cran: MCL | Projects | Ecosyste.ms: Papers

10.1016/j.xpro.2020.100085

Protocol for Identification and Removal of Doublets with DoubletDecon
Cited by: 7
Author(s): Erica A. K. DePasquale, Daniel Schnell, Kashish Chetal, Nathan Salomonis
Software Mentions: 25
Published: over 3 years ago

10.1186/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: almost 5 years ago

10.1128/mSystems.00903-19

manta: a Clustering Algorithm for Weighted Ecological Networks
Cited by: 7
Author(s): Lisa Röttjers, Karoline Faust
Software Mentions: 12
Published: over 4 years ago

10.1186/s13104-017-2607-8

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks
Cited by: 28
Author(s): Θεοδόσιος Θεοδοσίου, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C. Kyrpides, Pantelis G. Bagos, Ioannis Iliopoulos, Georgios A. Pavlopoulos
Software Mentions: 11
Published: almost 7 years ago

10.1371/journal.pone.0041762

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Cited by: 7
Author(s): Matthew P Davis, Cei Abreu‐Goodger, Stijn van Dongen, Dong Lu, P. Täte, Nenad Bartoniček, Claudia Kutter, Pentao Liu, William C. Skarnes, Anton J. Enright, Ian Dunham
Software Mentions: 10
Published: over 12 years ago

10.1093/gigascience/giy014

Bipartite graphs in systems biology and medicine: a survey of methods and applications
Cited by: 116
Author(s): Georgios A. Pavlopoulos, Panagiota I. Kontou, Athanasia Pavlopoulou, Costas Bouyioukos, Evripides Markou, Pantelis G. Bagos
Software Mentions: 10
Published: about 6 years ago

10.1002/advs.201901850

Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta
Cited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: over 4 years ago

10.1128/mSystems.00474-21

Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved Metatranscriptomics
Cited by: 12
Author(s): Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie K. Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Software Mentions: 9
Published: over 2 years ago

10.1186/s12915-018-0518-3

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
Cited by: 21
Author(s): Angelika Schmidt, Francesco Marabita, Narsis A. Kiani, Catharina C. Groß, Henrik J. Johansson, Szabolcs Éliás, Sini Rautio, Matilda Eriksson, Sunjay Jude Fernandes, Gilad Silberberg, Ubaid Ullah, Urvashi Bhatia, Harri Lähdesmäki, Janne Lehtiö, David Gomez-Cabrero, Heinz Wiendl, Riitta Lahesmaa, Jesper Tegnér
Software Mentions: 9
Published: about 6 years ago

10.3389/fcimb.2020.582187

Virome Sequencing of the Human Intestinal Mucosal–Luminal Interface
Cited by: 11
Author(s): Austin Yan, James Butcher, David Mack, Alain Stintzi
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0212248

Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti
Cited by: 17
Author(s): Ruvini V. Lelwala, Pasi K. Korhonen, Neil D. Young, Jason B. Scott, Peter K. Ades, Robin B. Gasser, P. W. J. Taylor
Software Mentions: 8
Published: almost 5 years ago

10.1093/gigascience/giz003

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
Cited by: 21
Author(s): Stefan Prost, Ellie E. Armstrong, Johan A. A. Nylander, Gregg W.C. Thomas, Alexander Suh, Bent Petersen, Love Dalén, Brett W. Benz, Mozes P. K. Blom, Eleftheria Palkopoulou, Per G. P. Ericson, Martin Irestedt
Software Mentions: 8
Published: over 5 years ago

10.1186/s13742-015-0077-2

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
Cited by: 83
Author(s): Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Θεοδόσιος Θεοδοσίου, Anton J. Enright, Ioannis Iliopoulos
Software Mentions: 7
Published: over 8 years ago

10.3389/fgene.2021.722981

Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
Cited by: 6
Author(s): Jing Li, Urminder Singh, Zebulun Arendsee, Eve Syrkin Wurtele
Software Mentions: 7
Published: almost 3 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Cited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: over 3 years ago

10.1128/mSystems.00264-19

A Genome-Based Species Taxonomy of the Lactobacillus Genus Complex
Cited by: 46
Author(s): Stijn Wittouck, Sander Wuyts, Conor J. Meehan, Vera van Noort, Sarah Lebeer
Software Mentions: 7
Published: over 4 years ago

10.1111/tpj.14349

The genome of cowpea (Vigna unguiculata [L.] Walp.)
Cited by: 215
Author(s): Stefano Lonardi, María Muñoz‐Amatriaín, Qihua Liang, Shengqiang Shu, Steve Wanamaker, Sassoum Lo, Jaakko Tanskanen, Alan H. Schulman, Tingting Zhu, Ming‐Cheng Luo, Hind Alhakami, Rachid Ounit, Abid Hasan, Jérôme Verdier, Philip A. Roberts, Jansen Rodrigo Pereira Santos, Arsenio Ndeve, Jaroslav Doležel, Jan Vrána, S. Hokin, Andrew Farmer, Steven B. Cannon, Timothy J. Close
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41396-020-00736-6

The saccharibacterium TM7x elicits differential responses across its host range
Cited by: 26
Author(s): Daniel R. Utter, Xuesong He, Colleen M. Cavanaugh, Jeffrey S. McLean, Batbileg Bor
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-015-2324-4

Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout
Cited by: 10
Author(s): Henrique César Pereira Figueiredo, Siomar C. Soares, Felipe Luiz Pereira, Fernanda Alves Dorella, Alex F. Carvalho, Júnia Pacheco Teixeira, Vasco Azevedo, Carlos Augusto Gomes Leal
Software Mentions: 6
Published: over 8 years ago

10.7554/eLife.30860

A high-resolution mRNA expression time course of embryonic development in zebrafish
Cited by: 218
Author(s): Richard White, John Collins, Ian Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek L. Stemple, Daniel N. Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J. Enright, Elisabeth M Busch-Nentwich
Software Mentions: 6
Published: over 6 years ago

10.1093/gbe/evz245

The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)
Cited by: 42
Author(s): Valerie L. Soza, Dale Lindsley, Adam Waalkes, Elizabeth Ramage, Rupali P Patwardhan, Joshua N. Burton, Andrew Adey, Akash Kumar, Ruolan Qiu, Jay Shendure, Benjamin D. Hall
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms22094598

Combined Transcriptomic and Proteomic Analysis of Perk Toxicity Pathways
Cited by: 6
Author(s): Rebeka Popovic, Ivana Celardo, Yao Yu, Ana Carolina Oliveira Costa, Samantha H. Y. Loh, L. Miguel Martins
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pcbi.1008769

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
Cited by: 1
Author(s): Song He, Xinyu Song, Xisheng Yang, Jianyang Yu, Yao Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo
Software Mentions: 6
Published: about 3 years ago

10.3390/pathogens10040396

Nanopore-Sequencing Characterization of the Gut Microbiota of Melolontha melolontha Larvae: Contribution to Protection against Entomopathogenic Nematodes?
Cited by: 4
Author(s): Ewa Sajnaga, Marcin Skowronek, Agnieszka Kalwasińska, Waldemar Kazimierczak, Karolina Ferenc, Magdalena Lis, Adrian Wiater
Software Mentions: 6
Published: about 3 years ago

10.1186/s12976-019-0103-7

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans
Cited by: 19
Author(s): Juan Castro, Iván Valdés, Laura González-García, Giovanna Danies, Silvia Cañas, Flávia Vischi Winck, Carlos Eduardo Ñústez, Silvia Restrepo, Diego Mauricio Riaño‐Pachón
Software Mentions: 5
Published: about 5 years ago

10.1186/s12870-018-1329-y

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
Cited by: 39
Author(s): Ji Huang, Jue-Fei Zheng, Hui Yuan, Karen M. McGinnis
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2229-8-99

Regulon organization of Arabidopsis
Cited by: 95
Author(s): Wieslawa I. Mentzen, Eve Syrkin Wurtele
Software Mentions: 5
Published: over 16 years ago

10.1038/s42003-018-0122-7

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish
Cited by: 44
Author(s): Marianna Pauletto, Tereza Manousaki, Serena Ferraresso, Massimiliano Babbucci, Alexandros Tsakogiannis, Bruno Louro, Nicola Vitulo, Viet Ha Quoc, R. Carraro, Daniela Bertotto, Rafaella Franch, Francesco Maroso, Muhammad Aslam, Anna K. Sonesson, Barbara Simionati, G Malacrida, Alessandro Cestaro, Stefano Caberlotto, Elena Sarropoulou, C. C. Mylonas, Deborah M. Power, Tomaso Patarnello, Adelino V.M. Canário, Costas S. Tsigenopoulos, Luca Bargelloni
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12920-016-0201-x

Single and multi-subject clustering of flow cytometry data for cell-type identification and anomaly detection
Cited by: 7
Author(s): Maziyar Baran Pouyan, Vasu Jindal, Javad Birjandtalab, Mehrdad Nourani
Software Mentions: 5
Published: almost 8 years ago

10.1186/1471-2105-11-403

Data reduction for spectral clustering to analyze high throughput flow cytometry data
Cited by: 142
Author(s): Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan R. Brinkman
Software Mentions: 5
Published: almost 14 years ago

10.1186/1471-2164-15-946

Conservation analysis of the CydX protein yields insights into small protein identification and evolution
Cited by: 35
Author(s): Rondine J. Allen, Evan P. Brenner, Caitlin E. VanOrsdel, Jessica J. Hobson, David J. Hearn, Matthew R. Hemm
Software Mentions: 5
Published: over 9 years ago

10.1128/mBio.01870-17

Gene Co-occurrence Networks Reflect Bacteriophage Ecology and Evolution
Cited by: 40
Author(s): Jason W. Shapiro, Catherine Putonti
Software Mentions: 5
Published: about 6 years ago

10.3389/fmicb.2020.01663

Cultivation and Genomics Prove Long-Term Colonization of Donor’s Bifidobacteria in Recurrent Clostridioides difficile Patients Treated With Fecal Microbiota Transplantation
Cited by: 7
Author(s): Hanne Jouhten, Aki Ronkainen, Juhani Aakko, Seppo Salminen, Eero Mattila, Perttu Arkkila, Reetta Satokari
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-020-79359-y

Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece
Cited by: 9
Author(s): Panos Bravakos, Manolis Mandalakis, Paraskevi Nomikou, Thekla I. Anastasiou, Jon Bent Kristoffersen, M. Stavroulaki, Stephanos P. Kilias, Georgios Kotoulas, Antoniοs Magoulas, Paraskevi N. Polymenakou
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0175330

Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis
Cited by: 8
Author(s): Xuehua Wan, Kent J. Koster, Lishi Qian, Edward Desmond, Richard Brostrom, Shaobin Hou, James T. Douglas
Software Mentions: 5
Published: about 7 years ago

10.15252/msb.20167490

Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes
Cited by: 163
Author(s): Kevin Drew, Chanjae Lee, Ryan L. Huizar, Fan Tu, Blake Borgeson, Claire D. McWhite, Yun Ma, John B. Wallingford, Edward M. Marcotte
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1006017

Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes
Cited by: 42
Author(s): Kévin Lebrigand, Le He, Nishant Thakur, Marie-Jeanne Arguel, Jolanta Polanowska, Bernard Henrissat, Éric Record, Ghislaine Magdelenat, Valérie Barbe, Sylvain Raffaele, Pascal Barbry, Jonathan J. Ewbank
Software Mentions: 5
Published: about 8 years ago

10.1186/1471-2164-8-191

C-terminal motif prediction in eukaryotic proteomes using comparative genomics and statistical over-representation across protein families
Cited by: 15
Author(s): Ryan E Austin, Nicholas J. Provart, Sean R. Cutler
Software Mentions: 5
Published: almost 17 years ago

10.7717/peerj.11950

Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies
Cited by: 2
Author(s): Jason W. Shapiro, Catherine Putonti
Software Mentions: 5
Published: almost 3 years ago

10.1371/journal.pcbi.1007564

Regulatory context drives conservation of glycine riboswitch aptamers
Cited by: 6
Author(s): Matt Crum, Nikhil Ram-Mohan, Michelle M. Meyer
Software Mentions: 5
Published: over 4 years ago

10.1111/1751-7915.12757

Relative abundance of ‘ Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community
Cited by: 25
Author(s): Anthony P. Malanoski, Baochuan Lin, Brian J. Eddie, Zheng Wang, W. Judson Hervey, Sarah M. Glaven
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-018-1536-8

Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data
Cited by: 111
Author(s): Basel Abu‐Jamous, Steven Kelly
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-014-0560-6

Gateways to the FANTOM5 promoter level mammalian expression atlas
Cited by: 634
Author(s): Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J. Mungall, Peter Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D. Diehl, Emmanuel Dimont, Tom C. Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F. Meehan, Koro Nishikata, Ono Hiromasa, Michael Rehli, Albin Sandelin, Erik Schultes, Peter A.C. ’t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W. Wright, Carsten O. Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-019-2861-y

miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules
Cited by: 31
Author(s): Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li, Thuc Duy Le
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.ppat.1008717

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys
Cited by: 17
Author(s): Eerik Aunin, Ulrike Böhme, Theo Sanderson, Noah D. Simons, Tony L. Goldberg, Nelson Ting, Colin A. Chapman, Chris Newbold, Matthew Berriman, Adam J. Reid
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2019.00725

Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics
Cited by: 4
Author(s): Caio Rafael do Nascimento Santiago, Renata de Almeida Barbosa Assis, Leandro Márcio Moreira, Luciano Antônio Digiampietri
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-019-2800-y

Integrating data and knowledge to identify functional modules of genes: a multilayer approach
Cited by: 10
Author(s): Lifan Liang, Vicky Chen, Kunju Zhu, Xiao-Nan Fan, Xinghua Lu, Songjian Lu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-016-1191-6

Protein complex prediction for large protein protein interaction networks with the Core&Peel method
Cited by: 35
Author(s): Marco Pellegrini, Miriam Baglioni, Filippo Geraci
Software Mentions: 4
Published: over 7 years ago

10.3389/fcimb.2017.00031

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life
Cited by: 10
Author(s): Tjerko Kamminga, Jasper J. Koehorst, Paul Vermeij, Simen-Jan Slagman, Vítor A. P. Martins dos Santos, Jetta J. E. Bijlsma, Peter J. Schaap
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-15-1047

De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets
Cited by: 13
Author(s): Meng Niu, Ehsan Tabari, Zhengchang Su
Software Mentions: 4
Published: over 9 years ago

10.1186/s13578-017-0138-6

Comparative analysis of pre- and post-parasitic transcriptomes and mining pioneer effectors of Heterodera avenae
Cited by: 20
Author(s): Dan Yang, Changlong Chen, Qian Liu, Heng Jian
Software Mentions: 4
Published: over 7 years ago

10.1093/database/bav096

Ensembl comparative genomics resources
Cited by: 315
Author(s): Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo I. Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, M Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha, Andy Yates, Paul Flicek
Software Mentions: 4
Published: over 8 years ago

10.1074/mcp.RA120.002275

On the Robustness of Graph-Based Clustering to Random Network Alterations
Cited by: 7
Author(s): R. Greg Stacey, Michael A. Skinnider, Leonard J. Foster
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-015-1825-5

Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates
Cited by: 124
Author(s): Nan Zhang, Dongqing Yang, Dandan Wang, Youzhi Miao, Jiahui Shao, Xuan Zhou, Zhihui Xu, Qing Li, Haichao Feng, Shuqing Liu, Qirong Shen, Ruifu Zhang
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-016-3286-x

Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
Cited by: 91
Author(s): Ann C. Gregory, Sergei A. Solonenko, J. Cesar Ignacio‐Espinoza, Kurt LaButti, Alex Copeland, Sebastian Sudek, Ashley Maitland, Lauren Chittick, Filipa Santos, Joshua S. Weitz, Alexandra Z. Worden, Tanja Woyke, Matthew B. Sullivan
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-017-1820-8

An effective approach to detecting both small and large complexes from protein-protein interaction networks
Cited by: 18
Author(s): Bin Xu, Yan Wang, Zewei Wang, Jiaogen Zhou, Shuigeng Zhou, Jihong Guan
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0068551

A Systems-Genetics Approach and Data Mining Tool to Assist in the Discovery of Genes Underlying Complex Traits in Oryza sativa
Cited by: 17
Author(s): Stephen P. Ficklin, F. Alex Feltus
Software Mentions: 4
Published: almost 11 years ago

10.1186/1471-2164-15-549

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species
Cited by: 239
Author(s): Cene Gostinčar, Robin A. Ohm, Tina Kogej, Silva Sonjak, Monika Turk, Janja Zajc, Polona Zalar, Martín Grube, Hui Sun, James Han, Aarti Sharma, Jennifer Chiniquy, Chew Yee Ngan, Anna Lipzen, Kerrie Barry, Igor V. Grigoriev, Nina Gunde‐Cimerman
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0236348

Unraveling the molecular pathobiology of vocal fold systemic dehydration using an in vivo rabbit model
Cited by: 8
Author(s): Naíla Cannes do Nascimento, Andrea Pires dos Santos, M. Preeti Sivasankar, Abigail Cox
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2105-12-S1-S25

GARNET – gene set analysis with exploration of annotation relations
Cited by: 10
Author(s): Kyoohyoung Rho, Bumjin Kim, Yeongjun Jang, Sang‐Hyun Lee, Taejeong Bae, Jihae Seo, Chae Hwa Seo, Ji‐Hyun Lee, Hyun‐Jung Kang, Ungsik Yu, Sung Hoon Kim, Sanghyuk Lee, Wankyu Kim
Software Mentions: 4
Published: over 13 years ago

10.1186/s12859-018-2555-x

Protein complexes identification based on go attributed network embedding
Cited by: 21
Author(s): Bo Xu, Kun Li, Wei Zheng, Xiaoxia Liu, Yijia Zhang, Zhehuan Zhao, Zengyou He
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-5629-x

The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata
Cited by: 82
Author(s): Daniele Armaleo, Olaf Müller, François Lutzoni, Ólafur S. Andrésson, Guillaume Blanc, Helge B. Bode, F. Collart, Francesco Dal Grande, Fred S. Dietrich, Igor V. Grigoriev, Suzanne Joneson, Alan Kuo, Peter E. Larsen, John M. Logsdon, David López, Francis Martin, Susan May, Tami McDonald, Sabeeha Merchant, Vivian Miao, Emmanuelle Morin, Ryoko Oono, Matteo Pellegrini, Nimrod D. Rubinstein, M. Virginia Sanchez‐Puerta, Elizabeth Savelkoul, Imke Schmitt, Jason C. Slot, Darren M. Soanes, Péter Szövényi, Nicholas J. Talbot, Claire Veneault‐Fourrey, Basil Britto Xavier
Software Mentions: 4
Published: almost 5 years ago

10.1101/2021.06.22.449395

Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks
Cited by: 3
Author(s): Meghana Venkata Palukuri, Edward M. Marcotte
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12859-018-2309-9

Predicting overlapping protein complexes based on core-attachment and a local modularity structure
Cited by: 23
Author(s): Rongquan Wang, Caixia Wang, Lingtao Su, Liankun Sun
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-25998-1

FACS-Seq analysis of Pax3-derived cells identifies non-myogenic lineages in the embryonic forelimb
Cited by: 8
Author(s): Arun Singh, Cheng-Chi Chang, Hsiao-Yen Ma, Stephen A. Ramsey, Theresa M. Filtz, Chrissa Kioussi
Software Mentions: 4
Published: about 6 years ago

10.1038/sdata.2018.154

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments
Cited by: 73
Author(s): Paul M. Berube, Steven J. Biller, Thomas Hackl, Brandon M. Satinsky, Jamie W. Becker, Rogier Braakman, Sara B. Collins, Libusha Kelly, Jessie W Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W. Chisholm
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0009719

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex
Cited by: 6
Author(s): Luisa Berná, Gonzalo Greif, Sebastián Pita, Paula Faral-Tello, Florencia Díaz-Viraqué, Rita de Cássia Moreira de Souza, Gustavo Adolfo Vallejo, Fernando Álvarez-Valín, Carlos Robello
Software Mentions: 4
Published: over 2 years ago

10.1038/srep30115

Genomic content typifying a prevalent clade of bovine mastitis-associated Escherichia coli
Cited by: 39
Author(s): Robert Goldstone, Susan R. Harris, David George Emslie Smith
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pbio.2005359

Comparative genomics and the nature of placozoan species
Cited by: 63
Author(s): Michael Eitel, Warren R. Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A. Williams, Bernd Schierwater, Gert Wörheide
Software Mentions: 4
Published: almost 6 years ago

10.1155/2019/3726721

Identifying Protein Complexes from Dynamic Temporal Interval Protein-Protein Interaction Networks
Cited by: 1
Author(s): Jinxiong Zhang, Cheng Zhong, Hai Lin, Mian Wang
Software Mentions: 4
Published: over 4 years ago

10.1099/mgen.0.000108

A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli
Cited by: 18
Author(s): Robert Goldstone, David George Emslie Smith
Software Mentions: 4
Published: about 7 years ago

10.1093/gbe/evz100

PopNetD3—A Network-Based Web Resource for Exploring Population Structure
Cited by: 1
Author(s): Javi Zhang, John Parkinson
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2009-10-3-r33

Reconstructing the ubiquitin network - cross-talk with other systems and identification of novel functions
Cited by: 30
Author(s): Thiago M. Venancio, S. Balaji, Lakshminarayan M. Iyer, L. Aravind
Software Mentions: 4
Published: over 15 years ago

10.3390/genes10090714

NCBI’s Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements
Cited by: 13
Author(s): Ryan Connor, Rodney Brister, Jan P. Buchmann, Ward Deboutte, Robert A. Edwards, Joan Martí-Carreras, Michael J. Tisza, Vadim Zalunin, Juan S. Andrade-Martínez, Adrian Cantu, Michael D’Amour, Alexandre Efremov, Lydia Fleischmann, Laura Milena Forero‐Junco, Sanzhima Garmaeva, Melissa Giluso, Cody Glickman, Margaret Henderson, Benjamin P. Kellman, David M. Kristensen, Carl Leubsdorf, Kyle Levi, Shane Levi, Suman B. Pakala, Vikas Peddu, Alise J. Ponsero, Eldred A. Ribeiro, Farrah Roy, Lindsay Rutter, Surya Saha, Migun Shakya, Ryan C. Shean, Matthew Miller, Benjamin J. Tully, Christopher J R Turkington, Ken Youens‐Clark, Bert Vanmechelen, Ben Busby
Software Mentions: 4
Published: over 4 years ago

10.1186/1756-0381-6-17

Using random walks to identify cancer-associated modules in expression data
Cited by: 32
Author(s): Deanna Petrochilos, Ali Shojaie, John H. Gennari, Neil F. Abernethy
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-015-0721-2

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
Cited by: 2,420
Author(s): David Emms, Steven Kelly
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12862-019-1364-9

Evolution of salivary glue genes in Drosophila species
Cited by: 15
Author(s): Jean-Luc Da Lage, Gregg W.C. Thomas, Magalie Bonneau, Virginie Courtier‐Orgogozo
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0159923

BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes
Cited by: 8
Author(s): Amir Lakizadeh, Saeed Jalili
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12870-017-1077-4

Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response
Cited by: 23
Author(s): Shisong Ma, Zehong Ding, Pinghua Li
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2021.679409

Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export
Cited by: 5
Author(s): Elif Koeksoy, Oliver Bezuidt, Timm Bayer, Clara S. Chan, David Emerson
Software Mentions: 4
Published: almost 3 years ago

10.1186/s13059-016-1145-3

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
Cited by: 539
Author(s): Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Bâa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamás Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara López-Gomollón, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel D. Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock van Oosterhout, David Swarbreck, Saskia A. Hogenhout
Software Mentions: 4
Published: over 7 years ago

10.1093/gigascience/giaa036

Chromosome-level reference genome of the jellyfish Rhopilema esculentum
Cited by: 16
Author(s): Yunfeng Li, Lei Gao, Yongjia Pan, Meilin Tian, Yulong Li, Chongbo He, Ying Dong, Yamin Sun, Zunchun Zhou
Software Mentions: 4
Published: about 4 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: almost 5 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: over 2 years ago

10.1007/s00438-014-0959-5

RNase E in the γ-Proteobacteria: conservation of intrinsically disordered noncatalytic region and molecular evolution of microdomains
Cited by: 41
Author(s): Soraya Aït‐Bara, Agamemnon J. Carpousis, Yves Quentin
Software Mentions: 3
Published: over 9 years ago

10.1186/s40168-016-0221-y

Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age
Cited by: 39
Author(s): Gabriele Andrea Lugli, Christian Milani, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Sabrina Duranti, Douwe van Sinderen, Marco Ventura
Software Mentions: 3
Published: over 7 years ago

10.3390/molecules22071223

Neighbor Affinity-Based Core-Attachment Method to Detect Protein Complexes in Dynamic PPI Networks
Cited by: 7
Author(s): Xiujuan Lei, Jing Liang
Software Mentions: 3
Published: almost 7 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: over 6 years ago

10.1371/journal.pone.0119627

Phylogenomic Analyses of Echinodermata Support the Sister Groups of Asterozoa and Echinozoa
Cited by: 81
Author(s): Adrian Reich, Casey W. Dunn, Koji Akasaka, Gary M. Wessel
Software Mentions: 3
Published: about 9 years ago

10.1074/mcp.RA117.000445

Infection by the Helminth Parasite Fasciola hepatica Requires Rapid Regulation of Metabolic, Virulence, and Invasive Factors to Adjust to Its Mammalian Host
Cited by: 70
Author(s): Krystyna Cwiklinski, Heather Jewhurst, Paul McVeigh, Tara Barbour, Aaron G. Maule, José F. Tort, Sandra M. O’Neill, Mark W. Robinson, Sheila Donnelly, John P. Dalton
Software Mentions: 3
Published: about 6 years ago

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: over 10 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 2 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: over 17 years ago

10.1186/1471-2164-10-419

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation
Cited by: 32
Author(s): Sergei A. Manakov, Seth G. N. Grant, Anton J. Enright
Software Mentions: 3
Published: over 14 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: over 10 years ago

10.1371/journal.pone.0154882

An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants
Cited by: 18
Author(s): Li Zhang, Shibo Wang, Qi-Gang Li, Jian Song, Yuqi Hao, Ling Zhou, Huanquan Zheng, J. M. Dunwell, Yuanming Zhang
Software Mentions: 3
Published: about 8 years ago

10.12688/f1000research.9416.3

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
Cited by: 4
Author(s): Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vítor A. P. Martins dos Santos, María Suárez-Diez
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0099193

Discovering Functional Modules across Diverse Maize Transcriptomes Using COB, the Co-Expression Browser
Cited by: 26
Author(s): Robert J. Schaefer, Roman Briskine, Nathan M. Springer, Chad L. Myers
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2148-11-154

BEL/Pao retrotransposons in metazoan genomes
Cited by: 44
Author(s): Nicole de la Chaux, Andreas Wagner
Software Mentions: 3
Published: almost 13 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: over 3 years ago

Projects: cran: MCL

Papers Mentioning MCL 563