Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: MCL

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/MCL

Markov Cluster Algorithm
1 version
Latest release: over 9 years ago
2 dependent packages
398 downloads last month

Papers Mentioning MCL 563

10.1371/journal.pone.0080870
Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships
Cited by: 69
Author(s): Zhenxiang Xi, Joshua S. Rest, Charles C. Davis
Software Mentions: 3
Published: about 11 years ago
10.1371/journal.pone.0072366
C-element: A New Clustering Algorithm to Find High Quality Functional Modules in PPI Networks
Cited by: 1
Author(s): Mahdieh Ghasemi, Maseud Rahgozar, Gholamreza Bidkhori, Ali Masoudi‐Nejad
Software Mentions: 3
Published: about 11 years ago
10.1093/molbev/msaa303
Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques
Cited by: 10
Author(s): Gregg W.C. Thomas, Richard J. Wang, Jelena Nguyen, R. Alan Harris, Muthuswamy Raveendran, Jeffrey Rogers, Matthew W. Hahn
Software Mentions: 3
Published: almost 4 years ago
10.3390/ijms21020483
Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes
Cited by: 25
Author(s): Wei Liu, Yingli Cai, Qianqian Zhang, Shu Fang, Lianfu Chen, Xiaolong Ma, Yinbing Bian
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12859-021-04279-1
Consensus clustering applied to multi-omics disease subtyping
Cited by: 23
Author(s): Galadriel Brière, Élodie Darbo, Patricia Thébault, Raluca Uricaru
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2164-8-426
e-Fungi: a data resource for comparative analysis of fungal genomes
Cited by: 29
Author(s): Cornelia Hedeler, Han Min Wong, Michael Cornell, Intikhab Álam, Darren M. Soanes, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, Norman W. Paton
Software Mentions: 3
Published: almost 18 years ago
10.1128/mSphere.00694-20
Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome
Cited by: 15
Author(s): Louis‐Marie Bobay, Emily F. Wissel, Kasie Raymann
Software Mentions: 3
Published: about 4 years ago
10.1128/mSystems.00075-18
Metapopulation Structure of CRISPR-Cas Immunity in <i>Pseudomonas aeruginosa</i> and Its Viruses
Cited by: 21
Author(s): Whitney England, Ted Kim, Rachel J. Whitaker
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pgen.1004078
Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus
Cited by: 229
Author(s): Kui Lin, Erik Limpens, Zhonghua Zhang, Sergey Ivanov, Diane G. O. Saunders, Desheng Mu, Erli Pang, Huifen Cao, Hwangho Cha, Tao Lin, Qian Zhou, Yi Shang, Ying Liu, Teena Sharma, Robin van Velzen, N.C.A. de Ruijter, Duur K. Aanen, Joe Win, Sophien Kamoun, Ton Bisseling, René Geurts, Sanwen Huang
Software Mentions: 3
Published: almost 11 years ago
10.1107/S0907444913027157
An estimated 5% of new protein structures solved today represent a new Pfam family
Cited by: 12
Author(s): Jaina Mistry, Edda Kloppmann, Burkhard Rost, Marco Punta
Software Mentions: 3
Published: about 11 years ago
10.3390/s21123972
Development of Magnetic-Based Navigation by Constructing Maps Using Machine Learning for Autonomous Mobile Robots in Real Environments
Cited by: 3
Author(s): Takumi Takebayashi, Renato Miyagusuku, Koichi Ozaki
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pntd.0005559
MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni
Cited by: 32
Author(s): Anna V. Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J. Collins, Anton J. Enright, Matthew Berriman
Software Mentions: 3
Published: over 7 years ago
10.3390/s21020665
Multi-Zone Authentication and Privacy-Preserving Protocol (MAPP) Based on the Bilinear Pairing Cryptography for 5G-V2X
Cited by: 12
Author(s): Shimaa A. Abdel Hakeem, HyungWon Kim
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pgen.1003840
Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways
Cited by: 66
Author(s): Shisong Ma, Smit Shah, Hans J. Bohnert, M Snyder, Savithramma P. Dinesh‐Kumar
Software Mentions: 3
Published: about 11 years ago
10.1038/s41598-020-66194-4
Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence
Cited by: 28
Author(s): Stavria Panayidou, Kaliopi Georgiades, Theodoulakis Christofi, Stella Tamana, Vasilis J. Promponas, Yiorgos Apidianakis
Software Mentions: 3
Published: over 4 years ago
10.1186/s42523-020-00063-3
The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance
Cited by: 6
Author(s): Bachar Cheaib, Hamza Seghouani, Martin S. Llewellyn, Katherine Vandal-Lenghan, Pierre-Luc Mercier, Nicolas Derôme
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-020-60737-5
L-HetNetAligner: A novel algorithm for Local Alignment of Heterogeneous Biological Networks
Cited by: 18
Author(s): Marianna Milano, Tijana Milenković, Mario Cannataro, Pietro Hiram Guzzi
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-017-11543-z
Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans
Cited by: 13
Author(s): Misty M. Attwood, Arunkumar Krishnan, Markus Sällman Almén, Helgi B. Schiöth
Software Mentions: 3
Published: about 7 years ago
10.1038/s41598-017-18341-7
Discovering viral genomes in human metagenomic data by predicting unknown protein families
Cited by: 13
Author(s): Mauricio Barrientos‐Somarribas, David N. Messina, Christian Pou, Fredrik Lysholm, Annelie Bjerkner, Tobias Allander, Björn Andersson, Erik L. L. Sonnhammer
Software Mentions: 3
Published: almost 7 years ago
10.1371/journal.pbio.3001026
Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides
Cited by: 66
Author(s): Alexander Kloosterman, Peter Cimermančič, E. A. Aboutabl, Congcong Du, Michalis Hadjithomas, Mohamed S. Donia, Michael A. Fischbach, Gilles P. van Wezel, Marnix H. Medema
Software Mentions: 3
Published: almost 4 years ago
10.7717/peerj.4691
Sexually dimorphic venom proteins in long-jawed orb-weaving spiders (<i>Tetragnatha</i>) comprise novel gene families
Cited by: 18
Author(s): Pamela A. Zobel-Thropp, Emily A. Bulger, Matthew Cordes, Greta J. Binford, Rosemary G. Gillespie, Michael S. Brewer
Software Mentions: 3
Published: over 6 years ago
10.1186/1471-2105-14-18
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
Cited by: 9
Author(s): Phillip Seitzer, Tu Anh Ngoc Huynh, Marc T. Facciotti
Software Mentions: 3
Published: almost 12 years ago
10.1186/1477-5956-10-S1-S18
Filtering Gene Ontology semantic similarity for identifying protein complexes in large protein interaction networks
Cited by: 17
Author(s): Jian Wang, Dong Xie, Hongfei Lin, Zhihao Yang, Yijia Zhang
Software Mentions: 3
Published: almost 13 years ago
10.1186/1471-2164-14-S5-S15
PLW: Probabilistic Local Walks for detecting protein complexes from protein interaction networks
Cited by: 11
Author(s): Daniel Lin-Kit Wong, Xiaoli Li, Min Wu, Jie Zheng, See-Kiong Ng
Software Mentions: 3
Published: almost 12 years ago
10.1093/molbev/msab152
A Chromosome-Level Assembly of Blunt Snout Bream (<i>Megalobrama amblycephala</i>) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish
Cited by: 29
Author(s): Han Liu, Chunhai Chen, Mao-Lin Lv, Ning Liu, Yafei Hu, Hailin Zhang, Erik D Enbody, Zexia Gao, Leif C. Andersson, Weimin Wang
Software Mentions: 3
Published: over 3 years ago
10.1002/mbo3.583
Characterization of Swedish<i>Campylobacter coli</i>clade 2 and clade 3 water isolates
Cited by: 5
Author(s): Anna Nilsson, Astrid Skarp, Cecilia Johansson, René Kaden, Lars Engstrand, Hilpi Rautelin
Software Mentions: 3
Published: almost 7 years ago
10.1186/1471-2164-14-608
Predicting whole genome protein interaction networks from primary sequence data in model and non-model organisms using ENTS
Cited by: 26
Author(s): Eli Rodgers-Melnick, Mark V. Culp, Stephen P. DiFazio
Software Mentions: 3
Published: about 11 years ago
10.1093/gigascience/giaa062
CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems
Cited by: 27
Author(s): Victor Alexandre Padilha, Omer S. Alkhnbashi, Shiraz A. Shah, André C. P. L. F. de Carvalho, Rolf Backofen
Software Mentions: 3
Published: over 4 years ago
10.1155/2017/1016305
Identification of Pharmacologically Tractable Protein Complexes in Cancer Using the R-Based Network Clustering and Visualization Program MCODER
Cited by: 4
Author(s): Gino Kwon, Hyosil Kim
Software Mentions: 3
Published: almost 8 years ago
10.7717/peerj.8778
Co-expression clustering across flower development identifies modules for diverse floral forms in<i>Achimenes</i>(Gesneriaceae)
Cited by: 3
Author(s): Wade R. Roberts, Eric H. Roalson
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2164-15-S9-S6
Transcriptome alterations of mitochondrial and coagulation function in schizophrenia by cortical sequencing analysis
Cited by: 25
Author(s): Kuo-Chuan Huang, Ko-Chun Yang, Han Lin, Theresa Tsun-Hui Tsao, Sheng-An Lee
Software Mentions: 3
Published: almost 10 years ago
10.1371/journal.ppat.1003037
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Cited by: 489
Author(s): Robin A. Ohm, Nicolas Feau, Bernard Henrissat, Conrad L. Schoch, Benjamin A. Horwitz, Kerrie Barry, Bradford Condon, Alex Copeland, Braham Dhillon, Fabian Glaser, Cedar Hesse, Idit Kosti, Kurt LaButti, Erika Lindquist, Susan Lucas, Asaf Salamov, Rosie E. Bradshaw, Lynda M. Ciuffetti, Richard Hamelin, G.H.J. Kema, Christopher B. Lawrence, James A. Scott, Joseph W. Spatafora, B. Gillian Turgeon, P.J.G.M. de Wit, Shaobin Zhong, Stephen B. Goodwin, Igor V. Grigoriev
Software Mentions: 3
Published: almost 12 years ago
10.1534/g3.120.401037
Draft Genome Assembly of <i>Floccularia luteovirens</i>, an Edible and Symbiotic Mushroom on Qinghai-Tibet Plateau
Cited by: 3
Author(s): Xiaolong Gan, Dong Cao, Zhenyu Zhang, Shu Cheng, Lin Wei, Shiming Li, Baolong Liu
Software Mentions: 3
Published: over 4 years ago
10.1186/1471-2164-11-S1-S3
Computational approaches for detecting protein complexes from protein interaction networks: a survey
Cited by: 281
Author(s): Xiaoli Li, Min Wu, Chee-Keong Kwoh, See-Kiong Ng
Software Mentions: 3
Published: almost 15 years ago
10.3389/fpls.2021.666342
Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain
Cited by: 36
Author(s): Pradeep Ruperao, Nepolean Thirunavukkarasu, Prasad Gandham, Sivasubramani Selvanayagam, Mahalingam Govindaraj, Baloua Nebié, Eric Manyasa, Rajeev Gupta, Roma Rani Das, Damaris Achieng Odeny, Harish Gandhi, David Edwards, Santosh Deshpande, Abhishek Rathore
Software Mentions: 3
Published: over 3 years ago
10.3389/fmicb.2018.00276
Genome-Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors
Cited by: 52
Author(s): David Lopez, Sébastien Ribeiro, Philippe Label, Boris Fumanal, Jean-Stéphane Venisse, Annegret Kohler, Ricardo Ribeiro de Oliveira, Kurt LaButti, Anna Lipzen, Kathleen Lail, Diane Bauer, Robin A. Ohm, Kerrie Barry, Joseph W. Spatafora, Igor V. Grigoriev, Francis Martin, Valérie Pujade-Renaud
Software Mentions: 3
Published: over 6 years ago
10.3389/fmicb.2019.00910
Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters
Cited by: 20
Author(s): Víctor González, Rosa I. Santamaría, Patricia Bustos, Olga María Pérez-Carrascal, Pablo Vinuesa, Soledad Juárez, Irma Martínez-Flores, Miguel A. Cevallos, Susana Brom, Esperanza Martínez‐Romero, David Romero
Software Mentions: 3
Published: over 5 years ago
10.3390/microorganisms8050653
Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae
Cited by: 33
Author(s): Jamie McGowan, Richard O’Hanlon, Rebecca A. Owens, David A. Fitzpatrick
Software Mentions: 3
Published: over 4 years ago
10.1186/1756-0500-4-549
Which clustering algorithm is better for predicting protein complexes?
Cited by: 26
Author(s): Charalampos Moschopoulos, Georgios A. Pavlopoulos, Ernesto Iacucci, Jan Aerts, Spiridon D. Likothanassis, Reinhard Schneider, Σοφία Κοσσίδα
Software Mentions: 3
Published: almost 13 years ago
10.1186/1471-2105-15-S2-S6
Prediction of heterotrimeric protein complexes by two-phase learning using neighboring kernels
Cited by: 18
Author(s): Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
Software Mentions: 3
Published: almost 11 years ago
10.3389/fpls.2016.01186
Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus
Cited by: 31
Author(s): Xiaoming Song, Jinpeng Wang, Xiao Ma, Yuxian Li, Tianyu Lei, Li Wang, Weina Ge, Di Guo, Zhenyi Wang, Chunjin Li, Zhao Jian-jun, Xiyin Wang
Software Mentions: 3
Published: over 8 years ago
10.3389/fpls.2016.00186
Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association
Cited by: 134
Author(s): Ki Tae Kim, Jongbum Jeon, Jaeyoung Choi, Kwang Ho Cheong, Hyeunjeong Song, Gobong Choi, Seogchan Kang, Yong Hwan Lee
Software Mentions: 3
Published: almost 9 years ago
10.1186/1471-2164-14-75
Draft genome sequence of the rubber tree Hevea brasiliensis
Cited by: 214
Author(s): Azimah Abd Rahman, Abhilash O Usharraj, Biswapriya B. Misra, Gincy P. Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz, Anton Yuryev, Bjarne Knudsen, Alexandre Dionne‐Laporte, Nokuthula Peace Mchunu, Qingyi Yu, Brennick J. Langston, Tracey Freitas, Aaron G. Young, Rui Chen, Lei Wang, Nazalan Najimudin, Jennifer A. Saito, Maqsudul Alam
Software Mentions: 3
Published: almost 12 years ago
10.1186/s12864-016-2547-z
Bioinformatic analyses in early host response to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) reveals pathway differences between pigs with alternate genotypes for a major host response QTL
Cited by: 24
Author(s): Martine Schroyen, Christopher J. Eisley, James E. Koltes, Eric R. Fritz-Waters, Igseo Choi, Graham Plastow, Leluo Guan, Paul Stothard, Hua Bao, Arun Kommadath, James M. Reecy, Joan K. Lunney, R. Rowland, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 3
Published: over 8 years ago
10.1186/s12870-021-03173-5
A pan-genomic approach to genome databases using maize as a model system
Cited by: 75
Author(s): Margaret R. Woodhouse, Ethalinda K. S. Cannon, John L. Portwood, Lisa C. Harper, Jack M. Gardiner, Mary L. Schaeffer, Carson M. Andorf
Software Mentions: 3
Published: over 3 years ago
10.3389/fgene.2021.701331
Modularity in Biological Networks
Cited by: 17
Author(s): Sergio Antonio Alcalá-Corona, Santiago Sandoval-Motta, Jesús Espinal-Enríquez, Enrique Hernández‐Lemus
Software Mentions: 3
Published: about 3 years ago
10.3389/fgene.2017.00165
New Tools in Orthology Analysis: A Brief Review of Promising Perspectives
Cited by: 55
Author(s): Bruno Thiago de Lima Nichio, Jeroniza Nunes Marchaukoski, Roberto Tadeu Raittz
Software Mentions: 3
Published: about 7 years ago
10.1186/1752-0509-8-34
Network and matrix analysis of the respiratory disease interactome
Cited by: 3
Author(s): Benjamin J. Garcia, Gargi Datta, Gregory P. Cosgrove, Michael Strong
Software Mentions: 3
Published: over 10 years ago
10.3389/fgene.2019.00668
A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis)
Cited by: 28
Author(s): Rachel Young, Lucas Lefèvre, Stephen J. Bush, Akshay Joshi, Shailesh Kumar Singh, Santosh Kumar Jadhav, Dhanikachalam Velu, Zofia M. Lisowski, Daniela Iamartino, Kim M. Summers, J. L. Williams, Alan Archibald, S. B. Gokhale, Satish Kumar, David Hume
Software Mentions: 3
Published: over 5 years ago
10.1093/gbe/evw047
<i>In-silico</i>identification of candidate genes for fertility restoration in cytoplasmic male sterile perennial ryegrass (<i>Lolium perenne</i>L.)
Cited by: 13
Author(s): Timothy Sykes, Steven Yates, Istvàn Nagy, Torben Asp, Ian Small, Bruno Studer
Software Mentions: 3
Published: over 8 years ago
10.1186/gb-2007-8-4-r61
Evolutionary conservation of sequence and secondary structures in CRISPR repeats
Cited by: 403
Author(s): Victor Kunin, Rotem Sorek, Philip Hugenholtz
Software Mentions: 3
Published: almost 18 years ago
10.1371/journal.ppat.1004365
Comparative Phenotypic Analysis of the Major Fungal Pathogens Candida parapsilosis and Candida albicans
Cited by: 100
Author(s): Linda Holland, Markus Schröder, Siobhán A. Turner, Heather T. Taff, David R. Andes, Zsuzsanna Grózer, Attila Gácser, Lauren Ames, Ken Haynes, Desmond G. Higgins, Geraldine Butler
Software Mentions: 3
Published: about 10 years ago
10.1186/s12859-019-2670-3
WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
Cited by: 17
Author(s): Yongzhi Yang, Ying Liu, Chunming Qiao, Yongshuai Sun, Zhiqiang Lu
Software Mentions: 2
Published: almost 6 years ago
10.1186/1471-2105-13-264
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
Cited by: 23
Author(s): Thomas J. Sharpton, Guillaume Jospin, Dongying Wu, Morgan G. I. Langille, Katherine S. Pollard, Jonathan A. Eisen
Software Mentions: 2
Published: about 12 years ago
10.1186/1471-2105-14-163
Protein complex detection using interaction reliability assessment and weighted clustering coefficient
Cited by: 126
Author(s): Nazar Zaki, Dmitry Efimov, Jose Berengueres
Software Mentions: 2
Published: over 11 years ago
10.1186/s12859-016-1054-1
Construction of dynamic probabilistic protein interaction networks for protein complex identification
Cited by: 25
Author(s): Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang
Software Mentions: 2
Published: over 8 years ago
10.1111/eva.12798
Experimental evolution of phytoplankton fatty acid thermal reaction norms
Cited by: 13
Author(s): Daniel R. O'Donnell, Zhi‐Yan Du, Elena Litchman
Software Mentions: 2
Published: over 5 years ago
10.1186/1471-2105-14-S16-S8
Identifying conserved protein complexes between species by constructing interolog networks
Cited by: 32
Author(s): Phi Vu Nguyen, Sriganesh Srihari, Hon Wai Leong
Software Mentions: 2
Published: about 11 years ago
10.3390/cancers12102823
Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling
Cited by: 5
Author(s): Ian M. Overton, Andrew H. Sims, Jeremy A. Owen, Bret S.E. Heale, Matthew J. Ford, Alexander L R Lubbock, Erola Pairo-Castineira, Abdelkader Essafi
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0053197
Benchmarking Human Protein Complexes to Investigate Drug-Related Systems and Evaluate Predicted Protein Complexes
Cited by: 14
Author(s): Min Wu, Qi Yu, Xiaoli Li, Jie Zheng, Jing‐Fei Huang, Chee Keong Kwoh
Software Mentions: 2
Published: almost 12 years ago
10.1186/s12859-014-0445-4
Evaluation and improvements of clustering algorithms for detecting remote homologous protein families
Cited by: 24
Author(s): Juliana Silva Bernardes, Fabio Rocha Jimenez Vieira, Lygia M M Costa, Gerson Zaverucha
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0184880
Large-scale cross-species chemogenomic platform proposes a new drug discovery strategy of veterinary drug from herbal medicines
Cited by: 7
Author(s): Chao Huang, Yang Yang, Xuetong Chen, Chao Wang, Yan Li, Chunli Zheng, Yonghua Wang
Software Mentions: 2
Published: about 7 years ago
10.1186/s12859-017-1877-4
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks
Cited by: 20
Author(s): Le Ou-Yang, Hong Yan, Xiaofei Zhang
Software Mentions: 2
Published: about 7 years ago
10.1186/s13015-015-0053-5
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison
Cited by: 9
Author(s): Wei Peng, Jianxin Wang, Fang‐Xiang Wu, Yi Pan
Software Mentions: 2
Published: over 9 years ago
10.1186/s40478-019-0847-7
Comparative profiling of the synaptic proteome from Alzheimer’s disease patients with focus on the APOE genotype
Cited by: 50
Author(s): Raphael Hesse, Maica Llavero Hurtado, Rosemary J. Jackson, Samantha L. Eaton, Abigail G. Herrmann, Martí Colom‐Cadena, Makis Tzioras, Declan King, Jamie Rose, Jane Tulloch, Chris-Anne McKenzie, Colin Smith, Christopher M. Henstridge, Douglas J. Lamont, Thomas M. Wishart, Tara L. Spires‐Jones
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2105-14-347
Heterodimeric protein complex identification by naïve Bayes classifiers
Cited by: 7
Author(s): Osamu Maruyama
Software Mentions: 2
Published: almost 11 years ago
10.1371/journal.pone.0102319
Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice
Cited by: 15
Author(s): Amit Kumar, Thomas F. Harrelson, Nathan E. Lewis, Emily J. Gallagher, Joseph Shiloach, Michael J. Betenbaugh
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0178650
Community detection in sequence similarity networks based on attribute clustering
Cited by: 3
Author(s): Janamejaya Chowdhary, Frank E. Löffler, Jeremy C. Smith
Software Mentions: 2
Published: over 7 years ago
10.1186/s12859-019-3256-9
Detecting overlapping protein complexes in weighted PPI network based on overlay network chain in quotient space
Cited by: 6
Author(s): Jie Zhao, Xiujuan Lei
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pone.0194124
Predicting protein complexes using a supervised learning method combined with local structural information
Cited by: 11
Author(s): Yadong Dong, Yeneng Sun, Chao Qin
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-019-6281-1
Genomic insights into mite phylogeny, fitness, development, and reproduction
Cited by: 22
Author(s): Yanxuan Zhang, Xia Chen, Jieping Wang, Zhiqiang Zhang, Hui Wei, Haiyan Yu, Hongkun Zheng, Yong Chen, Lisheng Zhang, Jian Lin, Li Sun, Dongyuan Liu, Juan Tang, Lei Yan, Xuming Li, Min Liu
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12864-016-2496-6
Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets
Cited by: 79
Author(s): Peter Thorpe, Peter J. A. Cock, Jorunn I. B. Bos
Software Mentions: 2
Published: over 8 years ago
10.3390/molecules190914723
Challenges and Opportunities of MicroRNAs in Lymphomas
Cited by: 25
Author(s): Giacoma De Tullio, Valentina Fazio, Nicola Sgherza, Carla Minoia, Simona Serratì, Francesca Merchionne, Giacomo Loseto, Angela Iacobazzi, Antonello Rana, P. Petrillo, Nicola Silvestris, Pasquale Iacopino, Attilio Giacosa
Software Mentions: 2
Published: about 10 years ago
10.1186/s12862-014-0266-0
Concatenated alignments and the case of the disappearing tree
Cited by: 48
Author(s): Thorsten Thiergart, Giddy Landan, William Martin
Software Mentions: 2
Published: almost 10 years ago
10.1186/s40168-015-0067-8
A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes
Cited by: 82
Author(s): Nurdyana Abdul Rahman, Donovan H. Parks, Dana Willner, Anna Engelbrektson, Shana K. Goffredi, Falk Warnecke, Rudolf H. Scheffrahn, Philip Hugenholtz
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0199947
Minor taxa in human skin microbiome contribute to the personal identification
Cited by: 25
Author(s): Hikaru Watanabe, Issei Nakamura, Sayaka Mizutani, Yumiko Kurokawa, Hiroshi Mori, Ken Kurokawa, Takuji Yamada
Software Mentions: 2
Published: over 6 years ago
10.1371/journal.pone.0041430
Mapping the Mutual Information Network of Enzymatic Families in the Protein Structure to Unveil Functional Features
Cited by: 34
Author(s): Daniel Aguilar, Baldo Oliva, Cristina Marino-Buslje
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0043092
Exploring Overlapping Functional Units with Various Structure in Protein Interaction Networks
Cited by: 20
Author(s): Xiaofei Zhang, Dao‐Qing Dai, Le Ou-Yang, Mengyun Wu
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0062158
Protein Complex Detection via Weighted Ensemble Clustering Based on Bayesian Nonnegative Matrix Factorization
Cited by: 29
Author(s): Le Ou-Yang, Dao‐Qing Dai, Xiaofei Zhang
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0016219
Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift
Cited by: 120
Author(s): Zhihua Hua, Cheng Zou, Shin-Han Shiu, Richard D. Vierstra
Software Mentions: 2
Published: almost 14 years ago
10.1371/journal.pone.0180570
A density-based approach for detecting complexes in weighted PPI networks by semantic similarity
Cited by: 9
Author(s): Huanfu Zhou, Jie Liu, Junhuai Li, WenCong Duan
Software Mentions: 2
Published: over 7 years ago
10.1186/s12920-017-0314-x
iOPTICS-GSO for identifying protein complexes from dynamic PPI networks
Cited by: 7
Author(s): Xiujuan Lei, Huan Li, Aidong Zhang, Fang‐Xiang Wu
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pone.0209411
Coastal complexity: Ancient human diets inferred from Bayesian stable isotope mixing models and a primate analogue
Cited by: 17
Author(s): Matthew C. Lewis, Judith Sealy
Software Mentions: 2
Published: almost 6 years ago
10.1186/1755-8794-7-S2-S3
Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection
Cited by: 9
Author(s): Zhi Yang, Feng Yu, Hong Fei Lin, Jian Wang
Software Mentions: 2
Published: almost 11 years ago
10.1186/1471-2105-12-192
MINE: Module Identification in Networks
Cited by: 86
Author(s): Kahn Rhrissorrakrai, Kristin C. Gunsalus
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0023973
One Carbon Metabolism in SAR11 Pelagic Marine Bacteria
Cited by: 164
Author(s): Jing Sun, Laura Steindler, J. Cameron Thrash, Kimberly H. Halsey, Daniel P. Smith, Amy E. Carter, Zachary C. Landry, Stephen J. Giovannoni
Software Mentions: 2
Published: about 13 years ago
10.1371/journal.pone.0013348
Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks
Cited by: 18
Author(s): Recep Çolak, Flavia Moser, Jeffrey Shih-Chieh Chu, Alexander Schönhuth, Nansheng Chen, Martin Ester
Software Mentions: 2
Published: about 14 years ago
10.1371/journal.pone.0011604
Phylogenomic Analysis of Marine Roseobacters
Cited by: 22
Author(s): Kai Tang, Hongzhan Huang, Nianzhi Jiao, Cathy H. Wu
Software Mentions: 2
Published: over 14 years ago
10.1371/journal.pone.0020085
OrthoList: A Compendium of C. elegans Genes with Human Orthologs
Cited by: 375
Author(s): Daniel D. Shaye, Iva Greenwald
Software Mentions: 2
Published: over 13 years ago
10.1371/journal.pone.0018011
Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees
Cited by: 96
Author(s): Dongying Wu, Martin Wu, Aaron L. Halpern, Douglas B. Rusch, Shibu Yooseph, M.E. Frazier, J. Craig Venter, Jonathan A. Eisen
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2105-16-S12-S3
Protein complex detection in PPI networks based on data integration and supervised learning method
Cited by: 11
Author(s): Feng Yu, Zhi Yang, Xiao Hu, Youhong Sun, Hong Fei Lin, Jian Wang
Software Mentions: 2
Published: about 9 years ago
10.1371/journal.pone.0091856
Detecting Overlapping Protein Complexes by Rough-Fuzzy Clustering in Protein-Protein Interaction Networks
Cited by: 46
Author(s): Hao Wu, Lin Gao, Jiuying Dong, Xiaofei Yang
Software Mentions: 2
Published: over 10 years ago
10.1186/1471-2164-11-557
Genome-wide expression patterns in physiological cardiac hypertrophy
Cited by: 17
Author(s): Ignat Drozdov, Sophia Tsoka, Christos A. Ouzounis, Ajay M. Shah
Software Mentions: 2
Published: about 14 years ago
10.1186/s12859-019-2649-0
Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks
Cited by: 8
Author(s): Xiujuan Lei, Ming Fang, Ling Guo, Fang‐Xiang Wu
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pone.0126468
What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated
Cited by: 90
Author(s): Benoı̂t Valot, Christophe Guyeux, Julien Yves Rolland, Kamel Mazouzi, Xavier Bertrand, Didier Hocquet
Software Mentions: 2
Published: over 9 years ago
10.1186/s12859-020-3447-4
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions
Cited by: 35
Author(s): Guannan Wang, Dong-Ha Oh, Maheshi Dassanayake
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0062077
Construction of Ontology Augmented Networks for Protein Complex Prediction
Cited by: 16
Author(s): Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0065265
Prediction of Heterodimeric Protein Complexes from Weighted Protein-Protein Interaction Networks Using Novel Features and Kernel Functions
Cited by: 22
Author(s): Peiying Ruan, Morihiro Hayashida, Osamu Maruyama, Tatsuya Akutsu
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0160435
CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design
Cited by: 5
Author(s): Shaoqiang Zhang, Yong Chen
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0061692
Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem
Cited by: 88
Author(s): Sheila Podell, Juan A. Ugalde, Priya Narasingarao, Jillian F. Banfield, Karla B. Heidelberg, Eric E. Allen
Software Mentions: 2
Published: over 11 years ago