bioconductor: SPIA | Projects | Ecosyste.ms: Papers

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

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

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.1186/s12920-015-0114-0

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma
Cited by: 12
Author(s): Vinay Randhawa, Vishal Acharya
Software Mentions: 17
Published: over 9 years ago

10.3390/biom10121606

A Customizable Analysis Flow in Integrative Multi-Omics
Cited by: 14
Author(s): Samuel M. Lancaster, Akshay Sanghi, Si Wu, M Snyder
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: about 9 years ago

10.1186/s13059-019-1790-4

Identifying significantly impacted pathways: a comprehensive review and assessment
Cited by: 113
Author(s): Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen, Sorin Drăghici
Software Mentions: 12
Published: about 5 years ago

10.1038/srep18871

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Cited by: 37
Author(s): Xinran Dong, Yun Huang, Xiao Wang, Weidong Tian
Software Mentions: 12
Published: almost 9 years ago

10.1371/journal.pcbi.1008979

netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis
Cited by: 4
Author(s): Michael Hellstern, Jing Ma, Kun Yue, Ali Shojaie
Software Mentions: 12
Published: over 3 years ago

10.1371/journal.pone.0041169

Global Transcriptome Analysis in Influenza-Infected Mouse Lungs Reveals the Kinetics of Innate and Adaptive Host Immune Responses
Cited by: 93
Author(s): Claudia Pommerenke, Esther Wilk, Barkha Srivastava, Annika Schulze, Natalia Novoselova, Robert Geffers, Klaus Schughart
Software Mentions: 11
Published: over 12 years ago

10.1016/j.csbj.2015.08.004

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
Cited by: 73
Author(s): Daniel Spies, Constance Ciaudo
Software Mentions: 11
Published: almost 10 years ago

10.1371/journal.pone.0131656

iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data
Cited by: 1
Author(s): Ashis Saha, Minji Jeon, Aik Choon Tan, Jaewoo Kang
Software Mentions: 10
Published: over 9 years ago

10.1186/s12859-019-3146-1

A comparative study of topology-based pathway enrichment analysis methods
Cited by: 51
Author(s): Jing Ma, Ali Shojaie, George Michailidis
Software Mentions: 10
Published: about 5 years ago

10.3389/fphys.2013.00278

Methods and approaches in the topology-based analysis of biological pathways
Cited by: 162
Author(s): Cristina Mitrea, Zeinab Taghavi, Behzad Bokanizad, Samer Najeeb Hanoudi, Rebecca Tagett, Michèle Donato, Călin Voichiţa, Sorin Drăghici
Software Mentions: 9
Published: almost 12 years ago

10.1371/journal.pone.0056024

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning
Cited by: 14
Author(s): Alex Gutteridge, J. Michael Rukstalis, Daniel Ziemek, Mark Tié, Lin Ji, Rebeca Ramos-Zayas, Nancy A. Nardone, Lisa D. Norquay, Martin Brenner, Kim San Tang, John D. McNeish, Rebecca K. Rowntree
Software Mentions: 9
Published: almost 12 years ago

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: over 4 years ago

10.1038/s41598-019-39019-2

Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data
Cited by: 10
Author(s): Marcela Franco, Ashwini Jeggari, Sylvain Peuget, Franziska Böttger, Galina Selivanova, Andrey Alexeyenko
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12859-021-04124-5

Popularity and performance of bioinformatics software: the case of gene set analysis
Cited by: 21
Author(s): Chengshu Xie, Shaurya Jauhari, Antonio M. Mora
Software Mentions: 8
Published: over 3 years ago

10.1016/j.celrep.2019.10.018

Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells
Cited by: 91
Author(s): Christopher Piper, Elizabeth C. Rosser, Kristīne Oļeiņika, Kiran Nistala, Thomas Krausgruber, André F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Software Mentions: 8
Published: about 5 years ago

10.7554/eLife.65228

Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice
Cited by: 8
Author(s): Diptendu Mukherjee, Ben J. Gonzales, Reut Ashwal-Fluss, Hagit Turm, Maya Groysman, Ami Citri
Software Mentions: 8
Published: over 3 years ago

10.1186/1471-2105-13-20

graphite - a Bioconductor package to convert pathway topology to gene network
Cited by: 157
Author(s): Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi
Software Mentions: 7
Published: almost 13 years ago

10.1186/s13040-018-0166-8

Gene set analysis methods: a systematic comparison
Cited by: 57
Author(s): Ravi Mathur, Daniel M. Rotroff, Ma Jun, Ali Shojaie, Alison A. Motsinger‐Reif
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2105-15-132

Investigating perturbed pathway modules from gene expression data via structural equation models
Cited by: 19
Author(s): Daniele Pepe, Mario Grassi
Software Mentions: 7
Published: over 10 years ago

10.3389/fmolb.2020.565530

Cross-Sectional Transcriptional Analysis of the Aging Murine Heart
Cited by: 4
Author(s): Matthew Greenig, Andrew Melville, Derek Huntley, Mark Isalan, Michał Mielcarek
Software Mentions: 7
Published: about 4 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: over 3 years ago

10.1186/s12864-019-6155-6

A framework using topological pathways for deeper analysis of transcriptome data
Cited by: 0
Author(s): Yue Zhao, Stephanie Piekos, Tham H. Hoang, Dong-Guk Shin
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0191154

A critical comparison of topology-based pathway analysis methods
Cited by: 51
Author(s): Ivana Ihnatová, Vlad Popovici, Eva Budínská
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12859-015-0751-5

Comparative study on gene set and pathway topology-based enrichment methods
Cited by: 61
Author(s): Michaela Bayerlová, Klaus Jung, Frank Krämer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth
Software Mentions: 6
Published: about 9 years ago

10.1186/1745-6150-7-44

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods
Cited by: 21
Author(s): Frank Emmert‐Streib, Shailesh Tripathi, Ricardo de Matos Simoes
Software Mentions: 6
Published: almost 13 years ago

10.1080/21623945.2019.1595269

Transcriptome profiling reveals association of peripheral adipose tissue pathology with type-2 diabetes in Asian Indians
Cited by: 17
Author(s): Aditya Saxena, Prabhat Tiwari, Nitin Wahi, Arpana Soni, Ram Chandra Bansiwal, Anshul Kumar, Balram Sharma, Prakash P Punjabi, Nidhi Gupta, Babita Malik, Krishna Mohan Medicherla, Prashanth Suravajhala, Sandeep Kumar Mathur
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0101581

Analysis of the Transcriptome in Hyperoxic Lung Injury and Sex-Specific Alterations in Gene Expression
Cited by: 25
Author(s): Krithika Lingappan, Chandramouleeswaran Srinivasan, Weiwu Jiang, Lihua Wang, Xanthi I. Couroucli, Bhagavatula Moorthy
Software Mentions: 6
Published: over 10 years ago

10.3389/fgene.2019.01203

The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling
Cited by: 67
Author(s): Sarah Mubeen, Charles Tapley Hoyt, André Gemünd, Martin Hofmann‐Apitius, Holger Fröhlich, Daniel Domingo‐Fernándéz
Software Mentions: 6
Published: almost 5 years ago

10.1007/s00018-020-03485-z

Anti-adipogenic signals at the onset of obesity-related inflammation in white adipose tissue
Cited by: 17
Author(s): Tiziana Caputo, Van Du T. Tran, Nasim Bararpour, Carine Winkler, Gabriela Aguileta, Bao Khanh Trang, Greta Maria Paola Giordano Attianese, Anne Wilson, Aurélien Thomas, Marco Pagni, Nicolas Guex, Béatrice Desvergne, Federica Gilardi
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0164542

IGSA: Individual Gene Sets Analysis, including Enrichment and Clustering
Cited by: 3
Author(s): Lingxiang Wu, Xiujie Chen, Denan Zhang, Wubing Zhang, Lei Liu, Hongzhe Ma, Jingbo Yang, Hongbo Xie, Bo Liu, Qing Jin
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0092111

Transcriptome Analysis Reveals Differential Splicing Events in IPF Lung Tissue
Cited by: 69
Author(s): Tracy Nance, Kevin S. Smith, Vanessa Anaya, Rhea Richardson, Lawrence Ho, Mauro Pala, Sara Mostafavi, Alexis Battle, Carol Feghali‐Bostwick, Glenn D. Rosen, Stephen B. Montgomery
Software Mentions: 6
Published: over 10 years ago

10.3390/cancers11040489

Functional Effects of let-7g Expression in Colon Cancer Metastasis
Cited by: 9
Author(s): Che Mai Chang, Henry Sung Ching Wong, Chien‐Yu Huang, Wen Li Hsu, Zhi Feng Maio, Siou Jin Chiu, Yao Ting Tsai, Ben Kuen Chen, Yu Wan, Jaw‐Yuan Wang, Wei Chiao Chang
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2020.00654

Gene Set Analysis: Challenges, Opportunities, and Future Research
Cited by: 98
Author(s): Farhad Maleki, Katie Ovens, Daniel J. Hogan, Anthony Kusalik
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-78288-0

Common and personal target genes of the micronutrient vitamin D in primary immune cells from human peripheral blood
Cited by: 19
Author(s): Andrea Hanel, Antonio Neme, Marjo Malinen, Emmi Hämäläinen, Henna-Riikka Malmberg, Stéphane Etheve, Tomi‐Pekka Tuomainen, Jyrki K. Virtanen, Igor Bendik, Carsten Carlberg
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-018-37098-1

Comparison between dopaminergic and non-dopaminergic neurons in the VTA following chronic nicotine exposure during pregnancy
Cited by: 9
Author(s): Renee F. Keller, Tina Kazemi, Andrei Dragomir, Yasemin M. Akay, Metin Akay
Software Mentions: 5
Published: almost 6 years ago

10.1038/s41598-018-34412-9

RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ
Cited by: 29
Author(s): Marta Pulido-Salgado, José M. Vidal-Taboada, Gerardo Garcıa-Dıaz Barriga, Carme Solà, Josep Saura
Software Mentions: 5
Published: about 6 years ago

10.1038/srep21911

Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: over 8 years ago

10.1186/s13058-017-0814-9

DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms
Cited by: 28
Author(s): David J. Lemler, Miranda L. Lynch, Lia Tesfay, Zhiyong Deng, Bibbin T. Paul, Xiaohong Wang, Poornima Hegde, David H. Manz, Suzy V. Torti, Frank M. Torti
Software Mentions: 5
Published: over 7 years ago

10.1002/1878-0261.12070

Synergistic activity of everolimus and 5-aza-2′-deoxycytidine in medullary thyroid carcinoma cell lines
Cited by: 23
Author(s): Giovanna Mantovani, Alessandra Dicitore, Daniele Pepe, Davide Gentilini, Elisa Grassi, Maria Orietta Borghi, Giulia Gelmini, Maria Celeste Cantone, Germano Gaudenzi, Gabriella Misso, Anna Maria Di Blasio, Leo J. Hofland, Michele Caraglia, Luca Persani
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pcbi.1008550

CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models
Cited by: 9
Author(s): Lillian R Thistlethwaite, Varduhi Petrosyan, Xiqi Li, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pcbi.1005187

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways
Cited by: 24
Author(s): Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pone.0179613

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells
Cited by: 7
Author(s): Benjamin Ulfenborg, Alexander Karlsson, Maria Riveiro, Caroline Améen, Karolina Åkesson, Christian X. Andersson, Peter Sartipy, Jane Synnergren
Software Mentions: 5
Published: over 7 years ago

10.1038/srep13044

ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis
Cited by: 24
Author(s): Junwei Han, Xinrui Shi, Yunpeng Zhang, Yanjun Xu, Ying Jiang, Chunlong Zhang, Feng Li, Haixiu Yang, Desi Shang, Zeguo Sun, Fei Su, Chunquan Li, Xia Li
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0024351

Molecular Insights into Reprogramming-Initiation Events Mediated by the OSKM Gene Regulatory Network
Cited by: 63
Author(s): Nancy Mah, Ying Wang, Mei-Chih Liao, Alessandro Prigione, Justyna Józefczuk, Björn Lichtner, Katharina Wolfrum, Manuela Haltmeier, Max Flöttmann, Martin H. Schaefer, Alexander Hahn, Ralf Mrowka, Edda Klipp, Miguel A. Andrade‐Navarro, James Adjaye
Software Mentions: 5
Published: about 13 years ago

10.1016/j.isci.2020.101249

Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Triple-Negative Breast Cancer
Cited by: 5
Author(s): Asha Nair, Xiaojia Tang, Kevin J. Thompson, Peter T. Vedell, Krishna R. Kalari, Subbaya Subramanian
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0171689

Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock
Cited by: 10
Author(s): Samanwoy Mukhopadhyay, Pravat Kumar Thatoi, AK Pandey, B. K. Das, Balachandran Ravindran, Samsiddhi Bhattacharjee, Saroj Kant Mohapatra
Software Mentions: 5
Published: almost 8 years ago

10.3390/cancers12082257

A Global Gene Body Methylation Measure Correlates Independently with Overall Survival in Solid Cancer Types
Cited by: 1
Author(s): Dietmar Pils, Elisabeth Steindl, Anna Bachmayr-Heyda, Sabine Dekan, Stefanie Aust
Software Mentions: 5
Published: over 4 years ago

10.18632/oncotarget.11038

Role of the immune system in the peritoneal tumor spread of high grade serous ovarian cancer
Cited by: 33
Author(s): Katharina Auer, Anna Bachmayr-Heyda, Nyamdelger Sukhbaatar, Stefanie Aust, Klaus G. Schmetterer, Samuel M. Meier, Christopher Gerner, Christoph Grimm, Reinhard Horvat, Dietmar Pils
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-61177-x

RNA-seq analysis reveals TRPC genes to impact an unexpected number of metabolic and regulatory pathways
Cited by: 10
Author(s): Karina Formoso, Sebastián Susperreguy, Marc Freichel, Lutz Birnbaumer
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-16-S8-S6

NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases
Cited by: 15
Author(s): Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio
Software Mentions: 4
Published: over 9 years ago

10.1007/s13238-017-0480-9

TDP-43 regulates cancer-associated microRNAs
Cited by: 28
Author(s): Xiaowei Chen, Zhen Fan, W Ambrose McGee, Mengmeng Chen, Ruirui Kong, Pushuai Wen, Tengfei Xiao, Xiaomin Chen, Jianghong Liu, Li Zhu, Runsheng Chen, Jane Y. Wu
Software Mentions: 4
Published: about 7 years ago

10.1186/s12918-014-0121-3

Understanding disease mechanisms with models of signaling pathway activities
Cited by: 42
Author(s): Patricia Sebastián-León, Enrique Vidal, Pablo Mínguez, Ana Conesa, Sonia Tarazona, Alicia Amadoz, Leandro Pardo, Francisco Salavert, António Vidal-Puig, David Montaner, Joaquín Dopazo
Software Mentions: 4
Published: about 10 years ago

10.1038/s41598-019-50271-4

Fractional Deletion of Compound Kushen Injection Indicates Cytokine Signaling Pathways are Critical for its Perturbation of the Cell Cycle
Cited by: 9
Author(s): Thazin Nwe Aung, Saeed Nourmohammadi, Zhibo Qu, Yuka Harata-Lee, Jingang Cui, Hao Shen, Andrea J. Yool, Tara L. Pukala, Hongling Du, R. Daniel Kortschak, Wenxin Wei, David L. Adelson
Software Mentions: 4
Published: about 5 years ago

10.18632/oncotarget.11788

Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: about 8 years ago

10.1038/srep33956

A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes
Cited by: 19
Author(s): Alan Mueller, Simon R. Tew, Olga Vasieva, Peter Clegg, Elizabeth G. Canty‐Laird
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0084955

Clustering Gene Expression Regulators: New Approach to Disease Subtyping
Cited by: 30
Author(s): Mikhail A. Pyatnitskiy, Ilya Mazo, Maria Shkrob, Elena Schwartz, Ekaterina Kotelnikova
Software Mentions: 4
Published: almost 11 years ago

10.3390/cancers11050698

NECTIN4 (PVRL4) as Putative Therapeutic Target for a Specific Subtype of High Grade Serous Ovarian Cancer—An Integrative Multi-Omics Approach
Cited by: 25
Author(s): Christine Bekos, Besnik Muqaku, Sabine Dekan, Reinhard Horvat, Stephan Polterauer, Christopher Gerner, Stefanie Aust, Dietmar Pils
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2019.00858

pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks
Cited by: 189
Author(s): Ege Ülgen, Özan Özışık, Uğur Sezerman
Software Mentions: 4
Published: about 5 years ago

10.1186/1751-0473-7-10

PathNet: a tool for pathway analysis using topological information
Cited by: 62
Author(s): Bhaskar Dutta, Anders Wallqvist, Jaques Reifman
Software Mentions: 4
Published: about 12 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: over 9 years ago

10.21203/rs.3.rs-287183/v1

Rapid Identification of Druggable Targets and the Power of the PHENotype SIMulator for Effective Drug Repurposing in COVID-19
Cited by: 1
Author(s): Naomi I. Maria, Rosaria Valentina Rapicavoli, Salvatore Alaimo, Evelyne Bischof, Alessia Stasuzzo, Jantine A.C. Broek, Alfredo Pulvirenti, Bud Mishra, Ashley J. Duits, Alfredo Ferro
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0107629

Tracking Difference in Gene Expression in a Time-Course Experiment Using Gene Set Enrichment Analysis
Cited by: 4
Author(s): Pui Shan Wong, Michihiro Tanaka, Yoshihiko Sunaga, Masayoshi Tanaka, Tadatsugu Taniguchi, Tomoko Yoshino, Tsuyoshi Tanaka, Wataru Fujibuchi, Sachiyo Aburatani
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0041541

Identification of Pathway Deregulation – Gene Expression Based Analysis of Consistent Signal Transduction
Cited by: 16
Author(s): Jakub Mieczkowski, Karolina Swiatek-Machado, Bożena Kamińska
Software Mentions: 3
Published: over 12 years ago

10.1186/s12859-019-2635-6

FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods
Cited by: 5
Author(s): Fatemeh Mansoori, Maseud Rahgozar, Kaveh Kavousi
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-014-0358-2

A MATLAB tool for pathway enrichment using a topology-based pathway regulation score
Cited by: 10
Author(s): M Ibrahim, Sabah Jassim, Michael A. Cawthorne, Kenneth Langlands
Software Mentions: 3
Published: about 10 years ago

10.1186/s12859-019-2829-y

GeneSurrounder: network-based identification of disease genes in expression data
Cited by: 5
Author(s): Sahil D. Shah, Rosemary Braun
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0173331

Bayesian model of signal rewiring reveals mechanisms of gene dysregulation in acquired drug resistance in breast cancer
Cited by: 12
Author(s): A. K. M. Azad, Alfons Lawen, Jonathan M. Keith
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2019.00314

Effect of Compound Kushen Injection, a Natural Compound Mixture, and Its Identified Chemical Components on Migration and Invasion of Colon, Brain, and Breast Cancer Cell Lines
Cited by: 41
Author(s): Saeed Nourmohammadi, Thazin Nwe Aung, Jingang Cui, Jinxin V. Pei, Michael L. De Ieso, Yuka Harata-Lee, Zhibo Qu, David L. Adelson, Andrea J. Yool
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.652017

Transplanted Erythropoietin-Expressing Mesenchymal Stem Cells Promote Pro-survival Gene Expression and Protect Photoreceptors From Sodium Iodate-Induced Cytotoxicity in a Retinal Degeneration Model
Cited by: 4
Author(s): Avin Ee-Hwan Koh, Hiba Amer Alsaeedi, Munirah Binti Abd Rashid, Chenshen Lam, Mohd Hairul Nizam Harun, Min Hwei Ng, Hazlita Mohd Isa, K. Then, Mae-Lynn Catherine Bastion, Aisha Farhana, Mohammad Khursheed Alam, Suresh Kumar Subbiah, Pooi Ling Mok
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2019.00632

Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection With Transcriptome Analysis
Cited by: 21
Author(s): Hao Shen, Zhibo Qu, Yuka Harata-Lee, Thazin Nwe Aung, Jingang Cui, Wei Wang, R. Daniel Kortschak, David L. Adelson
Software Mentions: 3
Published: over 5 years ago

10.1038/srep37651

Immune signatures of protective spleen memory CD8 T cells
Cited by: 11
Author(s): Lilia Brinza, Sophia Djebali, Martine Tomkowiak, Julien Mafille, Céline Loiseau, Pierre Emmanuel Jouve, Simon Bernard, Laurent Buffat, Bruno Lina, Michèle Ottmann, Manuel Rosa‐Calatrava, Stéphane Schicklin, Nathalie Bonnefoy, Grégoire Lauvau, Morgan Grau, Mélanie Wencker, Christophe Arpin, Thierry Walzer, Yann Leverrier, Jacqueline Marvel
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12859-020-03568-5

PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures
Cited by: 11
Author(s): Mohammad Asif Emon, Daniel Domingo‐Fernándéz, Charles Tapley Hoyt, Martin Hofmann‐Apitius
Software Mentions: 3
Published: over 4 years ago

10.1038/srep40450

Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways
Cited by: 12
Author(s): Abhinav Kaushik, Shakir Ali, Dinesh Gupta
Software Mentions: 3
Published: almost 8 years ago

10.1111/jcmm.13997

ce-Subpathway: Identification of ceRNA-mediated subpathways via joint power of ceRNAs and pathway topologies
Cited by: 9
Author(s): Chenchen Feng, Chao Song, Ziyu Ning, Bo Ai, Qiuyu Wang, Yong Xu, Meng Li, Xuefeng Bai, Jian Zhao, Yuejuan Liu, Xuecang Li, Jian Zhang, Chunquan Li
Software Mentions: 3
Published: about 6 years ago

10.1186/s12920-015-0095-z

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Cited by: 11
Author(s): Tobias Meißner, Kathleen Fisch, Louis Gioia, Andrew I. Su
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-14-770

The periodontal pathogen Porphyromonas gingivalis changes the gene expression in vascular smooth muscle cells involving the TGFbeta/Notch signalling pathway and increased cell proliferation
Cited by: 28
Author(s): Boxi Zhang, Ali Ateia Elmabsout, Hazem Khalaf, Vladimir Basic, Kartheyaene Jayaprakash, Robert L. Kruse, Torbjörn Bengtsson, Allan Sirsjö
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-017-09490-w

The epigenetic modifier Fam208a is required to maintain epiblast cell fitness
Cited by: 6
Author(s): Shohag Bhargava, Brian Cox, Christiana Polydorou, Veronika Gresakova, Vladimír Kořínek, Hynek Strnad, Radislav Sedláček, Trevor Epp, Kallayanee Chawengsaksophak
Software Mentions: 3
Published: about 7 years ago

10.3389/fncel.2016.00230

Altered Expression of Genes Encoding Neurotransmitter Receptors in GnRH Neurons of Proestrous Mice
Cited by: 32
Author(s): Csaba Vastagh, Annie Rodolosse, Norbert Solymosi, Zsolt Liposits
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-019-2863-9

PathMe: merging and exploring mechanistic pathway knowledge
Cited by: 38
Author(s): Daniel Domingo‐Fernándéz, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann‐Apitius
Software Mentions: 3
Published: over 5 years ago

10.1016/j.omtn.2021.01.015

miR-130a activates the VEGFR2/STAT3/HIF1α axis to potentiate the vasoregenerative capacity of endothelial colony-forming cells in hypoxia
Cited by: 7
Author(s): Jasenka Guduric-Fuchs, Edoardo Pedrini, Judith Lechner, Sean Chambers, Christina O'Neill, Joana Mendes Lopes de Melo, Varun Pathak, Rachel H. Church, Stuart McKeown, James Bojdo, Kiran J. McLoughlin, Alan W. Stitt, Reinhold J. Medina
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.9695

Identifying disease-associated signaling pathways through a novel effector gene analysis
Cited by: 1
Author(s): Zhenshen Bao, Bing Zhang, Li Li, Qinyu Ge, Wanjun Gu, Ya Mei Bai
Software Mentions: 3
Published: over 4 years ago

10.1186/s12885-018-5061-7

Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma
Cited by: 18
Author(s): Diāna Andrējeva, Jan-Michael Kugler, Thanh Hung Nguyen, Anders Malmendal, Magnus Holm, Birgitte Groenkaer Toft, Anand C Loya, Stephen M. Cohen
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers12061460

Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer
Cited by: 1
Author(s): Shamim Sarhadi, Ali Salehzadeh‐Yazdi, Mehdi Damaghi, Nosratollah Zarghami, Olaf Wolkenhauer, Hedayatollah Hosseini
Software Mentions: 3
Published: over 4 years ago

10.3389/fphys.2015.00383

Pathway Analysis: State of the Art
Cited by: 170
Author(s): Miguel Angel García-Campos, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-45304-x

BioTarget: A Computational Framework Identifying Cancer Type Specific Transcriptional Targets of Immune Response Pathways
Cited by: 7
Author(s): Tham H. Hoang, Yue Zhao, Y. W. Lam, Stephanie Piekos, Yueh-Chiang Han, Cameron Reilly, Pujan Joshi, Seung-Hyun Hong, Chang Ohk Sung, Charles Giardina, Dong-Guk Shin
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0234993

The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells
Cited by: 9
Author(s): Derick Thompson, Jordyn Sorenson, Jacob R. Greenmyer, Catherine A. Brissette, John A. Watt
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0175844

Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection
Cited by: 55
Author(s): Chetan Seshadri, Nafiseh Sedaghat, Monica Campo, Glenna J. Peterson, Richard D. Wells, Gregory S. Olson, David R. Sherman, Catherine M. Stein, Harriet Mayanja‐Kizza, Ali Shojaie, W. Henry Boom, Thomas R. Hawn
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0144398

The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington’s Disease
Cited by: 47
Author(s): Xianjun Dong, Junko Tsuji, Adam Labadorf, Panos Roussos, Jiang‐Fan Chen, Richard H. Myers, Schahram Akbarian, Zhiping Weng
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0145322

Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer
Cited by: 31
Author(s): Jennifer S. Myers, Ariana von Lersner, Charles J. Robbins, Qing‐Xiang Amy Sang
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0132813

Subpathway Analysis based on Signaling-Pathway Impact Analysis of Signaling Pathway
Cited by: 39
Author(s): Xianbin Li, Liangzhong Shen, Xuequn Shang, Wenbin Liu
Software Mentions: 3
Published: over 9 years ago

10.1186/s12977-016-0248-y

TLR8 regulation of LILRA3 in monocytes is abrogated in human immunodeficiency virus infection and correlates to CD4 counts and virus loads
Cited by: 8
Author(s): Hui Zhi Low, Gerrit Ahrenstorf, Claudia Pommerenke, Nadine Habermann, Klaus Schughart, David Ordóñez, Renata Stripecke, Esther Wilk, Torsten Witte
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.16110

Robust <i>in-silico</i> identification of cancer cell lines based on next generation sequencing
Cited by: 12
Author(s): Raik Otto, Christine Sers, Ulf Leser
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-12-403

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference
Cited by: 26
Author(s): Yan Jiao, Katherine Lawler, Gargi Patel, Arnie Purushotham, Annete F. Jones, Anita Grigoriadis, Andrew Tutt, Tony Ng, Andrew E. Teschendorff
Software Mentions: 2
Published: about 13 years ago

10.1186/s12859-016-1333-x

A network-based pathway-expanding approach for pathway analysis
Cited by: 4
Author(s): Qiaosheng Zhang, Jie Li, Haozhe Xie, Hanqing Xue, Yadong Wang
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-021-04297-z

Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data
Cited by: 5
Author(s): Giuseppe Agapito, Mario Cannataro
Software Mentions: 2
Published: about 3 years ago

Projects: bioconductor: SPIA

Papers Mentioning SPIA 155