cran: MCL | Projects | Ecosyste.ms: Papers

10.1186/1756-0500-6-107

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks
Cited by: 0
Author(s): Michel Bellis
Software Mentions: 1
Published: over 11 years ago

10.1186/1472-6807-11-31

Dynamical Basis for Drug Resistance of HIV-1 Protease
Cited by: 20
Author(s): Yi Mao
Software Mentions: 1
Published: almost 14 years ago

PPI network analyses of human WD40 protein family systematically reveal their tendency to assemble complexes and facilitate the complex predictions
Cited by: 8
Author(s): Xudong Zou, Ke An, Yun Na Wu, Zhiqiang Ye
Software Mentions: 1
Published: over 6 years ago

10.1186/1752-0509-5-134

Biological interaction networks are conserved at the module level
Cited by: 36
Author(s): Guy Zinman, Shan Zhong, Ziv Bar‐Joseph
Software Mentions: 1
Published: over 13 years ago

10.1186/1752-0509-6-S3-S4

Detection of protein complexes from affinity purification/mass spectrometry data
Cited by: 10
Author(s): Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang
Software Mentions: 1
Published: almost 12 years ago

10.1186/1752-0509-4-8

A general co-expression network-based approach to gene expression analysis: comparison and applications
Cited by: 201
Author(s): Jianhua Ruan, Angela K Dean, Weixiong Zhang
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12918-017-0405-5

Finding low-conductance sets with dense interactions (FLCD) for better protein complex prediction
Cited by: 6
Author(s): Yijie Wang, Xiaoning Qian
Software Mentions: 1
Published: over 7 years ago

10.1186/1752-0509-5-25

A new computational method to split large biochemical networks into coherent subnets
Cited by: 21
Author(s): W.S. Verwoerd
Software Mentions: 1
Published: almost 14 years ago

10.1186/1752-0509-6-S1-S6

Discovering protein complexes in protein interaction networks via exploring the weak ties effect
Cited by: 22
Author(s): Xiaoke Ma, Lin Gao
Software Mentions: 1
Published: almost 13 years ago

10.1186/1752-0509-3-63

The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti
Cited by: 11
Author(s): Ignacio D. Rodríguez‐Llorente, Miguel A. Caviedes, Mohammed Dary, Antonio J. Palomares, Francisco M. Cánovas, José M. Peregrín-Alvarez
Software Mentions: 1
Published: over 15 years ago

10.1186/1752-0509-8-S1-S9

Joint clustering of protein interaction networks through Markov random walk
Cited by: 8
Author(s): Yijie Wang, Xiaoning Qian
Software Mentions: 1
Published: almost 11 years ago

10.1186/s41044-016-0019-8

PorthoMCL: Parallel orthology prediction using MCL for the realm of massive genome availability
Cited by: 28
Author(s): Ehsan Tabari, Zhengchang Su
Software Mentions: 1
Published: almost 8 years ago

10.3390/bioengineering6030083

Finite Element Driven Design Domain Identification of a Beating Left Ventricular Simulator
Cited by: 3
Author(s): Utku Gülbulak, A. Ertaş
Software Mentions: 1
Published: about 5 years ago

10.1093/bioinformatics/bts370

Identifying functional modules in interaction networks through overlapping Markov clustering
Cited by: 95
Author(s): Yu-Keng Shih, S. Parthasarathy
Software Mentions: 1
Published: about 12 years ago

10.1186/1745-6150-1-38

Cited by: 6
Author(s): Emmanuel Jaspard
Software Mentions: 1
Published: almost 19 years ago

10.1155/2021/6656365

Genome Assembly and Analyses of the Macrofungus Macrocybe gigantea
Cited by: 3
Author(s): Ling Kui, Zhe Zhang, Yangzi Wang, Yesheng Zhang, Shiming Li, Dong Xiao, Qiuju Xia, Jun Sheng, Jian Wang, Yang Dong
Software Mentions: 1
Published: almost 4 years ago

10.1155/2014/354539

A Novel Algorithm for Detecting Protein Complexes with the Breadth First Search
Cited by: 10
Author(s): Xiwei Tang, Jianxin Wang, Min Li, Yiming He, Yi Pan
Software Mentions: 1
Published: almost 11 years ago

10.3390/biom9110656

A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes
Cited by: 0
Author(s): Suyu Mei, Kun Zhang
Software Mentions: 1
Published: about 5 years ago

10.3390/biom11070950

Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase
Cited by: 3
Author(s): Mirna Hajj, Petra S. Langendijk-Genevaux, Manon Batista, Yves Quentin, Sébastien Laurent, Régine Capeyrou, Ziad Abdel-Razzak, Didier Flament, Hala Chamieh, Gwennaële Fichant, Béatrice Clouet‐d’Orval, Marlène Bouvier
Software Mentions: 1
Published: over 3 years ago

10.1186/s13068-016-0670-3

Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype
Cited by: 85
Author(s): Jesse Traller, Shawn J. Cokus, David López, Olga Gaidarenko, Sarah R. Smith, John P. McCrow, Sean D. Gallaher, Sheila Podell, Michael J. Thompson, Orna Cook, Marco Morselli, Artur Jaroszewicz, Eric E. Allen, Andrew E. Allen, Sabeeha Merchant, Matteo Pellegrini, Mark Hildebrand
Software Mentions: 1
Published: almost 8 years ago

10.3390/life6010007

Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch
Cited by: 2
Author(s): Oleg A. Zverkov, А. В. Селиверстов, Vassily Lyubetsky
Software Mentions: 1
Published: almost 9 years ago

10.1097/MD.0000000000000078

Truview EVO2 and Standard Macintosh Laryngoscope for Tracheal Intubation During Cardiopulmonary Resuscitation
Cited by: 5
Author(s): Ewelina Gaszyńska, Tomasz Gaszyński
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pbio.1000096

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Cited by: 333
Author(s): Pingzhao Hu, Sarath Chandra Janga, Mohan Babu, J. Javier Díaz-Mejía, Gareth Butland, Wenhong Yang, Oxana Pogoutse, Xinghua Guo, Sadhna Phanse, Patrick Wong, Shamanta Chandran, Constantine Christopoulos, Anaies Nazarians-Armavil, Negin Karimi Nasseri, Gabriel Musso, Mehrab Ali, Nazila Nazemof, Veronika Eroukova, Ashkan Golshani, Alberto Paccanaro, Jack Greenblatt, Gabriel Moreno‐Hagelsieb, Andrew Emili
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1000641

Associating Genes and Protein Complexes with Disease via Network Propagation
Cited by: 742
Author(s): Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pcbi.1002752

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life
Cited by: 50
Author(s): Marc P. Hoeppner, Paul P. Gardner, Anthony M. Poole
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pcbi.1004016

A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis
Cited by: 149
Author(s): Marnix H. Medema, Peter Cimermančič, Andrej Šali, Eriko Takano, Michael A. Fischbach
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pcbi.0030066

Towards Complete Sets of Farnesylated and Geranylgeranylated Proteins
Cited by: 148
Author(s): Sebastian Maurer‐Stroh, Manfred Koranda, Wolfgang Benetka, Georg Schneider, Fernanda L. Sirota, Frank Eisenhaber
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pcbi.0030206

Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data
Cited by: 220
Author(s): Tom C. Freeman, Leon Goldovsky, Markus Brosch, Stijn van Dongen, Pierre Mazière, Russell Grocock, Shiri Freilich, Janet M. Thornton, Anton J. Enright
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pcbi.1000788

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks
Cited by: 42
Author(s): Karine Audouze, Agnieszka Sierakowska Juncker, Francisco S. Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen, Søren Brunak
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1002983

The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems
Cited by: 239
Author(s): Sophie S. Abby, Eduardo P. C. Rocha
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1002222

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation
Cited by: 321
Author(s): Julien Guglielmini, Leonor Quintais, M. Pilar Garcillán-Barcia, Fernando de la Cruz, Eduardo P. C. Rocha
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pgen.1005614

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin
Cited by: 176
Author(s): Guangxi Wu, He Zhao, Chenhao Li, Menaka Priyadarsani Rajapakse, William Wong, Jingying Xu, Charles W. Saunders, Nancy L. Reeder, Raymond Reilman, Annika Scheynius, Sheng Sun, R. Blake Billmyre, Wenjun Li, Anna Floyd Averette, Piotr A. Mieczkowski, Joseph Heitman, Bart Theelen, Markus Schröder, Paola Flórez de Sessions, Geraldine Butler, Sebastian Maurer‐Stroh, Teun Boekhout, Niranjan Nagarajan, Thomas L. Dawson
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1002357

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont
Cited by: 189
Author(s): Araceli Lamelas, María José Gosalbes, Alejandro Manzano-Marı́n, Juli Peretó, Andrés Moya, Amparo Latorre
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pgen.1003825

Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability
Cited by: 41
Author(s): Louis‐Marie Bobay, Marie Touchon, Eduardo P. C. Rocha
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pntd.0000269

Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus with the Free-living Caenorhabditis elegans
Cited by: 38
Author(s): Yong Yin, John Martin, Sahar Abubucker, Alan L. Scott, James P. McCarter, Richard K. Wilson, Douglas P. Jasmer, Makedonka Mitreva
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pntd.0004446

A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions
Cited by: 56
Author(s): Carine Makendi, Andrew J. Page, Brendan W. Wren, Tu Le Thi Phuong, Simon Clare, Christine Hale, David Goulding, Elizabeth J. Klemm, Derek Pickard, Chinyere K. Okoro, Martin Hunt, Corinne N. Thompson, Nguyen Phu Huong Lan, Nhu Tran Do Hoang, Guy Thwaites, Simon Le Hello, Anne Brisabois, François‐Xavier Weill, Stephen Baker, Gordon Dougan
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0094608

ModuleRole: A Tool for Modulization, Role Determination and Visualization in Protein-Protein Interaction Networks
Cited by: 5
Author(s): Gui Peng Li, Ming Li, Yi Wei Zhang, Dong Wang, Rong Li, Roger Guimerà, Juntao Gao, Michael Q. Zhang
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0025381

Profiling the Trypanosoma cruzi Phosphoproteome
Cited by: 65
Author(s): Fabrício Klerynton Marchini, Lyris Martins Franco de Godoy, Rita de Cássia Pontello Rampazzo, Daniela Parada Pavoni, Christian M. Probst, Florian Gnad, Matthias Mann, Marco Aurélio Krieger
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0203670

CASS: A distributed network clustering algorithm based on structure similarity for large-scale network
Cited by: 5
Author(s): Jungrim Kim, Mincheol Shin, Jeongwoo Kim, Chihyun Park, Sujin Lee, Jaemin Woo, Hyerim Kim, Dongmin Seo, Soo‐Chang Yu, Sang‐Hyun Park
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0121248

Modes of Interaction between Individuals Dominate the Topologies of Real World Networks
Cited by: 4
Author(s): Insuk Lee, Eiru Kim, Edward M. Marcotte
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0012623

Diffusion Model Based Spectral Clustering for Protein-Protein Interaction Networks
Cited by: 26
Author(s): Kentaro Inoue, Weijiang Li, Hiroyuki Kurata
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0017300

New Implications on Genomic Adaptation Derived from the Helicobacter pylori Genome Comparison
Cited by: 19
Author(s): Edgar E. Lara-Ramírez, Aldo Segura‐Cabrera, Xianwu Guo, Guoying Karen Yu, Carlos A. García-Pérez, Mario A. Rodríguez‐Pérez
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0151651

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens
Cited by: 116
Author(s): Tomasz Suchan, Camille Pitteloud, Н. Г. Герасимова, Anna Kostikova, Sarah Schmid, Nils Arrigo, Mila Pajkovic, Michał Ronikier, Nadir Alvarez
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0020892

MultiMSOAR 2.0: An Accurate Tool to Identify Ortholog Groups among Multiple Genomes
Cited by: 19
Author(s): Guanqun Shi, Meng-Chih Peng, Tao Jiang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0153967

Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression
Cited by: 12
Author(s): Xin Shen, Yang Li, Xingpeng Jiang, Tingting He, Xiaohua Hu, Jincai Yang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0125585

A Modularity-Based Method Reveals Mixed Modules from Chemical-Gene Heterogeneous Network
Cited by: 3
Author(s): Jianglong Song, Shi-Huan Tang, Xi Liu, Yibo Gao, Hongjun Yang, Peng Lu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0236950

Dietary supplementation with a microencapsulated blend of organic acids and botanicals alters the kinome in the ileum and jejunum of Gallus gallus
Cited by: 9
Author(s): Christina L. Swaggerty, Ryan J. Arsenault, Casey Johnson, Andrea Piva, Ester Grilli
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0066213

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System
Cited by: 1,460
Author(s): Sujeevan Ratnasingham, Paul D. N. Hebert
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0060224

Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia spumigena CCY9414 Based on a Genome-Transcriptome Analysis
Cited by: 76
Author(s): Björn Voß, Henk Bolhuis, David P. Fewer, Matthias Kopf, Fred Möke, Fabian B. Haas, Rehab El-Shehawy, Paul K. Hayes, Birgitta Bergman, Kaarina Sivonen, Elke Dittmann, David J. Scanlan, Martin Hagemann, Lucas J. Stal, Wolfgang R. Hess
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0172393

Preload-based Starling-like control of rotary blood pumps: An in-vitro evaluation
Cited by: 13
Author(s): Majdi Mansouri, Shaun D. Gregory, Robert F. Salamonsen, Nigel H. Lovell, Michael C. Stevens, Jo P. Pauls, Rini Akmeliawati, Einly Lim
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0002567

A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria
Cited by: 58
Author(s): Lisa Crossman, Santiago Castillo-Ramírez, Craig McAnnula, Luis Lozano, Georgios S. Vernikos, José Luís Acosta, Zara Ghazoui, Ismael Hernández-González, Georgina E. Meakin, Alan W. Walker, Michael F. Hynes, J. Peter W. Young, J. Allan Downie, David Romero, Andrew Johnston, Guillermo Dávila, Julian Parkhill, Víctor González
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0223438

Comparison of transcriptomes of an orthotospovirus vector and non-vector thrips species
Cited by: 5
Author(s): Anita Shrestha, Donald E. Champagne, A. K. Culbreath, Mark Abney, Rajagopalbabu Srinivasan
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0000085

The Evolution of Mammalian Gene Families
Cited by: 292
Author(s): Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0195994

Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution
Cited by: 5
Author(s): Chen Chen, Linfeng Wu, Qinghua Cao, Huanhuan Shao, Xuedan Li, Yizheng Zhang, Haiyan Wang, Xuemei Tan
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0173163

The amyloid interactome: Exploring protein aggregation
Cited by: 23
Author(s): Konstantina V. Biza, Katerina C. Nastou, Paraskevi L. Tsiolaki, Chara V. Mastrokalou, Stavros J. Hamodrakas, Vassiliki A. Iconomidou
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0003358

Discovery and Expansion of Gene Modules by Seeking Isolated Groups in a Random Graph Process
Cited by: 4
Author(s): Jochen Brumm, Elizabeth Conibear, Wyeth W. Wasserman, Jenny Bryan
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0177977

A dual-strategy expression screen for candidate connectivity labels in the developing thalamus
Cited by: 12
Author(s): Olivia Bibollet-Bahena, Tatsuya Okafuji, Karsten Hokamp, Guy Tear, Kevin J. Mitchell
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0084796

Lactococcus garvieae: Where Is It From? A First Approach to Explore the Evolutionary History of This Emerging Pathogen
Cited by: 41
Author(s): Chiara Ferrario, Giovanni Ricci, Christian Milani, Gabriele Andrea Lugli, Marco Ventura, Giovanni Eraclio, Francesca Borgo, María Grazia Fortina
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0095480

Community-Based Network Study of Protein-Carbohydrate Interactions in Plant Lectins Using Glycan Array Data
Cited by: 19
Author(s): Adeel Malik, Juyong Lee, Jooyoung Lee
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0020124

Gene Network Landscape of the Ciliate Tetrahymena thermophila
Cited by: 30
Author(s): Jie Xiong, Dan Yuan, Jeffrey Fillingham, Jyoti Garg, Xianbo Lu, Yue Chang, Yifan Liu, Chengjie Fu, Ronald E. Pearlman, Wei Miao
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0100999

Elucidation of Operon Structures across Closely Related Bacterial Genomes
Cited by: 3
Author(s): Chunkui Zhou, Qin Ma, Guojun Li
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0183460

Protein complex prediction via dense subgraphs and false positive analysis
Cited by: 10
Author(s): Cecilia Hernández, Carlos Mella, Gonzalo Navarro, Álvaro Olivera-Nappa, Jaime E. Araya
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0133597

Network Analysis for the Identification of Differentially Expressed Hub Genes Using Myogenin Knock-down Muscle Satellite Cells
Cited by: 20
Author(s): Adeel Malik, Eun Ju Lee, Arif Tasleem Jan, Sarafraz Ahmad, Kyung‐Hyun Cho, Jihoe Kim, Inho Choi
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0148889

Comparative Analysis of Lacinutrix Genomes and Their Association with Bacterial Habitat
Cited by: 3
Author(s): Yung Mi Lee, Mi-Kyeong Kim, Do Hwan Ahn, Han-Woo Kim, Hyun Park, Seung Chul Shin
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41419-020-2498-9

MCL-1Matrix maintains neuronal survival by enhancing mitochondrial integrity and bioenergetic capacity under stress conditions
Cited by: 54
Author(s): Ujval Anilkumar, Mireille Khacho, Alexanne Cuillerier, Richard Harris, David A. Patten, Maria Bilen, Mohamed Ariff Iqbal, Ding Yuan Guo, Louis-Éric Trudeau, David Park, Mary‐Ellen Harper, Yan Burelle, Ruth S. Slack
Software Mentions: 1
Published: over 4 years ago

10.1016/j.celrep.2019.03.096

Regional Molecular Mapping of Primate Synapses during Normal Healthy Aging
Cited by: 16
Author(s): Laura C. Graham, Michael J. Naldrett, Steven G. Kohama, Colin Smith, Douglas J. Lamont, Barry W. McColl, Thomas H. Gillingwater, Paul Skehel, Henryk F. Urbanski, Thomas M. Wishart
Software Mentions: 1
Published: over 5 years ago

10.3390/cells10020402

Knowledge-Guided “Community Network” Analysis Reveals the Functional Modules and Candidate Targets in Non-Small-Cell Lung Cancer
Cited by: 10
Author(s): Fan Wang, Shengcheng Han, Jicheng Yang, Wenying Yan, Guang Hu
Software Mentions: 1
Published: almost 4 years ago

10.1155/2017/5924270

Finding Solvable Units of Variables in Nonlinear ODEs of ECM Degradation Pathway Network
Cited by: 1
Author(s): Shuji Kawasaki, Dhisa Minerva, Keiko Itano, Takashi Suzuki
Software Mentions: 1
Published: almost 8 years ago

10.1186/1742-6413-3-24

Cited by: 37
Author(s): Pranab Dey, Thasneem Amir, Aisha Al Jassar, Salem Al Shemmari, Sanjay Jogai, Ganapathi Bhat M, Aisha Al Quallaf, Zahia Al Shammari
Software Mentions: 1
Published: almost 19 years ago

10.1093/database/bax092

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases
Cited by: 8
Author(s): Sook Jung, Taein Lee, Cuixia Cheng, Stephen P. Ficklin, Jing Yu, Jodi L. Humann, Dorrie Main
Software Mentions: 1
Published: almost 8 years ago

10.1093/database/baab023

Tripal MegaSearch: a tool for interactive and customizable query and download of big data
Cited by: 7
Author(s): Sook Jung, Cuixia Cheng, Katheryn Buble, Taein Lee, Jodi L. Humann, Jing Yu, James Crabb, Heidi Hough, Dorrie Main
Software Mentions: 1
Published: almost 4 years ago

10.1093/database/baz122

UPObase: an online database of unspecific peroxygenases
Cited by: 4
Author(s): Muniba Faiza, Dongming Lan, Shengfeng Huang, Yonghua Wang
Software Mentions: 1
Published: almost 6 years ago

10.1155/2015/497314

The Mechanism Research of Qishen Yiqi Formula by Module-Network Analysis
Cited by: 3
Author(s): Shu Zheng, Zhang Yan-ling, Yanjiang Qiao
Software Mentions: 1
Published: almost 10 years ago

10.1017/erm.2015.3

Cooperative integration between HEDGEHOG-GLI signalling and other oncogenic pathways: implications for cancer therapy
Cited by: 70
Author(s): Silvia Pandolfi, Barbara Stecca
Software Mentions: 1
Published: almost 10 years ago

10.1002/2211-5463.13287

Unraveling the relevance of the polyadenylation factor EhCFIm25 in <i>Entamoeba histolytica</i> through proteomic analysis
Cited by: 1
Author(s): América Itzallana Salgado-Martínez, Rodolfo Gamaliel Avila-Bonilla, Esther Ramírez‐Moreno, Carlos Alberto Castañón-Sánchez, César López‐Camarillo, Laurence A. Marchat
Software Mentions: 1
Published: about 3 years ago

10.3389/fgene.2021.609766

Protein Complexes Form a Basis for Complex Hybrid Incompatibility
Cited by: 11
Author(s): Krishna B S Swamy, Scott C. Schuyler, Jun‐Yi Leu
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2018.00738

Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia
Cited by: 24
Author(s): Sofya K. Garushyants, Alexandra Beliavskaia, Dmitry B. Malko, Maria D. Logacheva, Maria Rautian, Mikhail S. Gelfand
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2015.00713

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle
Cited by: 218
Author(s): Karen E. Nelson, James C. Stegen
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2015.01110

A combined bioinformatics and functional metagenomics approach to discovering lipolytic biocatalysts
Cited by: 16
Author(s): Thorsten Masuch, Anna Kusnezowa, Sebastian Nilewski, José Terrón Bautista, Robert Kourist, Lars I. Leichert
Software Mentions: 1
Published: about 9 years ago

10.3389/fmicb.2021.664476

IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context
Cited by: 3
Author(s): Stefani Díaz-Valerio, Anat Lev Hacohen, Raphael Schöppe, Heiko Liesegang
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2018.01548

The Endophytic Strain Klebsiella michiganensis Kd70 Lacks Pathogenic Island-Like Regions in Its Genome and Is Incapable of Infecting the Urinary Tract in Mice
Cited by: 12
Author(s): Karina I Dantur, Nadia Regina Chalfoun, Maria P Claps, María L. Tortora, Clara Silva, Ángela Jure, Norma Porcel, María I. Bianco, Adrián Alberto Vojnov, Atilio Pedro Castagnaro, Björn Welin
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2020.00369

Genome Insights of the Plant-Growth Promoting Bacterium Cronobacter muytjensii JZ38 With Volatile-Mediated Antagonistic Activity Against Phytophthora infestans
Cited by: 33
Author(s): Abdul Aziz Eida, Salim Bougouffa, Floriane L’Haridon, Intikhab Álam, Laure Weisskopf, Vladimir B. Bajic, Maged M. Saad, Heribert Hirt
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.680920

Genetic Dissection of a Prevalent Plasmid-Encoded Conjugation System in Lactococcus lactis
Cited by: 5
Author(s): Guillermo Ortíz Charneco, Philip Kelleher, Andrius Buivydas, Hugo Streekstra, Emiel Ver Loren van Themaat, Paul P. de Waal, Jennifer Mahony, Douwe van Sinderen
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2016.00118

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database
Cited by: 120
Author(s): James J. Davis, Svetlana Gerdes, Gary J. Olsen, Robert Olson, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Hyunseung Yoo
Software Mentions: 1
Published: almost 9 years ago

10.3389/fnbot.2018.00011

Hierarchical Spatial Concept Formation Based on Multimodal Information for Human Support Robots
Cited by: 15
Author(s): Yoshinobu Hagiwara, Masashi Inoue, Hiroyoshi Kobayashi, Tadahiro Taniguchi
Software Mentions: 1
Published: over 6 years ago

10.3389/fpls.2015.00579

Candidate effector proteins of the necrotrophic apple canker pathogen Valsa mali can suppress BAX-induced PCD
Cited by: 46
Author(s): Zhengpeng Li, Zhiyuan Yin, Yanyun Fan, Ming Xu, Zhensheng Kang, Lili Huang
Software Mentions: 1
Published: over 9 years ago

10.3389/fpls.2013.00228

Effector candidates in the secretome of Piriformospora indica, a ubiquitous plant-associated fungus
Cited by: 42
Author(s): Maryam Rafiqi, Lukas Jelonek, Ndifor Fidele Akum, Feng Zhang, Karl-Heinz Kögel
Software Mentions: 1
Published: almost 12 years ago

10.3389/fpubh.2020.557587

Blood Transcriptome Response to Environmental Metal Exposure Reveals Potential Biological Processes Related to Alzheimer's Disease
Cited by: 9
Author(s): Julian Krauskopf, Ingvar A. Bergdahl, Anders Johansson, Domenico Palli, Thomas Lundh, Soterios A. Kyrtopoulos, Theo M. de Kok, Jos Kleinjans
Software Mentions: 1
Published: about 4 years ago

10.3389/frobt.2019.00031

Semantic Mapping Based on Spatial Concepts for Grounding Words Related to Places in Daily Environments
Cited by: 9
Author(s): Yuki Katsumata, Akira Taniguchi, Yoshinobu Hagiwara, Tadahiro Taniguchi
Software Mentions: 1
Published: over 5 years ago

10.3390/genes3040576

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation
Cited by: 64
Author(s): Florence Wisniewski‐Dyé, Luis Lozano, Erika Acosta-Cruz, Stéphanie Borland, Benoît Drogue, Claire Prigent‐Combaret, Zoé Rouy, Valérie Barbe, Alberto Herrera, Víctor González, Patrick Mavingui
Software Mentions: 1
Published: about 12 years ago

10.3390/genes2041017

Plant-Bacteria Association and Symbiosis: Are There Common Genomic Traits in Alphaproteobacteria?
Cited by: 67
Author(s): Francesco Pini, Marco Galardini, Marco Bazzicalupo, Alessio Mengoni
Software Mentions: 1
Published: almost 13 years ago

10.3390/genes12091421

Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
Cited by: 6
Author(s): Yuqiang Zhao, Yanxin Wang, Chengyao Xia, Lixin Xu, Xianfeng Ye, Qi‐Wen Fan, Yan Huang, Zhoukun Li, Cancan Zhu, Zhongli Cui
Software Mentions: 1
Published: about 3 years ago

10.1002/gcc.22977

Increased complexity of t(11;14) rearrangements in plasma cell neoplasms compared with mantle cell lymphoma
Cited by: 1
Author(s): Joanna Dalland, James B. Smadbeck, Neeraj Sharma, Reid G. Meyer, Kathryn E. Pearce, Patricia T. Greipp, Jess F. Peterson, Santosh Kumar, Rhett P. Ketterling, Rebecca King, Linda B. Baughn
Software Mentions: 1
Published: over 3 years ago

10.1128/genomeA.00363-16

Genome Sequence of Penicillium solitum RS1, Which Causes Postharvest Apple Decay
Cited by: 16
Author(s): Jiujiang Yu, Guangxi Wu, Wayne M. Jurick, Verneta L. Gaskins, Yanbin Yin, Guohua Yin, Joan W. Bennett, Daniel R. Shelton
Software Mentions: 1
Published: over 8 years ago

10.1186/gb-2006-7-4-r31

Cited by: 157
Author(s): Tim Hulsen, Martijn A. Huynen, Jacob de Vlieg, Peter M.A. Groenen
Software Mentions: 1
Published: almost 19 years ago

10.1186/gb-2011-12-4-r40

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma
Cited by: 552
Author(s): Christian P. Kubicek, Alfredo Herrera-Estrella, Verena Seidl‐Seiboth, Diego Martínez, Irina S. Druzhinina, Michael R. Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A. Horwitz, Prasun K. Mukherjee, Mala Mukherjee, László Kredics, Luis David Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte Guadalupe Cervantes-Badillo, Jean F. Challacombe, Olga Chertkov, Kevin McCluskey, Fanny Coulpier, Nandan P. Deshpande, Hans von Döhren, Daniel J. Ebbole, Edgardo Ulises Esquivel-Naranjo, Erzsébet Fekete, Michel Flipphi, Fabian Glaser, Elida Yazmín Gómez-Rodríguez, Sabine Gruber, Cliff Han, Bernard Henrissat, Rosa Hermosa, Miguel Ángel Hernández‐Oñate, Levente Karaffa, Idit Kosti, Stéphane Le Crom, Erika Lindquist, Susan Lucas, Mette Lübeck, Peter Stephensen Lübeck, Antoine Margeot, Benjamin Metz, Monica Misra, Helena Nevalainen, Markus Omann, Nicolle H. Packer, Giancarlo Perrone, Edith Elena Uresti-Rivera, Asaf Salamov, Monika Schmoll, Bernhard Schink, Harris Shapiro, Serenella A. Sukno, Juan Antonio Tamayo-Ramos, Doris Tisch, Aric Wiest, Heather H. Wilkinson, Michael Zhang, Pedro M. Coutinho, Charles M. Kenerley, Enrique Monte, Scott E. Baker, Igor V. Grigoriev
Software Mentions: 1
Published: over 13 years ago

10.1186/s13059-014-0466-3

Genome of the house fly, Musca domestica L., a global vector of diseases with adaptations to a septic environment
Cited by: 228
Author(s): Jeffrey G. Scott, Wesley C. Warren, Leo W. Beukeboom, Daniel Bopp, Andrew G. Clark, Sarah D. Giers, Monika Hediger, Andrew K. Jones, Shinji Kasai, Cheryl A. Leichter, Ming Li, Richard P. Meisel, Patrick Minx, Terence Murphy, David R. Nelson, William Reid, Frank D. L. Rinkevich, Hugh M. Robertson, Timothy B. Sackton, David B. Sattelle, Françoise Thibaud‐Nissen, Chad Tomlinson, Louis van de Zande, Kimberly K. O. Walden, Richard K. Wilson, Nannan Liu
Software Mentions: 1
Published: about 10 years ago

10.1186/s13059-015-0607-3

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes
Cited by: 219
Author(s): Alastair Crisp, Chiara Boschetti, Malcolm Perry, Alan Tunnacliffe, Gos Micklem
Software Mentions: 1
Published: over 9 years ago

10.1186/s13059-017-1151-0

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus
Cited by: 357
Author(s): Ronald P. de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A. Braus‐Stromeyer, Camila Caldana, David Cánovas, Gustavo C. Cerqueira, Fusheng Chen, Wanping Chen, Cindy Choi, Alicia Clum, Renato Augusto Corrêa dos Santos, André Damásio, George Diallinas, Tamás Emri, Erzsébet Fekete, Michel Flipphi, Susanne Freyberg, Antonia Gallo, Christos Gournas, Rob Habgood, Matthieu Hainaut, María Harispe, Bernard Henrissat, Kristiina Hildén, Ryan Hope, Abeer Hossain, Eugenia Karabika, Levente Karaffa, Zsolt Karányi, Nada Kraševec, Alan Kuo, Harald Kusch, Kurt LaButti, Ellen Lagendijk, Alla Lapidus, Anthony Levasseur, Erika Lindquist, Anna Lipzen, Antonio F. Logrieco, Andrew MacCabe, Miia Mäkelä, Iran Malavazi, Petter Melin, Vera Meyer, Natalia Mielnichuk, Márton Miskei, Ákos Molnár, Giuseppina Mulè, Chew Yee Ngan, Margarita Orejas, Erzsébet Orosz, Jean Ouedraogo, Karin Overkamp, Hee-Soo Park, Giancarlo Perrone, François Piumi, Peter J. Punt, Arthur F. J. Ram, Ana Ramón, Stefan Rauscher, Éric Record, Diego Mauricio Riaño-Pachón, Vincent Robert, Julian Röhrig, Roberto Ruller, Asaf Salamov, Nadhira Salih, Robert A. Samson, Erzsébet Sándor, Manuel Sanguinetti, Tabea Schütze, Kristina Sepčić, Ekaterina Shelest, Gavin Sherlock, Vicky Sophianopoulou, Fábio M. Squina, Hui Sun, Antonia Susca, Richard B. Todd, Adrian Tsang, Shiela E. Unkles, Nathalie van de Wiele, Diana van Rossen-Uffink, Juliana Velasco de Castro Oliveira, Tammi Camilla Vesth, Jaap Visser, Jae‐Hyuk Yu, Miaomiao Zhou, Mikael Rørdam Andersen, David B. Archer, Scott E. Baker, Isabelle Benoit, Axel A. Brakhage, Gerhard H. Braus, Reinhard Fischer, Jens Christian Frisvad, Gustavo H. Goldman, Jos Houbraken, Berl R Oakley, István Pócsi, Claudio Scazzocchio, Bernhard Schink, Patricia A. vanKuyk, Jennifer Wortman, Paul S. Dyer, Igor V. Grigoriev
Software Mentions: 1
Published: almost 8 years ago

10.1093/gbe/evaa047

Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes
Cited by: 31
Author(s): Julia Brueckner, William Martin
Software Mentions: 1
Published: over 4 years ago

Projects: cran: MCL

Papers Mentioning MCL 563