, Shaobin Huang, Jun Guo
Software Mentions: 6
Published: about 5 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: about 3 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
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: about 10 years ago

10.3390/nu12092610

Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults
Cited by: 21
Author(s): Frida Fart, Sukithar Rajan, Rebecca Wall, Ignacio Rangel, John Peter Ganda-Mall, Lina Tingö, Robert Jan Brummer, Dirk Repsilber, Ida Schoultz, Carl Mårten Lindqvist
Software Mentions: 5
Published: almost 4 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: over 15 years ago

10.1186/1471-2105-10-203

Integrated analysis of DNA copy number and gene expression microarray data using gene sets
Cited by: 57
Author(s): Renée X. de Menezes, Marten Boetzer, Melle Sieswerda, Gert‐Jan B. van Ommen, Judith M. Boer
Software Mentions: 5
Published: about 15 years ago

10.1038/s41598-018-21874-0

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau
Cited by: 40
Author(s): Yunfu Gu, Yan Bai, Quanju Xiang, Xiumei Yu, Ke Zhao, Xiaoping Zhang, Chaonan Li, Songqin Liu, Qiang Chen
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-017-00641-7

SNPs in bone-related miRNAs are associated with the osteoporotic phenotype
Cited by: 16
Author(s): Laura De-Ugarte, Enrique Caro-Molina, Maria Rodríguez-Sanz, Miguel A. García‐Pérez, José M. Olmos, Manuel Sosa-Henríquez, Ramón Pérez‐Cano, Carlos Gómez‐Alonso, Luís Del Río, J. Mateo-Agudo, José Antonio Blázquez-Cabrera, Jesús González-Macı́as, Javier del Pino‐Montes, Manuel Muñoz‐Torres, Manuel Dı́az Curiel, Jorge Malouf, Antonio Cano, José Luis Pérez‐Castrillón, Xavier Nogués, Natalia Garcia‐Giralt, Adolfo Díez-Pérez
Software Mentions: 5
Published: over 7 years ago

10.1038/srep43465

Parasitism perturbs the mucosal microbiome of Atlantic Salmon
Cited by: 86
Author(s): Martin S. Llewellyn, S. Leadbeater, Carlos García, François‐Étienne Sylvain, María Custodio, Keng Pee Ang, Frank C. Powell, Gary R. Carvalho, Simon Creer, J. M. Elliot, Nicolas Derôme
Software Mentions: 5
Published: over 7 years ago

10.1038/srep31669

Organotypic culture in three dimensions prevents radiation-induced transformation in human lung epithelial cells
Cited by: 3
Author(s): Mariam El-Ashmawy, Melissa Coquelin, Krishna Luitel, Kimberly Batten, Jerry W. Shay
Software Mentions: 5
Published: almost 8 years ago

10.3389/fcell.2020.00557

Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric Cancer
Cited by: 10
Author(s): Nan Xiao, Yang Hu, Liran Juan
Software Mentions: 5
Published: about 4 years ago

10.1186/1471-2105-13-30

ICGE: an R package for detecting relevant clusters and atypical units in gene expression
Cited by: 7
Author(s): Itziar Irigoien, Basilio Sierra, C. Arenas
Software Mentions: 5
Published: over 12 years ago

10.1186/1471-2164-9-124

Can subtle changes in gene expression be consistently detected with different microarray platforms?
Cited by: 48
Author(s): Paola Pedotti, Peter A C ‘t Hoen, Erno Vreugdenhil, Geert J. Schenk, Rolf H. A. M. Vossen, Yavuz Ariyürek, Mattias de Hollander, Rowan Kuiper, G.J.B. van Ommen, Johan T. den Dunnen, Judith M. Boer, Renée X. de Menezes
Software Mentions: 5
Published: over 16 years ago

10.1371/journal.pone.0091828

Characterization of Changes in Gene Expression and Biochemical Pathways at Low Levels of Benzene Exposure
Cited by: 36
Author(s): Reuben Thomas, Alan Hubbard, Cliona M. McHale, Luoping Zhang, Stephen M. Rappaport, Qing Lan, Nathaniel Rothman, Roel Vermeulen, Kathryn Z. Guyton, Jennifer Jinot, Babasaheb Sonawane, Martyn T. Smith
Software Mentions: 5
Published: about 10 years ago

10.18632/aging.202634

Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 are associated with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients
Cited by: 5
Author(s): Lin Wang, Wen Zhu, Hui Ma, Liwei Wu, Hui Chen, Yijun Zhu, Liangfei Niu, Qihang Wu, Hongwei Li, Lei Shi, Leilei Li, Leiyi Wan, Jun Wang, Ka-Wing Wong, Yanzheng Song
Software Mentions: 4
Published: over 3 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: over 6 years ago

10.1186/1471-2105-7-533

Effect of various normalization methods on Applied Biosystems expression array system data
Cited by: 44
Author(s): Cátálin Bárbácioru, Yulei Wang, Roger D. Canales, Yongming Sun, David Keys, Felix Hon-Wai Chan, Karen Poulter, Raymond R. Samaha
Software Mentions: 4
Published: over 17 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: almost 14 years ago

10.1186/1471-2105-11-594

Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers
Cited by: 109
Author(s): Mohammed Dakna, Kate Harris, Alexandros Kalousis, Sébastien Carpentier, Walter Kölch, Joost P. Schanstra, Marion Haubitz, Antonia Vlahou, Harald Mischak, Mark Girolami
Software Mentions: 4
Published: over 13 years ago

10.1186/s12885-021-08218-4

MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker
Cited by: 5
Author(s): Sevan Omer Majed, Suhad Asad Mustafa
Software Mentions: 4
Published: about 3 years ago

10.1186/1471-2164-11-701

DNA methylation in glioblastoma: impact on gene expression and clinical outcome
Cited by: 176
Author(s): Amandine Etcheverry, Marc Aubry, Marie de Tayrac, Élodie Vauléon, Rachel Boniface, Frédérique Guénot, Stéphan Saïkali, Abderrahmane Hamlat, Laurent Riffaud, Philippe Menei, Véronique Quillien, Jean Mosser
Software Mentions: 4
Published: over 13 years ago

10.3390/microorganisms8020190

Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining
Cited by: 5
Author(s): Florian Centler, Sarah Günnigmann, Ingo Fetzer, Annelie Wendeberg
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0205179

Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana
Cited by: 10
Author(s): Rashmi R. Hazarika, Nikolina Šoštarić, Yi‐Feng Sun, Vera van Noort
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0199664

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients
Cited by: 32
Author(s): Bahtiyar Yılmaz, Marianne R. Spalinger, Luc Biedermann, Yannick Franc, Nicolas Fournier, Jean‐Benoît Rossel, Pascal Juillerat, Gerhard Rogler, Andrew J. Macpherson, Michael Scharl
Software Mentions: 4
Published: about 6 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: over 14 years ago

10.1371/journal.pone.0007556

An Eight-Gene Blood Expression Profile Predicts the Response to Infliximab in Rheumatoid Arthritis
Cited by: 92
Author(s): Antonio Julià, Alba Erra, Carles Palacio, Carlos Tomás, Xavier Sans, P Barceló, Sara Marsal
Software Mentions: 4
Published: almost 15 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: over 12 years ago

10.3390/cells9102257

Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD)
Cited by: 5
Author(s): Christina Kiel, Tobias Strunz, Felix Graßmann, Bernhard H. F. Weber
Software Mentions: 4
Published: almost 4 years ago

10.1289/ehp.1002546

Global Gene Expression Profiling of a Population Exposed to a Range of Benzene Levels
Cited by: 94
Author(s): Cliona M. McHale, Luoping Zhang, Qing Lan, Roel Vermeulen, Guilan Li, Alan Hubbard, Kristin E. Porter, Reuben Thomas, Christopher J. Portier, Min Shen, Stephen M. Rappaport, Shu Yin, Martyn T. Smith, Nathaniel Rothman
Software Mentions: 4
Published: about 13 years ago

10.1007/s11356-020-11597-z

Trace elements fingerprint of feathers differs between breeding and non-breeding areas in an Afro-Palearctic migratory bird, the barn swallow (Hirundo rustica)
Cited by: 4
Author(s): Marco Parolini, Michela Sturini, Federica Maraschi, Antonella Profumo, Alessandra Costanzo, Manuela Caprioli, Diego Rubolini, Roberto Ambrosini, Luca Canova
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2407-13-326

Interrogating differences in expression of targeted gene sets to predict breast cancer outcome
Cited by: 47
Author(s): Sarah A. Andres, Guy Brock, James L. Wittliff
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0013565

Ets-1 Regulates Energy Metabolism in Cancer Cells
Cited by: 48
Author(s): Meghan Verschoor, Leigh Wilson, Chris P. Verschoor, Gurmit Singh
Software Mentions: 3
Published: almost 14 years ago

10.1186/1471-2180-8-209

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro
Cited by: 53
Author(s): Philip A. Bronstein, Melanie J. Filiatrault, Christopher R. Myers, Michael Rutzke, David J. Schneider, Samuel Cartinhour
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0011044

Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients
Cited by: 391
Author(s): Michael J. Cox, Martin Allgaier, Byron Taylor, Marshall Baek, Yvonne J. Huang, Rebecca A. Daly, Ulaş Karaöz, Gary L. Andersen, Ronald C. Brown, Kei E. Fujimura, Brian Wu, Diem-Thy Tran, Jonathan L. Koff, Mary Ellen Kleinhenz, Dennis W. Nielson, Eoin L. Brodie, Susan V. Lynch
Software Mentions: 3
Published: about 14 years ago

10.3390/ijms21082689

A Circulating MicroRNA Profile in a Laser-Induced Mouse Model of Choroidal Neovascularization
Cited by: 8
Author(s): Christina Kiel, Patricia Berber, Marcus Karlstetter, Alexander Aslanidis, Tobias Strunz, Thomas Langmann, Felix Graßmann, Bernhard H. F. Weber
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-12-381

Discovering biological connections between experimental conditions based on common patterns of differential gene expression
Cited by: 21
Author(s): Adam C. Gower, Avrum Spira, Marc E. Lenburg
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0247495

Change detection of auditory tonal patterns defined by absolute versus relative pitch information. A combined behavioural and EEG study
Cited by: 3
Author(s): Nina Coy, M. K. M. Bader, Erich Schröger, Sabine Grimm
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0002987

Identification of Functional Networks of Estrogen- and c-Myc-Responsive Genes and Their Relationship to Response to Tamoxifen Therapy in Breast Cancer
Cited by: 90
Author(s): Elizabeth A. Musgrove, C. Marcelo Sergio, Sherene Loi, Claire K. Inman, Luke R. Anderson, M. Chehani Alles, Mark Pinese, C. Elizabeth Caldon, Judith Schütte, Margaret Gardiner-Garden, Christopher J. Ormandy, Grant A. McArthur, Alison J. Butt, Robert L. Sutherland
Software Mentions: 3
Published: almost 16 years ago

10.1186/1755-8794-5-66

Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines
Cited by: 199
Author(s): Andreas Schlicker, Garry Beran, Christine Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, D Castro, George M. Orphanides, Tim French, Lodewyk Wessels
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0133219

Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer
Cited by: 20
Author(s): James E. Korkola, Eric A. Collisson, Laura M. Heiser, Chris J. Oates, Nora Bayani, Solomon Itani, Amanda Esch, Wallace Thompson, Obi L. Griffith, Nicholas J. Wang, Wen‐Lin Kuo, Brian Cooper, Jessica I. Billig, Safiyyah Ziyad, Jenny L. Hung, Lakshmi R. Jakkula, Heidi S. Feiler, Yiling Lu, Gordon B. Mills, Paul T. Spellman, Claire J. Tomlin, Sach Mukherjee, Joe W. Gray
Software Mentions: 3
Published: about 9 years ago

10.1186/s13071-015-0939-6

Preliminary expression profile of cytokines in brain tissue of BALB/c mice with Angiostrongylus cantonensis infection
Cited by: 20
Author(s): Liping Yu, Xiaoying Wu, Jie Wei, Qi Liao, Liang Xu, Siqi Luo, Xiaofeng Zeng, Yi Zhao, Ziquan Lv, Zhongdao Wu
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.ppat.0030077

Epigenomic Modifications Predict Active Promoters and Gene Structure in Toxoplasma gondii
Cited by: 106
Author(s): Mathieu Gissot, Krystyna A. Kelly, James W. Ajioka, John M. Greally, Kami Kim
Software Mentions: 3
Published: about 17 years ago

10.1186/gb-2009-10-4-r38

Transcriptional features of genomic regulatory blocks
Cited by: 100
Author(s): Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O. Daub, Yoshihide Hayashizaki, Boris Lenhard
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2105-11-S9-S6

Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
Cited by: 21
Author(s): Alexander A. Morgan, Purvesh Khatri, Richard H. Jones, Minnie M. Sarwal, Atul J. Butte
Software Mentions: 3
Published: almost 14 years ago

10.1186/1752-0509-1-56

Gene regulatory networks in lactation: identification of global principles using bioinformatics
Cited by: 124
Author(s): Danielle G. Lemay, Margaret C. Neville, Michael C. Rudolph, Katherine S. Pollard, J. Bruce German
Software Mentions: 3
Published: over 16 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: over 17 years ago

10.3389/fpls.2018.01347

Genome-Wide Association Mapping in a Rice MAGIC Plus Population Detects QTLs and Genes Useful for Biofortification
Cited by: 74
Author(s): Gwen Iris L. Descalsota, B. P. Mallikarjuna Swamy, Hein Zaw, Mary Ann Inabangan-Asilo, Amery Amparado, Ramil Mauleon, Prabhjit Chadha-Mohanty, Emily C. Arocena, Chitra Raghavan, Hei Leung, Jose E. Hernandez, Antonio G. Lalusin, Merlyn S. Mendioro, Ma. Genaleen Q. Diaz, Russell Reinke
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-33323-z

Genome-wide expression profiling of glioblastoma using a large combined cohort
Cited by: 20
Author(s): Jing Tang, Deyan He, Pingrong Yang, Junquan He, Songsong Wang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-020-07494-w

Identification of common signatures in idiopathic pulmonary fibrosis and lung cancer using gene expression modeling
Cited by: 7
Author(s): Liubing Dong, Jiawen Yi, Maodong Xiang, Hongying Zhao, Yuhui Zhang
Software Mentions: 3
Published: almost 4 years ago

10.3389/fpls.2018.01453

Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation
Cited by: 12
Author(s): Yujiao Qu, Julia Legen, J Arndt, Stephanie Henkel, Galina Hoppe, Christopher Thieme, Giovanna Ranzini, Jose M. Muiño, Andreas Weihe, Uwe Ohler, Gert Weber, Oren Ostersetzer, Christian Schmitz‐Linneweber
Software Mentions: 3
Published: almost 6 years ago

10.3389/fimmu.2019.02651

Rapid Proteome Changes in Plasma and Cerebrospinal Fluid Following Bacterial Infection in Preterm Newborn Pigs
Cited by: 17
Author(s): Tik Muk, Allan Stensballe, Stanislava Pankratova, Duc Ninh Nguyen, Anders Brunse, Per Torp Sangild, Pingping Jiang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-018-4675-0

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction
Cited by: 31
Author(s): Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Sharon Benjamini, Shoval Miyara, M. Ruzal, Manfred Grabherr, Nima Rafati, Anna Maja Molin, Ken Pendavis, Shane C. Burgess, Leif Andersson, Miriam Friedman‐Einat
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-11-344

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays
Cited by: 18
Author(s): Cyril Dégletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, Paul Chuchana, Pierre Jouventin, Christian Gautier, Claude Duchamp
Software Mentions: 3
Published: about 14 years ago

10.1186/1756-8935-3-10

Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation
Cited by: 56
Author(s): Y. Amy Tang, Derek Huntley, Giovanni Montana, Andrea Cerase, Tatyana B. Nesterova, Neil Brockdorff
Software Mentions: 3
Published: about 14 years ago

10.1186/s12859-020-3388-y

ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles
Cited by: 64
Author(s): Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang, Guohua Wang
Software Mentions: 3
Published: over 4 years ago

10.1289/ehp.9843

Associations between Prenatal Exposure to Polychlorinated Biphenyls and Neonatal Thyroid-Stimulating Hormone Levels in a Mexican-American Population, Salinas Valley, California
Cited by: 89
Author(s): Jonathan Chevrier, Brenda Eskenazi, Asa Bradman, Laura Fenster, Dana Boyd Barr
Software Mentions: 3
Published: almost 17 years ago

10.1186/s12864-017-3667-9

Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes
Cited by: 23
Author(s): Leticia Díaz-Beltrán, Francisco J. Esteban, Maya Varma, Alp Ortuzk, Maude M. David, Dennis P. Wall
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.7451

Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment
Cited by: 21
Author(s): Jan Budczies, Nicole Pfarr, Albrecht Stenzinger, Denise Treue, Volker Endris, Fakher Ismaéel, Nikola Bangemann, Jens-Uwe Blohmer, Manfred Dietel, Sibylle Loibl, Frederick Klauschen, Wilko Weichert, Carsten Denkert
Software Mentions: 3
Published: over 8 years ago

10.3892/mmr.2015.3335

Analysis of mechanical ventilation and lipopolysaccharide-induced acute lung injury using DNA microarray analysis
Cited by: 4
Author(s): Yuqing Chen, Xin Zhou, Ling Rong
Software Mentions: 2
Published: over 9 years ago

10.1186/s12870-017-1068-5

Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana
Cited by: 64
Author(s): Carla Ibáñez, Yvonne Poeschl, Tom Peterson, Julia Bellstädt, Kathrin Denk, Andreas Gogol-Döring, Marcel Quint, Carolin Delker
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pgen.1002959

Determinants of Human Adipose Tissue Gene Expression: Impact of Diet, Sex, Metabolic Status, and Cis Genetic Regulation
Cited by: 49
Author(s): Nathalie Viguerie, Émilie Montastier, Jean‐José Maoret, Bruno Roussel, Marion Combes, Carine Valle, Nathalie Villa-Vialaneix, Jason S. Iacovoni, J. Martinez, Claus Holst, Arne Astrup, Hubert Vidal, Karine Clément, Jörg Hager, Wim H. M. Saris, Dominique Langin
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0158051

Post-Bariatric Surgery Changes in Quinolinic and Xanthurenic Acid Concentrations Are Associated with Glucose Homeostasis
Cited by: 21
Author(s): Marie Favennec, Benjamin Hennart, Marie Verbanck, Marie Pigeyre, Robert Caïazzo, Violeta Raverdy, Hélène Verkindt, Audrey Leloire, Gilles J. Guillemin, Loïc Yengo, Delphine Allorge, Philippe Froguel, François Pattou, Odile Poulain‐Godefroy
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0024205

Genome-Wide Functional Profiling Reveals Genes Required for Tolerance to Benzene Metabolites in Yeast
Cited by: 48
Author(s): Matthew North, Vickram J. Tandon, Reuben Thomas, Alex Loguinov, Inna Gerlovina, Alan Hubbard, Luoping Zhang, Martyn T. Smith, Chris D. Vulpe
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0215946

Does MHC heterozygosity influence microbiota form and function?
Cited by: 17
Author(s): M.A. Wadud Khan, W. Zac Stephens, Ahmed Dawood Mohammed, June L. Round, Jason L. Kubinak
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0025147

Phenotypic Landscape of Saccharomyces cerevisiae during Wine Fermentation: Evidence for Origin-Dependent Metabolic Traits
Cited by: 96
Author(s): Carole Camarasa, Isabelle Sanchez, Pascale Brial, Frédéric Bigey, Sylvie Dequin
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12859-019-2893-3

JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles
Cited by: 3
Author(s): Yi Li, Yanan Liu, Yiming Wu, Xudong Zhao
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0084772

Network Analysis Highlights Complex Interactions between Pathogen, Host and Commensal Microbiota
Cited by: 159
Author(s): Sébastien Boutin, Louis Bernatchez, Céline Audet, Nicolas Derôme
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-015-2259-9

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds
Cited by: 8
Author(s): Magali SanCristobal, Florian Rohart, Christine Lascor, Marcel Bouffaud, Lidwine Trouilh, Pascal G.P. Martin, Yannick Lippi, Thierry Tribout, Thomas Faraut, Marie‐José Mercat, Denis Milan, Laurence Liaubet
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-015-2024-0

Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize
Cited by: 86
Author(s): Chunxiao Fan, Zhiqiang Hao, Jiahong Yan, Guanglin Li
Software Mentions: 2
Published: almost 9 years ago

10.1002/ece3.2839

The evolution of the major histocompatibility complex in upstream versus downstream river populations of the longnose dace
Cited by: 3
Author(s): Erika Crispo, Haley R. Tunna, Noreen Hussain, Sergio Rodríguez, Scott A. Pavey, Leland J. Jackson, Sean M. Rogers
Software Mentions: 2
Published: over 7 years ago

10.1186/s12967-021-02848-9

Inhibition of CPT1a as a prognostic marker can synergistically enhance the antileukemic activity of ABT199
Cited by: 9
Author(s): Shihui Mao, Qing Ling, Jiajia Pan, Fenglin Li, Shujuan Huang, Wenle Ye, Wuran Wei, Xiangjie Lin, Yu Qin, Yungui Wang, Xin Huang, Jiansong Huang, Jinghan Wang, Jie Jin
Software Mentions: 2
Published: about 3 years ago

10.3389/fimmu.2020.565862

Early Protein Markers of Necrotizing Enterocolitis in Plasma of Preterm Pigs Exposed to Antibiotics
Cited by: 7
Author(s): Yannan Jiang, Tik Muk, Allan Stensballe, Duc Ninh Nguyen, Per Torp Sangild, Pingping Jiang
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2015.01443

Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon
Cited by: 81
Author(s): Acácio Aparecido Navarrete, Andressa Monteiro Venturini, Kyle Meyer, Ann M. Klein, James M. Tiedje, Brendan J. M. Bohannan, Klaus Nüsslein, Siu Mui Tsai, Jorge L. M. Rodrigues
Software Mentions: 2
Published: over 8 years ago

Projects: bioconductor: multtest

Papers Mentioning multtest 158