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: about 9 years ago
2 dependent packages
398 downloads last month

Papers Mentioning MCL 563

10.1186/s12859-020-3489-7
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
Cited by: 11
Author(s): Joseph Bergenstråhle, Ludvig Bergenstråhle, Joakim Lundeberg
Software Mentions: 2
Published: about 4 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: over 13 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: almost 14 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: almost 6 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: about 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: almost 12 years ago
10.1186/s12859-017-1672-2
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer
Cited by: 20
Author(s): Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li
Software Mentions: 2
Published: about 7 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: about 13 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: almost 10 years ago
10.1186/s12859-016-1096-4
Protein complexes predictions within protein interaction networks using genetic algorithms
Cited by: 19
Author(s): Emad Ramadan, Ahmed Naef, Moataz Ahmed
Software Mentions: 2
Published: almost 8 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: over 6 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: almost 7 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: over 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: over 3 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: almost 12 years ago
10.3390/ijms21072580
A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)
Cited by: 4
Author(s): Katarzyna B. Czyż, Michał Książkiewicz, Grzegorz Koczyk, Anna Szczepaniak, Jan Podkowiński, B. Naganowska
Software Mentions: 2
Published: about 4 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: about 11 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: over 5 years ago
10.1093/molbev/msu245
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
Cited by: 274
Author(s): Ya Yang, Stephen A. Smith
Software Mentions: 2
Published: almost 10 years ago
10.1186/s12859-019-2856-8
PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks
Cited by: 9
Author(s): Yongsub Lim, In-Jae Yu, Dongmin Seo, U Kang, Lee Sael
Software Mentions: 2
Published: almost 5 years ago
10.1371/journal.pcbi.1003898
A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
Cited by: 202
Author(s): Seth D. Axen, Onur Erbilgin, Cheryl A. Kerfeld
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-019-5680-7
Evolution and comparative genomics of the most common Trichoderma species
Cited by: 150
Author(s): Christian P. Kubicek, Andrei Stecca Steindorff, Komal Chenthamara, Gelsomina Manganiello, Bernard Henrissat, Jian Zhang, Feng Cai, Alexey G. Kopchinskiy, Eva M. Kubicek, Alan Kuo, Riccardo Baroncelli, Sabrina Sarrocco, Eliane Ferreira Noronha, Giovanni Vannacci, Igor V. Grigoriev, Irina S. Druzhinina
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41598-020-66383-1
Screening and functional identification of lncRNAs in antler mesenchymal and cartilage tissues using high-throughput sequencing
Cited by: 5
Author(s): Danyang Chen, Ren-feng Jiang, Yanjun Li, Mingxiao Liu, Lei Wu, Wei Hu
Software Mentions: 2
Published: almost 4 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: about 5 years ago
10.1186/1471-2164-15-199
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease
Cited by: 78
Author(s): Puneet Talwar, Yumnam Silla, Sandeep Grover, Meena Gupta, Rachna Agarwal, Suman Kushwaha, Ritushree Kukreti
Software Mentions: 2
Published: about 10 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: almost 7 years ago
10.1186/s12864-019-5956-y
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations
Cited by: 11
Author(s): Rongquan Wang, Caixia Wang, Liankun Sun
Software Mentions: 2
Published: almost 5 years ago
10.3389/fgene.2016.00033
Computational Detection of Stage-Specific Transcription Factor Clusters during Heart Development
Cited by: 12
Author(s): Sebastian Zeidler, Cornelia Meckbach, Rebecca Tacke, Farah Raad, Angelica Roa, Shizuka Uchida, Wolfram‐Hubertus Zimmermann, Edgar Wingender, Mehmet Gültaş
Software Mentions: 2
Published: about 8 years ago
10.3389/fgene.2018.00272
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network
Cited by: 13
Author(s): Bo Xu, Yu Liu, Chi Lin, Jie Dong, Xiaoxia Liu, Zengyou He
Software Mentions: 2
Published: almost 6 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: almost 11 years ago
10.3389/fgene.2020.00567
DPCT: A Dynamic Method for Detecting Protein Complexes From TAP-Aware Weighted PPI Network
Cited by: 10
Author(s): Ali SabziNezhad, Saeed Jalili
Software Mentions: 2
Published: almost 4 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: almost 9 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: over 13 years ago
10.3389/fmicb.2014.00666
Multitasking SecB chaperones in bacteria
Cited by: 63
Author(s): Ambre Sala, Patricia Bordes, Pierre Genevaux
Software Mentions: 2
Published: over 9 years ago
10.3389/fmicb.2017.01279
Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae
Cited by: 23
Author(s): Matthew J. Harke, Andrew R. Juhl, Sheean T. Haley, Harriet Alexander, Sonya T. Dyhrman
Software Mentions: 2
Published: almost 7 years ago
10.1371/journal.pcbi.1002217
Thousands of Rab GTPases for the Cell Biologist
Cited by: 171
Author(s): Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-Cadete, Miguel C. Seabra, José B. Pereira-Leal
Software Mentions: 2
Published: over 12 years ago
10.1371/journal.pone.0105015
Orthology Detection Combining Clustering and Synteny for Very Large Datasets
Cited by: 103
Author(s): Marcus Lechner, Maribel Hernández-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thévenin, Jens Stoye, Roland K. Hartmann, Sonja J. Prohaska, Peter F. Stadler
Software Mentions: 2
Published: almost 10 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: about 13 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: over 13 years ago
10.1371/journal.pcbi.1002958
A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs
Cited by: 19
Author(s): Philip Stegmaier, Alexander Kel, Edgar Wingender, Jürgen Borlak
Software Mentions: 2
Published: about 11 years ago
10.1093/molbev/msx173
Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination
Cited by: 62
Author(s): Rafal Mostowy, Nicholas J. Croucher, Nicola De Maio, Claire Chewapreecha, Susannah J. Salter, Paul Turner, David M. Aanensen, Stephen D. Bentley, Xavier Didelot, Christophe Fraser
Software Mentions: 2
Published: almost 7 years ago
10.1186/1471-2105-11-504
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure
Cited by: 62
Author(s): Sriganesh Srihari, Kang Ning, Hon Wai Leong
Software Mentions: 2
Published: over 13 years ago
10.3389/fnmol.2021.658339
Broad Influence of Mutant Ataxin-3 on the Proteome of the Adult Brain, Young Neurons, and Axons Reveals Central Molecular Processes and Biomarkers in SCA3/MJD Using Knock-In Mouse Model
Cited by: 7
Author(s): Kalina Wiatr, Łukasz Marczak, J. Pérot, Emmanuel Brouillet, Julien Flament, Maciej Figiel
Software Mentions: 2
Published: almost 3 years ago
10.3389/fphys.2018.01689
Complete Genome Sequencing of Lactobacillus plantarum ZLP001, a Potential Probiotic That Enhances Intestinal Epithelial Barrier Function and Defense Against Pathogens in Pigs
Cited by: 33
Author(s): Wei Zhang, Hai‐Feng Ji, Dongyan Zhang, Hui Liu, Sixin Wang, Jing Wang, Yamin Wang
Software Mentions: 2
Published: over 5 years ago
10.3389/fpls.2015.01157
Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice
Cited by: 57
Author(s): Shuchi Smita, Amit Katiyar, Viswanathan Chinnusamy, Dev Mani Pandey, Kailash C. Bansal
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2020.607893
Evolution of Tandem Repeats Is Mirroring Post-polyploid Cladogenesis in Heliophila (Brassicaceae)
Cited by: 11
Author(s): Mert Dogan, Milan Pouch, Terezie Mandáková, Petra Hloušková, Xi Guo, P.J.D. Winter, Zuzana Chumová, Adriaan van Niekerk, Klaus Mummenhoff, Ihsan A. Al‐Shehbaz, Ladislav Mucina, Martin A. Lysak
Software Mentions: 2
Published: over 3 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: over 10 years ago
10.1186/1471-2164-10-630
Identification of mammalian orthologs using local synteny
Cited by: 63
Author(s): Jin Woo Jun, Ion Măndoiu, Craig E. Nelson
Software Mentions: 2
Published: over 14 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: over 6 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: about 4 years ago
10.1534/g3.112.004044
Comparative Genomics of a Plant-Pathogenic Fungus,<i>Pyrenophora tritici-repentis</i>, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence
Cited by: 142
Author(s): Viola A. Manning, Iovanna Pandelova, Braham Dhillon, Larry J. Wilhelm, Stephen B. Goodwin, Aaron M. Berlin, Melania Figueroa, Michael Freitag, James K. Hane, Bernard Henrissat, Wade H. Holman, Chinnappa D. Kodira, Joel Martin, Richard P. Oliver, Barbara Robbertse, Wendy Schackwitz, David C. Schwartz, Joseph W. Spatafora, B. Gillian Turgeon, Chandri Yandava, Sarah Young, Shiguo Zhou, Qiandong Zeng, Igor V. Grigoriev, Lijun Ma, Lynda M. Ciuffetti
Software Mentions: 2
Published: over 11 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: almost 13 years ago
10.3390/genes3020291
The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence
Cited by: 10
Author(s): Fotis Psomopoulos, Victoria I. Siarkou, Nikolas Papanikolaou, Ioannis Iliopoulos, Athanasios Tsaftaris, Vasilis J. Promponas, Christos A. Ouzounis
Software Mentions: 2
Published: about 12 years ago
10.1371/journal.pone.0202369
Genome-wide identification of clusters of predicted microRNA binding sites as microRNA sponge candidates
Cited by: 13
Author(s): Xiaoyong Pan, Anne Wenzel, Lars Juhl Jensen, Jan Gorodkin
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pcbi.1000452
A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations
Cited by: 247
Author(s): Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pone.0038108
Coordinating Environmental Genomics and Geochemistry Reveals Metabolic Transitions in a Hot Spring Ecosystem
Cited by: 72
Author(s): Wesley D. Swingley, D. R. Meyer-Dombard, Everett L. Shock, Eric Alsop, Heinz Dieter Falenski, J. R. Havig, Jason Raymond
Software Mentions: 2
Published: almost 12 years ago
10.1186/1471-2229-12-138
Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis
Cited by: 51
Author(s): Shan Wang, Yanbin Yin, Qin Ma, Xiaojia Tang, Dongyun Hao, Ying Xu
Software Mentions: 2
Published: almost 12 years ago
10.1371/journal.pone.0083841
Protein Complex Identification by Integrating Protein-Protein Interaction Evidence from Multiple Sources
Cited by: 12
Author(s): Bo Xu, Hongfei Lin, Yang Chen, Zhihao Yang, Hongfang Liu
Software Mentions: 2
Published: over 10 years ago
10.1186/gb-2010-11-1-r1
Genomic characterization of the Yersinia genus
Cited by: 94
Author(s): Peter E. Chen, Constance E. Cook, Andrew C. Stewart, Niranjan Nagarajan, Dan Sommer, Mihai Pop, Brendan Thomason, Maureen P. Kiley Thomason, Shannon M. Lentz, Nichole Nolan, Shanmuga Sozhamannan, Alexander Sulakvelidze, Alfred Mateczun, Lei Du, Michael E. Zwick, Timothy D. Read
Software Mentions: 2
Published: over 14 years ago
10.1186/gb-2010-11-4-r38
Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants
Cited by: 20
Author(s): Xin Zhou, Zhenguo Lin, Hong Mā
Software Mentions: 2
Published: over 14 years ago
10.1186/1471-2229-14-186
Annotation of gene function in citrus using gene expression information and co-expression networks
Cited by: 37
Author(s): D. Wong, Crystal Sweetman, Christopher M. Ford
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pcbi.1009446
Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class
Cited by: 18
Author(s): Elzbieta Rembeza, Martin K. M. Engqvist
Software Mentions: 2
Published: over 2 years ago
10.1186/s13059-014-0546-4
Organization and evolution of transposable elements along the bread wheat chromosome 3B
Cited by: 82
Author(s): Josquin Daron, Natasha Glover, Lise Pingault, Sébastien Theil, Véronique Jamilloux, Etienne Paux, Valérie Barbe, Sophie Mangenot, Adriana Alberti, Patrick Wincker, Hadi Quesneville, Catherine Feuillet, Frédéric Choulet
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2105-11-10
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Cited by: 52
Author(s): Guanqun Shi, Liqing Zhang, Tao Jiang
Software Mentions: 2
Published: over 14 years ago
10.1371/currents.RRN1213
Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data
Cited by: 51
Author(s): Barbara Robbertse, Ryan J. Yoder, Alexander Boyd, John Reeves, Joseph W. Spatafora
Software Mentions: 2
Published: over 13 years ago
10.1186/1471-2164-16-S2-S4
Integrating experimental and literature protein-protein interaction data for protein complex prediction
Cited by: 10
Author(s): Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang
Software Mentions: 2
Published: over 9 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: about 11 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: about 9 years ago
10.1186/s13059-018-1606-y
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex
Cited by: 78
Author(s): Marcus M. Dillon, Shalabh Thakur, Renan N. D. Almeida, Pauline W. Wang, Bevan S. Weir, David S. Guttman
Software Mentions: 2
Published: over 5 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: about 10 years ago
10.1093/gbe/evv220
Comparative Genomics of the Genus<i>Porphyromonas</i>Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species<i>Porphyromonas cangingivalis</i>
Cited by: 21
Author(s): Ciaran O’Flynn, Oliver Deusch, Aaron E. Darling, Jonathan A. Eisen, Corrin Wallis, Ian J. Davis, Stephen Harris
Software Mentions: 2
Published: over 8 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: over 9 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
10.1186/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: over 4 years ago
10.3390/microorganisms9040834
Presence of Broad-Spectrum Beta-Lactamase-Producing Enterobacteriaceae in Zoo Mammals
Cited by: 7
Author(s): Chloë De Witte, Nick Vereecke, Sebastiaan Theuns, Claudia De Ruyck, Francis Vercammen, Tim Bouts, Filip Boyen, Hans Nauwynck, Freddy Haesebrouck
Software Mentions: 2
Published: about 3 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: about 13 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: almost 8 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: over 4 years ago
10.1371/journal.pgen.1009200
A spectrum of verticality across genes
Cited by: 17
Author(s): Falk S. P. Nagies, Julia Brueckner, Fernando D. K. Tria, William Martin
Software Mentions: 2
Published: over 3 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: over 4 years ago
10.1186/s13321-016-0135-5
Ligand cluster-based protein network and ePlatton, a multi-target ligand finder
Cited by: 1
Author(s): Yu Du, Tieliu Shi
Software Mentions: 2
Published: about 8 years ago
10.1186/1752-0509-4-63
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems
Cited by: 37
Author(s): Sobia Raza, Neil McDerment, Paul Lacaze, Kevin A. Robertson, Steven Watterson, Ying Chen, Michael Chisholm, Geοrgiοs Eleftheriadis, Stephanie L. Monk, Matthew L. O’Sullivan, Arran Turnbull, Douglas Roy, Athanasios Theocharidis, Peter Ghazal, Tom C. Freeman
Software Mentions: 2
Published: about 14 years ago
10.1186/s12864-017-3650-5
Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation
Cited by: 75
Author(s): Philip Kelleher, Francesca Bottacini, Jennifer Mahony, Kieran N. Kilcawley, Douwe van Sinderen
Software Mentions: 2
Published: about 7 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: about 11 years ago
10.1186/1752-0509-8-S5-S3
Discovery of small protein complexes from PPI networks with size-specific supervised weighting
Cited by: 32
Author(s): Chern Han Yong, Osamu Maruyama, Limsoon Wong
Software Mentions: 2
Published: over 10 years ago
10.1186/1477-5956-9-S1-S7
Ontology integration to identify protein complex in protein interaction networks
Cited by: 18
Author(s): Bo Xu, Hongfei Lin, Zhihao Yang
Software Mentions: 2
Published: over 13 years ago
10.1186/1752-0509-4-129
Protein complex prediction based on k-connected subgraphs in protein interaction network
Cited by: 38
Author(s): Mahnaz Habibi, Changiz Eslahchi, Limsoon Wong
Software Mentions: 2
Published: over 13 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: almost 9 years ago
10.1186/1752-0509-7-S6-S14
PPSampler2: Predicting protein complexes more accurately and efficiently by sampling
Cited by: 26
Author(s): Chasanah Kusumastuti Widita, Osamu Maruyama
Software Mentions: 2
Published: over 11 years ago
10.1186/1752-0509-6-S2-S13
Supervised maximum-likelihood weighting of composite protein networks for complex prediction
Cited by: 36
Author(s): Chern Han Yong, Guimei Liu, Hon Nian Chua, Limsoon Wong
Software Mentions: 2
Published: over 12 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: over 6 years ago
10.1038/sdata.2016.30
Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors
Cited by: 87
Author(s): Luisa Orsini, Donald G. Gilbert, Ram Podicheti, Mieke Jansen, James Brown, Omid Shams Solari, Katina I. Spanier, John K. Colbourne, Douglas B Rush, Ellen Decaestecker, Jana Asselman, Karel A.C. De Schamphelaere, Dieter Ebert, Christoph R. Haag, Jouni Kvist, Christian Laforsch, Adam Petrusek, Andrew P. Beckerman, Tom J. Little, Anurag Chaturvedi, Michael E. Pfrender, Luc De Meester, Mikko J. Frilander
Software Mentions: 2
Published: about 8 years ago
10.1128/JVI.02613-15
Defining the Microglia Response during the Time Course of Chronic Neurodegeneration
Cited by: 66
Author(s): James E. Vincenti, Lita Murphy, Kathleen Grabert, Barry W. McColl, Enrico Cancellotti, Tom C. Freeman, Jean Manson
Software Mentions: 1
Published: about 8 years ago
10.1186/1471-2105-11-S1-S25
A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles
Cited by: 37
Author(s): Chia Hao Chin, Shu Hwa Chen, Chin Wen Ho, Ming-Tat Ko, Chung Yen Lin
Software Mentions: 1
Published: over 14 years ago
10.1186/1471-2105-11-S11-S3
Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology
Cited by: 4
Author(s): Liping Jing, Michael K. Ng
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2105-12-116
Ultra-fast sequence clustering from similarity networks with SiLiX
Cited by: 250
Author(s): Vincent Miele, Simon Penel, Laurent Duret
Software Mentions: 1
Published: about 13 years ago
10.1186/1471-2105-13-276
Coral: an integrated suite of visualizations for comparing clusterings
Cited by: 11
Author(s): Darya Filippova, Aashish Gadani, Carl Kingsford
Software Mentions: 1
Published: over 11 years ago
10.1186/s40168-018-0499-z
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon
Cited by: 111
Author(s): Evan Starr, Shaojun Shi, Steven J. Blazewicz, Alexander J. Probst, Donald J. Herman, Mary K. Firestone, Jillian F. Banfield
Software Mentions: 1
Published: almost 6 years ago
10.3390/microorganisms8040608
Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture
Cited by: 15
Author(s): Juanjuan Zhao, Xia Zhao, Junru Wang, Qi Gong, Xiaoxia Zhang, Guishan Zhang
Software Mentions: 1
Published: about 4 years ago
10.1186/s13100-016-0057-9
Phylogenomic analysis reveals genome-wide purifying selection on TBE transposons in the ciliate Oxytricha
Cited by: 12
Author(s): Xiao Chen, Laura F. Landweber
Software Mentions: 1
Published: over 8 years ago