bioconductor: SPIA | Projects | Ecosyste.ms: Papers

10.1186/1472-6882-14-14

Sho-saiko-to, a traditional herbal medicine, regulates gene expression and biological function by way of microRNAs in primary mouse hepatocytes
Cited by: 11
Author(s): Kwang Hoon Song, Yun Hee Kim, Bu-Yeo Kim
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12918-018-0646-y

Integrating proteomic and phosphoproteomic data for pathway analysis in breast cancer
Cited by: 6
Author(s): Jie Ren, Bo Wang, Jing Li
Software Mentions: 2
Published: about 6 years ago

10.1155/2018/5670210

Pathway Network Analysis of Complex Diseases Based on Multiple Biological Networks
Cited by: 10
Author(s): Fang Zheng, Wei Le, Liang Zhao, Fuchuan Ni
Software Mentions: 2
Published: over 6 years ago

10.1002/cam4.1301

Biological signaling pathways and potential mathematical network representations: biological discovery through optimization
Cited by: 4
Author(s): Clara E. Isaza, Juan Miguel Pérez Rosas, Enery Lorenzo, Arlette Marrero, Cristina Ortiz, Michael Ortiz, Lynn Perez, Mauricio Cabrera‐Ríos
Software Mentions: 2
Published: over 6 years ago

10.1186/s40168-018-0439-y

Microbiome–host systems interactions: protective effects of propionate upon the blood–brain barrier
Cited by: 279
Author(s): Lesley Hoyles, Tom Snelling, Umm-Kulthum Ismail Umlai, Jeremy K. Nicholson, Simon R. Carding, Robert C. Glen, Simon McArthur
Software Mentions: 2
Published: over 6 years ago

10.1002/1878-0261.12480

Interferon‐regulated suprabasin is essential for stress‐induced stem‐like cell conversion and therapy resistance of human malignancies
Cited by: 9
Author(s): Soňa Hubáčková, Miroslav Přibyl, Lenka Kyjacová, Alena Moudrá, Rastislav Dzijak, Barbora Šalovská, Hynek Strnad, Vojtěch Tambor, Terezie Imrichová, Jiří Švec, Pavel Vodička, Radka Václavíková, Lukáš Rob, Jiří Bártek, Zdeněk Hodný
Software Mentions: 2
Published: over 5 years ago

10.3390/v10110649

Characterizing the Different Effects of Zika Virus Infection in Placenta and Microglia Cells
Cited by: 15
Author(s): Maria del Pilar Martinez Viedma, Brett E. Pickett
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1002967

Differential Expression Analysis for Pathways
Cited by: 65
Author(s): Winston Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins, Eugene Kolker
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0031428

p53-Dependent Transcriptional Responses to Interleukin-3 Signaling
Cited by: 7
Author(s): Anissa Jabbour, Lavinia Gordon, Carmel Patricia Daunt, Benjamin D Green, Chung Hoow Kok, Richard J. D’Andrea, Paul G. Ekert
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0138524

Integrative Analysis of Transcriptomic and Epigenomic Data to Reveal Regulation Patterns for BMD Variation
Cited by: 22
Author(s): Jigang Zhang, Lijun Tan, Chao Xu, Hao He, Qing Tian, Yu Zhou, Chuan Qiu, Xiang-Ding Chen, Hong‐Wen Deng
Software Mentions: 2
Published: about 9 years ago

10.3389/fgene.2019.00441

Identification of Cancer Dysfunctional Subpathways by Integrating DNA Methylation, Copy Number Variation, and Gene-Expression Data
Cited by: 10
Author(s): Siyao Liu, Buhong Zheng, Yuqi Sheng, Qingfei Kong, Ying Jiang, Yang Yang, Xudong Han, Cheng Liang, Yunpeng Zhang, Junwei Han
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2016.00381

Impact of Enriched Environment on Murine T Cell Differentiation and Gene Expression Profile
Cited by: 15
Author(s): Lorenza Rattazzi, Giuseppa Piras, Samuel Brod, Koval Smith, M. Ono, Fulvio D’Acquisto
Software Mentions: 2
Published: about 8 years ago

10.3390/genes9070323

DynSig: Modelling Dynamic Signaling Alterations along Gene Pathways for Identifying Differential Pathways
Cited by: 0
Author(s): Ming Shi, Yanwen Chong, Weiming Shen, Xueping Xie, Hongqiang Wang
Software Mentions: 2
Published: over 6 years ago

10.1186/s13073-014-0056-8

DawnRank: discovering personalized driver genes in cancer
Cited by: 194
Author(s): Jack P. Hou, Jian Ma
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-018-37489-4

Metabolism as an early predictor of DPSCs aging
Cited by: 26
Author(s): Dannie Macrin, Ammar Alghadeer, Yan Ting Zhao, Jason W. Miklas, Abdiasis M. Hussein, Damien Detraux, Aaron M. Robitaille, Anup Madan, Randall T. Moon, Yuliang Wang, Arikketh Devi, Julie Mathieu, Hannele Ruohola‐Baker
Software Mentions: 2
Published: almost 6 years ago

10.1038/tp.2013.54

CD4+ but not CD8+ T cells revert the impaired emotional behavior of immunocompromised RAG-1-deficient mice
Cited by: 73
Author(s): Lorenza Rattazzi, Giuseppa Piras, M. Ono, Robert M. J. Deacon, Carmine Pariante, Fulvio D’Acquisto
Software Mentions: 2
Published: over 11 years ago

10.18632/oncotarget.9788

Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification
Cited by: 36
Author(s): Salvatore Alaimo, Rosalba Giugno, Mario Acunzo, Dario Veneziano, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 2
Published: over 8 years ago

10.1155/2014/497046

Point of Care Technologies for HIV
Cited by: 39
Author(s): Mohan Kumar Haleyur Giri Setty, Indira Hewlett
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0102803

Bayesian Pathway Analysis of Cancer Microarray Data
Cited by: 14
Author(s): Melike Korucuoglu, Senol Isci, Arzucan Özgür, Hasan H. Otu
Software Mentions: 1
Published: over 10 years ago

10.1186/s12859-020-3444-7

Network hub-node prioritization of gene regulation with intra-network association
Cited by: 9
Author(s): Hung-Ching Chang, Chiao-Pei Chu, Shu-Ju Lin, Chuhsing Kate Hsiao
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0179063

Salsalate ameliorates metabolic disturbances by reducing inflammation in spontaneously hypertensive rats expressing human C-reactive protein and by activating brown adipose tissue in nontransgenic controls
Cited by: 6
Author(s): Jaroslava Trnovská, Jan Šilhavý, Ondřej Kuda, V. Landa, Václav Zı́dek, Petr Mlejnek, Miroslava Šimáková, Hynek Strnad, Vojtěch Škop, Olena Oliyarnyk, Ludmila Kazdová, Martin Haluzı́k, Michal Pravenec
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0101906

Fumaric Acid Esters Can Block Pro-Inflammatory Actions of Human CRP and Ameliorate Metabolic Disturbances in Transgenic Spontaneously Hypertensive Rats
Cited by: 20
Author(s): Jan Šilhavý, Václav Zı́dek, Petr Mlejnek, V. Landa, Miroslava Šimáková, Hynek Strnad, Olena Oliyarnyk, Vojtěch Škop, Ludmila Kazdová, Theodore W. Kurtz, Michal Pravenec
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0057662

Aberrant Gene Expression in Dogs with Portosystemic Shunts
Cited by: 27
Author(s): Frank G. van Steenbeek, Lindsay Van den Bossche, Guy C. M. Grinwis, Anne Kummeling, Ingrid H. M. van Gils, Marian J. A. Groot Koerkamp, Dik van Leenen, Frank C. P. Holstege, Louis C. Penning, J. Rothuizen, P.A.J. Leegwater, Bart Spee
Software Mentions: 1
Published: almost 12 years ago

10.1177/2045893217729096

Differential IL‐1 signaling induced by BMPR2 deficiency drives pulmonary vascular remodeling
Cited by: 21
Author(s): Josephine Pickworth, Alexander Rothman, James Iremonger, Helen Casbolt, Kay Hopkinson, Peter Hickey, Santhi Gladson, Sheila Shay, Nicholas W. Morrell, Sheila Francis, James West, Allan Lawrie
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0070093

Biphasic Functional Regulation in Hippocampus of Rat with Chronic Cerebral Hypoperfusion Induced by Permanent Occlusion of Bilateral Common Carotid Artery
Cited by: 32
Author(s): Jihye Bang, Won Kyung Jeon, In Sun Lee, Jung‐Soo Han, Bu-Yeo Kim
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0176950

Identifying biologically relevant putative mechanisms in a given phenotype comparison
Cited by: 5
Author(s): Samer Najeeb Hanoudi, Michèle Donato, Sorin Drăghici
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0026938

Functional Correlations of Pathogenesis-Driven Gene Expression Signatures in Tuberculosis
Cited by: 148
Author(s): Jeroen Maertzdorf, Martin O. C. Ota, Dirk Repsilber, Hans-Joachim Mollenkopf, January Weiner, Philip C. Hill, Stefan H. E. Kaufmann
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pmed.0040023

Prediction of Graft-Versus-Host Disease in Humans by Donor Gene-Expression Profiling
Cited by: 95
Author(s): Chantal Baron, Roland Somogyi, Larry D. Greller, Vincent Rineau, Peter Wilkinson, Carolyn R. Cho, Mark J. Cameron, David J. Kelvin, Pierre Chagnon, Denis‐Claude Roy, Lambert Busque, Rafick‐Pierre Sékaly, Claude Perreault
Software Mentions: 1
Published: almost 18 years ago

10.1038/s41416-019-0553-z

FXYD5 (Dysadherin) upregulation predicts shorter survival and reveals platinum resistance in high-grade serous ovarian cancer patients
Cited by: 21
Author(s): Renata Tassi, Angela Gambino, Laura Ardighieri, Eliana Bignotti, Paola Todeschini, Chiara Romani, Laura Zanotti, Mattia Bugatti, Fulvio Borella, Dionyssios Katsaros, Germana Tognon, Enrico Sartori, Franco Odicino, Chiara Romualdi, Antonella Ravaggi
Software Mentions: 1
Published: over 5 years ago

10.1155/2014/408683

Microarray Analysis of Serum mRNA in Patients with Head and Neck Squamous Cell Carcinoma at Whole-Genome Scale
Cited by: 6
Author(s): Markéta Čapková, Jana Šáchová, Hynek Strnad, Michal Kolář, Miluše Hroudová, Martin Chovanec, Zdeněk Čada, Martin Šteffl, Jaroslav Valach, Jan Kastner, Čestmı́r Vlček, Karel Smetana, Jan Plzák
Software Mentions: 1
Published: almost 11 years ago

10.1186/1752-0509-9-S6-S6

A model for gene deregulation detection using expression data
Cited by: 4
Author(s): Thomas Picchetti, Julien Chiquet, Mohamed Elati, Pierre Neuvial, Rémy Nicolle, Étienne Birmelé
Software Mentions: 1
Published: about 9 years ago

10.1186/1756-0500-7-516

An algorithm for score aggregation over causal biological networks based on random walk sampling
Cited by: 4
Author(s): Dmitry Vasilyev, Timothy M. Thomson, Brian P. Frushour, Florian Martin, Alain Sewer
Software Mentions: 1
Published: over 10 years ago

10.1038/srep42929

Absence of PD-L1 on tumor cells is associated with reduced MHC I expression and PD-L1 expression increases in recurrent serous ovarian cancer
Cited by: 47
Author(s): Stefanie Aust, Sophie Félix, Katharina Auer, Anna Bachmayr-Heyda, Lukas Kenner, Sabine Dekan, Samuel M. Meier, Christopher Gerner, Christoph Grimm, Dietmar Pils
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-016-2383-1

Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster
Cited by: 82
Author(s): Lucie Kučerová, Olga I. Kubrak, Jonas Bengtsson, Hynek Strnad, Sören Nylin, Ulrich Theopold, Dick R. Nässel
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-018-25947-y

Linking drug target and pathway activation for effective therapy using multi-task learning
Cited by: 36
Author(s): Meizhu Yang, Jaak Simm, Clk Lam, Pooya Zakeri, Gerard J. P. van Westen, Yves Moreau, Julio Sáez-Rodríguez
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-015-1918-1

Helveticoside is a biologically active component of the seed extract of Descurainia sophia and induces reciprocal gene regulation in A549 human lung cancer cells
Cited by: 13
Author(s): Bu-Yeo Kim, Jun Lee, No Soo Kim
Software Mentions: 1
Published: about 9 years ago

10.1186/s12863-016-0338-9

Focal exposure of limited lung volumes to high-dose irradiation down-regulated organ development-related functions and up-regulated the immune response in mouse pulmonary tissues
Cited by: 5
Author(s): Bu Yeo Kim, Hee Kyung Jin, Yoon Jin Lee, Ga Young Kang, Jaeho Cho, Yun Sil Lee
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2105-13-167

Network-enabled gene expression analysis
Cited by: 14
Author(s): D.J. Edwards, Lei Wang, Peter Sørensen
Software Mentions: 1
Published: over 12 years ago

10.1186/s12885-015-1265-2

Identification of sample-specific regulations using integrative network level analysis
Cited by: 11
Author(s): Chengyu Liu, Riku Louhimo, Marko Laakso, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 1
Published: over 9 years ago

10.1186/s12885-017-3462-7

Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins
Cited by: 5
Author(s): Jennifer S. Myers, Karin A. Vallega, Jason White, Kaixian Yu, Clayton Yates, Qing‐Xiang Amy Sang
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-015-1484-6

Pan-cancer analysis of TCGA data reveals notable signaling pathways
Cited by: 28
Author(s): Richard E. Neapolitan, Curt M. Horvath, Xia Jiang
Software Mentions: 1
Published: over 9 years ago

10.1186/s12915-015-0116-6

Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles
Cited by: 69
Author(s): Stephen M Blazie, Cody S. Babb, Henry Wilky, Alan Rawls, Jin G. Park, Marco Mangone
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12859-018-2411-z

Probabilistic prioritization of candidate pathway association with pathway score
Cited by: 4
Author(s): Shu-Ju Lin, Tzu-Pin Lu, Qi-You Yu, Chuhsing Kate Hsiao
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-021-90006-y

Development of a novel method for the in-situ dechlorination of immovable iron elements: optimization of Cl− extraction yield through experimental design
Cited by: 4
Author(s): Marco Veneranda, Nagore Prieto‐Taboada, José Antonio Carrero, Ilaria Costantini, Aitor Larrañaga, Kepa Castro, Gorka Arana, Juan Manuel Madariaga
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-12-133

The PathOlogist: an automated tool for pathway-centric analysis
Cited by: 33
Author(s): Sharon Greenblum, Sol Efroni, Carl F. Schaefer, Kenneth H. Buetow
Software Mentions: 1
Published: over 13 years ago

10.1186/s12859-020-03732-x

A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path
Cited by: 17
Author(s): Peng Xu, Qian Wu, Da-Yong Lu, Jing Yu, Yongsheng Rao, Zheng Kou, Gang Fang, Wenbin Liu, Henry Han
Software Mentions: 1
Published: about 4 years ago

10.7554/eLife.30224

Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells
Cited by: 20
Author(s): Krishna Kolluri, Constantine Alifrangis, Neelam Kumar, Yuki Ishii, Stacey Price, Magali Michaut, Steven P. Williams, Syd Barthorpe, Howard Lightfoot, Sara Busacca, Annabel J. Sharkey, Zhenqiang Yuan, EK Sage, Sabari Vallath, John Le Quesne, David A. Tice, Doraid Alrifai, S von Karstedt, Antonella Montinaro, Naomi Guppy, David Waller, Apostolos Nakas, Robert B. Good, Alan M. Holmes, Henning Walczak, Dean A. Fennell, Mathew J. Garnett, Francesco Iorio, Lodewyk Wessels, Ultan McDermott, Sam M. Janes
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12859-016-1040-7

Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis
Cited by: 23
Author(s): Panagiotis Chouvardas, George Kollias, Christoforos Nikolaou
Software Mentions: 1
Published: over 8 years ago

10.3389/fnins.2018.00808

Comparative Transcriptomics of Rat and Axolotl After Spinal Cord Injury Dissects Differences and Similarities in Inflammatory and Matrix Remodeling Gene Expression Patterns
Cited by: 11
Author(s): Jure Tica, Athanasios Didangelos
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2021.694468

Assembling Disease Networks From Causal Interaction Resources
Cited by: 3
Author(s): Gianni Cesareni, Livia Perfetto
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2020.585998

Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema
Cited by: 3
Author(s): Lokesh P. Tripathi, Mari Itoh, Yoshito Takeda, Kazuyuki Tsujino, Yasushi Kondo, Atsushi Kumanogoh, Kenji Mizuguchi
Software Mentions: 1
Published: almost 4 years ago

10.1155/2013/584604

Gene Expression Profile of the A549 Human Non-Small Cell Lung Carcinoma Cell Line following Treatment with the Seeds of<i>Descurainia sophia</i>, a Potential Anticancer Drug
Cited by: 15
Author(s): Bu-Yeo Kim, Jun Lee, Sung‐Joon Park, Ok‐Sun Bang, No Soo Kim
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0150924

Effects of Metformin on Tissue Oxidative and Dicarbonyl Stress in Transgenic Spontaneously Hypertensive Rats Expressing Human C-Reactive Protein
Cited by: 20
Author(s): Hana Malínská, Olena Oliyarnyk, Vojtěch Škop, Jan Šilhavý, V. Landa, Václav Zı́dek, Petr Mlejnek, Miroslava Šimáková, Hynek Strnad, Ludmila Kazdová, Michal Pravenec
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms22010388

System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation
Cited by: 2
Author(s): Nicolas Borisov, Yaroslav Ilnytskyy, Boseon Byeon, Olga Kovalchuk, Igor Kovalchuk
Software Mentions: 1
Published: almost 4 years ago

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