bioconductor: gage | Projects | Ecosyste.ms: Papers

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: about 3 years ago

10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: about 11 years ago

10.1242/jeb.210302

Time-critical influences of gestational diet in a seahorse model of male pregnancy
Cited by: 7
Author(s): Francisco Otero‐Ferrer, Freddy Lättekivi, James Ord, Ene Reimann, Sulev Kõks, Marisol Izquierdo, William V. Holt, Alireza Fazeli
Software Mentions: 11
Published: almost 6 years ago

10.1186/s12859-016-1125-3

Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysis
Cited by: 3
Author(s): Nathan James Allen Cormier, Tyler Kolisnik, Mark Bieda
Software Mentions: 10
Published: over 8 years ago

10.1186/s40246-019-0226-2

Size matters: how sample size affects the reproducibility and specificity of gene set analysis
Cited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Software Mentions: 10
Published: about 5 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: about 3 years ago

10.1186/s13073-020-00806-6

Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study
Cited by: 8
Author(s): Valborg Guðmundsdóttir, Helle Pedersen, Gianluca Mazzoni, Kristine H. Allin, Anna Artati, Joline W.J. Beulens, Karina Banasik, Caroline Brorsson, Henna Cederberg, Elizaveta Chabanova, Federico De Masi, Petra Elders, Ian Forgie, G Giordano, Harald Grallert, Ramneek Gupta, Mark Haid, Torben Hansen, Tue H. Hansen, Andrew T. Hattersley, Alison Heggie, Mun‐Gwan Hong, Angus G. Jones, Robert W. Koivula, Tarja Kokkola, Markku Laakso, Peter Løngreen, Anubha Mahajan, Andrea Mari, Colin N.A. Palmer, Donna McEvoy, Petra B. Musholt, Imre Pávó, Cornelia Prehn, Hartmut Ruetten, Martin Ridderstråle, Femke Rutters, Sapna Sharma, Roderick C. Slieker, Ali Syed, Juan Fernández Tajes, Cecilia Engel Thomas, Henrik S. Thomsen, Jagadish Vangipurapu, Henrik Vestergaard, Ana Viñuela, Agata Wesolowska-Andersen, Mark Walker, Jerzy Adamski, Jochen M. Schwenk, Mark McCarthy, Ewan R. Pearson, Emmanouil T. Dermitzakis, Paul W. Franks, Oluf Pedersen, Søren Brunak
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.csbj.2021.04.056

A computational analysis of transcriptional profiles from CD8(+) T lymphocytes reveals potential mechanisms of HIV/AIDS control and progression
Cited by: 3
Author(s): Sergey Ivanov, Dmitry Filimonov, O. Tarasova
Software Mentions: 7
Published: almost 4 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in <i>Drosophila</i> heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: about 8 years ago

10.1038/s41598-020-70173-0

Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers
Cited by: 17
Author(s): Sofia Paraskevopoulou, Alice B. Dennis, Guntram Weithoff, Ralph Tiedemann
Software Mentions: 7
Published: over 4 years ago

10.3390/ijms21165923

Oxidant-Induced Alterations in the Adipocyte Transcriptome: Role of the Na,K-ATPase Oxidant Amplification Loop
Cited by: 7
Author(s): Komal Sodhi, James Denvir, Jiang Liu, Juan Sanabria, Yiliang Chen, Roy L. Silverstein, Zijian Xie, Nader G. Abraham, Joseph I. Shapiro
Software Mentions: 7
Published: over 4 years ago

10.1093/bioinformatics/btx179

<i>Fuento</i>: functional enrichment for bioinformatics
Cited by: 5
Author(s): David Tobias Weichselbaum, Bojan Žagrović, Anton A. Polyansky
Software Mentions: 5
Published: over 7 years ago

10.3389/fimmu.2021.626098

GMP-Compliant Universal Antigen Presenting Cells (uAPC) Promote the Metabolic Fitness and Antitumor Activity of Armored Cord Blood CAR-NK Cells
Cited by: 18
Author(s): Enli Liu, Sonny Ang, Lucila Nassif Kerbauy, Rafet Basar, Indreshpal Kaur, Mecit Kaplan, Li Li, Yijiu Tong, May Daher, Emily L. Ensley, Nadima Uprety, Ana Karen Nunez Cortes, Ryan Z Yang, Ye Li, Hila Shaim, Francia Reyes Silva, Paul Lin, Vakul Mohanty, Sunil Acharya, Mayra Shanley, Luis Muniz-Feliciano, Pinaki P. Banerjee, Ken Chen, Richard E. Champlin, Elizabeth J. Shpall, Katayoun Rezvani
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-019-2870-x

anamiR: integrated analysis of MicroRNA and gene expression profiling
Cited by: 12
Author(s): Ti-Tai Wang, Chien‐Yueh Lee, Liang‐Chuan Lai, Mong‐Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-019-6127-x

Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake
Cited by: 9
Author(s): Haibo Li, Kristina M. Feye, Yet Nguyen, Anoosh Rakhshandeh, Crystal L. Loving, Jack C. M. Dekkers, Nicholas K. Gabler, Christopher K. Tuggle
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-019-5974-9

Comparison of gene expression profile of the spinal cord of sprouting-capable neonatal and sprouting-incapable adult mice
Cited by: 9
Author(s): Hiroshi Tsujioka, Toshio Yamashita
Software Mentions: 5
Published: over 5 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1006348

HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation
Cited by: 32
Author(s): Yoshiaki Nakano, Naoko Misawa, Guillermo Juarez-Fernandez, Miyu Moriwaki, Shinji Nakaoka, Takaaki Funo, Eri Yamada, Andrew Soper, Rokusuke Yoshikawa, Diako Ebrahimi, Yuuya Tachiki, Shingo Iwami, Reuben S. Harris, Yoshio Koyanagi, Kei Sato
Software Mentions: 4
Published: over 7 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0148818

Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis
Cited by: 14
Author(s): Wonjun Lee, Sang Cheol Kim, Jong Ho Yoon, Sang Jun Yoon, Jong-Tae Lim, You Sun Kim, Sung Won Kwon, Jeong Hill Park
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-020-64801-y

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels
Cited by: 7
Author(s): Po‐Yu Liu, An-Chi Cheng, Shu‐Mei Huang, Hsiao Pei Lu, Tatsuo Oshida, Wenhua Liu, Hongjun Yu
Software Mentions: 4
Published: over 4 years ago

10.1186/s13287-020-02111-w

Radiation-induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectum
Cited by: 11
Author(s): Felipe Rodriguez-Tirado, Payel Bhanja, Eduardo Castro-Nallar, Ximena Diaz Olea, Catalina Salamanca, Subhrajit Saha
Software Mentions: 4
Published: almost 4 years ago

10.18632/oncotarget.27678

Ewing sarcoma family of tumors-derived small extracellular vesicle proteomics identify potential clinical biomarkers
Cited by: 19
Author(s): Glenson Samuel, Jennifer Crow, Jon B. Klein, Michael L. Merchant, Emily Nissen, Devin C. Koestler, Kris Laurence, Xiaobo Liang, Kathleen Neville, Vincent S. Staggs, Atif Ahmed, Safinur Atay, Andrew K. Godwin
Software Mentions: 3
Published: over 4 years ago

10.3390/biology9120435

Transcriptome Analysis Reveals High Similarities between Adult Human Cardiac Stem Cells and Neural Crest-Derived Stem Cells
Cited by: 11
Author(s): Anna L. Höving, Katharina Sielemann, Johannes F. W. Greiner, Barbara Kaltschmidt, Cornelius Knabbe, Christian Kaltschmidt
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0126859

Increased Expression of Angiogenic and Inflammatory Proteins in the Vitreous of Patients with Ischemic Central Retinal Vein Occlusion
Cited by: 42
Author(s): Christoph Ehlken, Bastian Grundel, Daniel de Sousa Michels, Bernd Junker, Andreas Stahl, Günther Schlunck, Lutz L. Hansen, Nicolas Feltgen, Gottfried Martin, Hansjürgen Agostini, Amelie Pielen
Software Mentions: 3
Published: over 9 years ago

10.3389/fimmu.2019.03103

Interleukin-2-Inducible T-Cell Kinase Deficiency Impairs Early Pulmonary Protection Against Mycobacterium tuberculosis Infection
Cited by: 15
Author(s): Lu Huang, Kaixiong Ye, Michael C McGee, Natalie F. Nidetz, Jessica Elmore, Candice B Limper, Teresa Southard, David G. Russell, Avery August, Weishan Huang
Software Mentions: 3
Published: almost 5 years ago

10.3389/fmicb.2019.02411

A Short-Term Feeding of Dietary Casein Increases Abundance of Lactococcus lactis and Upregulates Gene Expression Involving Obesity Prevention in Cecum of Young Rats Compared With Dietary Chicken Protein
Cited by: 12
Author(s): Zhanming Fan, Shangxin Song, Yafang Ma, Xinglian Xu
Software Mentions: 3
Published: about 5 years ago

10.1002/ijc.32384

Transcriptomic profiling reveals three molecular phenotypes of adenocarcinoma at the gastroesophageal junction
Cited by: 15
Author(s): Jan Bornschein, Lorenz Wernisch, Maria Secrier, Ahmad Miremadi, Juliane Perner, Shona MacRae, Maria O’Donovan, Richard Newton, Suraj Menon, Lawrence Bower, Matthew Eldridge, Ginny Devonshire, Calvin Cheah, Richard Turkington, Richard Hardwick, Michael Selgrad, Marino Venerito, Peter Malfertheiner, Rebecca C. Fitzgerald
Software Mentions: 3
Published: over 5 years ago

10.1111/acel.13356

Bioenergetic and inflammatory systemic phenotypes in Alzheimer’s disease APOE ε4‐carriers
Cited by: 11
Author(s): Heather Wilkins, Xiaowan Wang, Blaise Menta, Scott J. Koppel, Rebecca Bothwell, Annette M. Becker, Heidi Anderson, Erich Schwartz, Dong Pei, Nanda Kumar Yellapu, Prabhakar Chalise, Cynthia M. Gouvion, Mohammad Haeri, Jeffrey M. Burns, Russell H. Swerdlow
Software Mentions: 2
Published: over 3 years ago

10.1186/s13058-019-1111-6

Imprint of parity and age at first pregnancy on the genomic landscape of subsequent breast cancer
Cited by: 22
Author(s): Bastien Nguyen, David Venet, Matteo Lambertini, Christine Desmedt, Roberto Salgado, Hugo M. Horlings, Françoise Rothé, Christos Sotiriou
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-76555-8

Transcriptome and methylome analysis reveals three cellular origins of pituitary tumors
Cited by: 22
Author(s): Keiko Taniguchi‐Ponciano, Sergio Andonegui-Elguera, Eduardo Peña-Martínez, Gloria Silva-Román, Sandra Vela-Patiño, Erick Gómez‐Apo, Laura Chávez-Macías, Guadalupe Vargas‐Ortega, Laura Espinosa-de-los-Monteros, Baldomero González‐Virla, Carolina Velázquez Pérez, Aldo Ferreira‐Hermosillo, Etual Espinosa-Cárdenas, Claudia Ramírez‐Rentería, Ernesto Sosa, Blas López-Félix, Gerardo Guinto, Daniel Marrero‐Rodríguez, Moisés Mercado
Software Mentions: 2
Published: about 4 years ago

10.1186/s13395-019-0210-5

Defective angiogenesis in CXCL12 mutant mice impairs skeletal muscle regeneration
Cited by: 12
Author(s): David Hardy, Mylène Fefeu, Aurore Besnard, David Briand, Paméla Gasse, Fernando Arenzana-Seisdedos, Pierre Rocheteau, Fabrice Chrétien
Software Mentions: 2
Published: about 5 years ago

10.1186/s12863-020-00858-y

Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions
Cited by: 4
Author(s): Beatrix Bicskei, John B. Taggart, James E. Bron, Kevin A. Glover
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2407-12-232

MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells
Cited by: 127
Author(s): Lea H. Gregersen, Anders Jacobsen, Lisa B. Frankel, Jiayu Wen, Anders Krogh, Anders H. Lund
Software Mentions: 2
Published: over 12 years ago

10.1038/s42003-020-01353-x

Single-cell analysis of AIMP2 splice variants informs on drug sensitivity and prognosis in hematologic cancer
Cited by: 5
Author(s): Jayoung Ku, Ryul Kim, Dongchan Kim, Daeyoon Kim, Seulki Song, Keonyong Lee, Namseok Lee, Min A Kim, Sung Soo Yoon, Nam Hoon Kwon, Sung Hoon Kim, Yoosik Kim, Youngil Koh
Software Mentions: 2
Published: about 4 years ago

10.3389/fnmol.2018.00219

Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model
Cited by: 20
Author(s): Tímea Aczél, József Kun, Éva Szőke, Tibor A. Rauch, Sini Junttila, Attila Gyenesei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.203509

Glutathione is an aging-related metabolic signature in the mouse kidney
Cited by: 6
Author(s): Eunyong Ahn, Jueun Lee, Jin Kyu Han, Seungmin Lee, Ki‐Sun Kwon, Geum‐Sook Hwang
Software Mentions: 1
Published: about 3 years ago

10.1186/s13024-018-0288-y

Progranulin reduces insoluble TDP-43 levels, slows down axonal degeneration and prolongs survival in mutant TDP-43 mice
Cited by: 32
Author(s): Sander Beel, Sarah Herdewyn, Raheem Fazal, Mathias De Decker, Matthieu Moisse, Wim Robberecht, Ludo Van Den Bosch, Philip Van Damme
Software Mentions: 1
Published: about 6 years ago

10.3390/microorganisms9040876

Immune Transcriptome of Cells Infected with Enterovirus Strains Obtained from Cases of Autoimmune Thyroid Disease
Cited by: 4
Author(s): Anello Marcello Poma, Sarah Salehi Hammerstad, Angelo Genoni, Alessio Basolo, Knut Dahl‐Jørgensen, Antonio Toniolo
Software Mentions: 1
Published: over 3 years ago

10.3390/microorganisms8071031

Immune Transcriptome of Cells Infected with Enterovirus Strains Obtained from Cases of Type 1 Diabetes
Cited by: 13
Author(s): Anello Marcello Poma, Angelo Genoni, Francesco Broccolo, Maria Denaro, Alberto Pugliese, Fulvio Basolo, Antonio Toniolo
Software Mentions: 1
Published: over 4 years ago

10.1093/bjsopen/zraa045

Use of gene expression profiling to identify candidate genes for pretherapeutic patient classification in acute appendicitis
Cited by: 11
Author(s): Natalie Kiss, Maximiliane I. Minderjahn, Josephine Reismann, Jan F. Svensson, Tomas Wester, Kathrin Hauptmann, Martina Schad, Jim Kallarackal, Horst von Bernuth, Marc Reismann
Software Mentions: 1
Published: almost 4 years ago

10.1038/srep39258

Transcriptomic profiling of microglia reveals signatures of cell activation and immune response, during experimental cerebral malaria
Cited by: 37
Author(s): Barbara Capuccini, Jing-wen Lin, Carlos Talavera-López, Shahid M. Khan, Jan Sodenkamp, Roberta Spaccapelo, Jean Langhorne
Software Mentions: 1
Published: almost 8 years ago

10.1093/bioinformatics/btt285

Pathview: an R/Bioconductor package for pathway-based data integration and visualization
Cited by: 1,316
Author(s): Weijun Luo, Cory Brouwer
Software Mentions: 1
Published: over 11 years ago

10.1186/s12864-021-07502-8

Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics
Cited by: 125
Author(s): Peter D. Karp, Peter E. Midford, Ron Caspi, Arkady B. Khodursky
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: gage

Papers Mentioning gage 45