bioconductor: BioNet | Projects | Ecosyste.ms: Papers

10.1186/s12868-019-0538-0

28th Annual Computational Neuroscience Meeting: CNS*2019
Cited by: 3
Author(s):
Software Mentions: 13
Published: about 5 years ago

PyRates—A Python framework for rate-based neural simulations
Cited by: 10
Author(s): Richard Gast, Daniel Rose, Christoph Salomon, Harald E. Möller, Nikolaus Weiskopf, Thomas R. Knösche
Software Mentions: 12
Published: almost 5 years ago

10.7554/eLife.44494

NetPyNE, a tool for data-driven multiscale modeling of brain circuits
Cited by: 101
Author(s): Salvador Dura‐Bernal, Benjamin A. Suter, Padraig Gleeson, Matteo Carandini, Adrián Quintana, Facundo Rodriguez, David J. Kedziora, George L. Chadderdon, Cliff C. Kerr, Samuel A. Neymotin, Robert A. McDougal, Michael L. Hines, Gordon M. Shepherd, William W. Lytton
Software Mentions: 10
Published: over 5 years ago

10.3390/ijms151221788

Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of Pigs
Cited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: almost 10 years ago

10.12688/f1000research.20887.3

RCy3: Network biology using Cytoscape from within R
Cited by: 72
Author(s): Julia Gustavsen, Shraddha Pai, Ruth Isserlin, Barry Demchak, Alexander R. Pico
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1008386

Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
Cited by: 28
Author(s): Kael Dai, Sergey L. Gratiy, Yazan N. Billeh, Richard Xu, Bin Cai, Nicholas Cain, Atle E Rimehaug, A. Stasik, Gaute T. Einevoll, Ştefan Mihalaş, Christof Koch, Anton Arkhipov
Software Mentions: 6
Published: almost 4 years ago

10.3389/fimmu.2020.00452

Influenza-Induced Interferon Lambda Response Is Associated With Longer Time to Delivery Among Pregnant Kenyan Women
Cited by: 1
Author(s): Christof Seiler, Nicholas Bayless, Rosemary Vergara, Jillian Pintye, John Kinuthia, Lusi Osborn, Daniel Matemo, Barbra A. Richardson, Grace John‐Stewart, Susan Holmes, Catherine A. Blish
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008819

Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer
Cited by: 3
Author(s): Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, Dominique Stoppa‐Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0201630

BioNet: A Python interface to NEURON for modeling large-scale networks
Cited by: 49
Author(s): Sergey L. Gratiy, Yazan N. Billeh, Kael Dai, Catalin Mitelut, David Feng, Nathan W. Gouwens, Nicholas Cain, Christof Koch, Costas A. Anastassiou, Anton Arkhipov
Software Mentions: 5
Published: over 6 years ago

10.3389/fninf.2019.00035

ELFENN: A Generalized Platform for Modeling Ephaptic Coupling in Spiking Neuron Models
Cited by: 9
Author(s): Aaron R. Shifman, John E. Lewis
Software Mentions: 4
Published: over 5 years ago

10.1186/2043-9113-1-34

Profiling the human response to physical exercise: a computational strategy for the identification and kinetic analysis of metabolic biomarkers
Cited by: 36
Author(s): Michael Netzer, Klaus M. Weinberger, Michael Handler, Michael Seger, Xuekun Fang, Karl G. Kugler, Armin Graber, Christian Baumgartner
Software Mentions: 4
Published: almost 14 years ago

10.1371/journal.pcbi.1003808

SANTA: Quantifying the Functional Content of Molecular Networks
Cited by: 56
Author(s): Alex J. Cornish, Florian Markowetz
Software Mentions: 4
Published: about 10 years ago

10.1186/1752-0509-6-72

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
Cited by: 12
Author(s): Daniela Beißer, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus Dittrich, Tobias Müller
Software Mentions: 4
Published: over 12 years ago

10.15252/msb.20209593

DOMINO: a network‐based active module identification algorithm with reduced rate of false calls
Cited by: 35
Author(s): Hagai Levi, Ran Elkon, Ron Shamir
Software Mentions: 4
Published: almost 4 years ago

10.3934/Neuroscience.2019.4.333

Identification of biomarkers associated with Parkinson’s disease by gene expression profiling studies and bioinformatics analysis
Cited by: 10
Author(s): Marios G. Krokidis
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-94005-x

Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer
Cited by: 5
Author(s): Dilara Uzuner, Yunus Akkoç, Nesibe Peker, Pınar Pir, Devrim Gözüaçık, Tunahan Çakır
Software Mentions: 3
Published: over 3 years ago

10.1186/1755-8794-5-27

Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics
Cited by: 19
Author(s): Diego Díez, Susumu Goto, John V. Fahy, David J. Erle, Prescott G. Woodruff, Åsa M. Wheelock, Craig E. Wheelock
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pcbi.1004293

Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma
Cited by: 22
Author(s): Julia C. Engelmann, Thomas Amann, Birgitta Ott-Rötzer, Margit Nützel, Yvonne Reinders, Jörg Reinders, Wolfgang E. Thasler, Theresa Kristl, Andreas Teufel, Christian G. Huber, Peter J. Oefner, Rainer Spang, Claus Hellerbrand
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-016-1402-1

Efficient randomization of biological networks while preserving functional characterization of individual nodes
Cited by: 32
Author(s): Francesco Iorio, Martí Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman, Julio Sáez-Rodríguez
Software Mentions: 3
Published: almost 8 years ago

10.3389/fgene.2019.00155

A Comprehensive Survey of Tools and Software for Active Subnetwork Identification
Cited by: 42
Author(s): Hung Son Nguyen, Sangam Shrestha, Duc Tran, Adib Shafi, Sorin Drăghici, Tin Nguyen
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0147475

Network-Based Meta-Analyses of Associations of Multiple Gene Expression Profiles with Bone Mineral Density Variations in Women
Cited by: 11
Author(s): Hao He, Shaolong Cao, Tianhua Niu, Yu Zhou, Lan Zhang, Yong Zeng, Wei Zhu, Yu Ping Wang, Hong‐Wen Deng
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0206686

Network assessment of demethylation treatment in melanoma: Differential transcriptome-methylome and antigen profile signatures
Cited by: 2
Author(s): Zhijie Jiang, Caterina Cinti, Monia Taranta, Elisabetta Mattioli, Elisa Schena, Sakshi Singh, Rimpi Khurana, Giovanna Lattanzi, Nicholas F. Tsinoremas, Enrico Capobianco
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-018-2513-7

Capturing context-specific regulation in molecular interaction networks
Cited by: 5
Author(s): Stephen Rush, Dirk Repsilber
Software Mentions: 3
Published: almost 6 years ago

10.1093/hmg/ddx036

GWAS of self-reported mosquito bite size, itch intensity and attractiveness to mosquitoes implicates immune-related predisposition loci
Cited by: 28
Author(s): Amy V. Jones, Mera Tilley, Alex Gutteridge, Craig Hyde, Michael W. Nagle, Daniel Ziemek, Donal Gorman, Eric B. Fauman, Xing Chen, Melissa R. Miller, Chao Tian, Youna Hu, David A. Hinds, Peter Cox, Serena Scollen
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pcbi.1006535

Visual physiology of the layer 4 cortical circuit in silico
Cited by: 68
Author(s): Anton Arkhipov, Nathan W. Gouwens, Yazan N. Billeh, Sergey L. Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael A. Buice, Nicholas Cain, Nuno da Costa, Saskia de Vries, Daniel J. Denman, Séverine Durand, David Feng, Tim Jarsky, Jérôme Lecoq, Brian Lee, Lü Li, Ştefan Mihalaş, Gabriel Koch Ocker, Shawn R. Olsen, R. Clay Reid, Gilberto Soler-Llavina, Staci A. Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch
Software Mentions: 2
Published: about 6 years ago

10.1186/s12859-017-1567-2

Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network
Cited by: 26
Author(s): Hao He, Dongdong Lin, Jigang Zhang, Yuping Wang, Hong‐Wen Deng
Software Mentions: 2
Published: over 7 years ago

10.1038/srep08117

PhenomeExpress: A refined network analysis of expression datasets by inclusion of known disease phenotypes
Cited by: 26
Author(s): Jamie Soul, Timothy E. Hardingham, Raymond P. Boot-Handford, Jean-Marc Schwartz
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-14-483

A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology
Cited by: 9
Author(s): Michael Seidl, Adrian Schneider, F. Govers, Berend Snel
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0013367

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases
Cited by: 110
Author(s): Igor Ulitsky, Akshay Krishnamurthy, Richard M. Karp, Ron Shamir
Software Mentions: 2
Published: about 14 years ago

10.1186/s12859-017-1477-3

SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information
Cited by: 23
Author(s): N. Ari Wijetunga, Andrew D. Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M. Greally
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13018-015-0275-8

Identification of genes associated with methotrexate resistance in methotrexate-resistant osteosarcoma cell lines
Cited by: 20
Author(s): Xiaorong Yang, Yan Xiong, Hong Duan, Renmin Gong
Software Mentions: 1
Published: about 9 years ago

10.1186/1471-2105-14-144

Steiner tree methods for optimal sub-network identification: an empirical study
Cited by: 24
Author(s): Afshin Sadeghi, Holger Fröhlich
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-020-03572-9

Markov chain Monte Carlo for active module identification problem
Cited by: 4
Author(s): Nikita Alexeev, Javlon E. Isomurodov, Vladimir Sukhov, G Korotkevich, Alexey Sergushichev
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-016-2909-6

Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network
Cited by: 6
Author(s): Jin Li, Ying Wang, Lei Wang, Xuefeng Dai, Cong Wang, Weixing Feng, Chengzhen Xu, Yulin Deng, Yue Wang, Todd C. Skaar, Hong Liang, Yunlong Liu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1002081

International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011
Cited by: 0
Author(s): Justin Mullins, BJ Morrison McKay
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0126986

Genome-Wide Association Analyses Point to Candidate Genes for Electric Shock Avoidance in Drosophila melanogaster
Cited by: 13
Author(s): Mirjam Appel, Claus‐Jürgen Scholz, Tobias Müller, Marcus Dittrich, Christian König, Marie Bockstaller, Tuba Oguz, Afshin Khalili, Emmanuel Antwi-Adjei, Tamás Schauer, Carla Margulies, Hiromu Tanimoto, Ayse Yarali
Software Mentions: 1
Published: over 9 years ago

10.1007/s00441-017-2734-5

Computational systems biology approaches for Parkinson’s disease
Cited by: 18
Author(s): Enrico Glaab
Software Mentions: 1
Published: almost 7 years ago

10.12688/f1000research.5984.2

Enhancement of COPD biological networks using a web-based collaboration interface
Cited by: 22
Author(s): Stéphanie Boué, Brett Fields, Julia Hoeng, Jennifer Park, Manuel C. Peitsch, Walter K. Schlage, Marja Talikka, Ilona Binenbaum, В. В. Бондаренко, Oleg V. Bulgakov, Vera Cherkasova, Norberto Díaz–Díaz, Larisa Fedorova, Svetlana V. Guryanova, Julia Guzova, G. I. Koroleva, Elena Kozhemyakina, Rahul Kumar, Noa Lavid, Qin Lu, Swapna Menon, Yael Ouliel, Samantha C. Peterson, Alexander V. Prokhorov, Edward B. Sanders, Sarah B. Schrier, Golan Schwaitzer Neta, Irina Shvydchenko, Aravind Tallam, Gema Villa-Fombuena, John Z. Wu, Ilya Yudkevich, Mariya Zelikman
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-14682-5

A Computational Method of Defining Potential Biomarkers based on Differential Sub-Networks
Cited by: 12
Author(s): Xin Huang, Xiaohui Lin, Jun Zeng, Lichao Wang, Peiyuan Yin, Lina Zhou, Chunxiu Hu, Wei Yao
Software Mentions: 1
Published: about 7 years ago

10.1021/acsnano.1c00353

Control of Nanoscale <i>In Situ</i> Protein Unfolding Defines Network Architecture and Mechanics of Protein Hydrogels
Cited by: 19
Author(s): Matt D. G. Hughes, Benjamin S. Hanson, Sophie Cussons, Najet Mahmoudi, David J. Brockwell, Lorna Dougan
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: BioNet

Papers Mentioning BioNet 40