pypi: mcl | Projects | Ecosyste.ms: Papers

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: over 8 years ago

10.1099/mgen.0.000174

The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements
Cited by: 19
Author(s): Matthew S. Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J. Sadowsky
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pcbi.1006373

Designing and running an advanced Bioinformatics and genome analyses course in Tunisia
Cited by: 6
Author(s): Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.devcel.2018.12.026

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis
Cited by: 32
Author(s): Toni Beltran, Consuelo Barroso, T. Y. Birkle, Lewis Stevens, Hillel T. Schwartz, Paul W. Sternberg, Hélène Fradin, Kristin C. Gunsalus, Fabio Piano, Garima Sharma, Chiara Cerrato, Julie Ahringer, Enrique Martínez-Pérez, Mark Blaxter, Peter Sarkies
Software Mentions: 5
Published: over 5 years ago

10.1186/s12862-017-1064-2

Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
Cited by: 45
Author(s): Fabrizio Menardo, Coraline R. Praz, Thomas Wicker, Beat Keller
Software Mentions: 5
Published: about 7 years ago

10.1093/gigascience/giz071

The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)
Cited by: 35
Author(s): Liang Qiang, Huayang Li, Shouke Li, Fuling Yuan, Jiantong Sun, Qicheng Duan, Qingyun Li, Rui Zhang, Ya Lin Sang, Nian Wang, Xiangwen Hou, Ke Yang, Jian Ning Liu, Long Yang
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2018.00297

Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks
Cited by: 10
Author(s): Tatiana V. Karpinets, Vancheswaran Gopalakrishnan, Jennifer A. Wargo, Andrew Futreal, Christopher W. Schadt, Jianhua Zhang
Software Mentions: 4
Published: over 6 years ago

10.1128/mBio.02391-19

Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi
Cited by: 25
Author(s): William C. Beckerson, Ricardo C. Rodrı́guez de la Vega, Fanny E. Hartmann, Marine Duhamel, Tatiana Giraud, Michael H. Perlin
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj.5902

Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions
Cited by: 21
Author(s): Carlos E. Santibáñez‐López, Ricardo Kriebel, Jesús A. Ballesteros, Nathaniel Rush, Zachary L. Witter, J. R. Williams, Daniel Janies, Prashant P. Sharma
Software Mentions: 4
Published: about 6 years ago

10.3390/toxins11110637

Hadrurid Scorpion Toxins: Evolutionary Conservation and Selective Pressures
Cited by: 8
Author(s): Carlos E. Santibáñez‐López, Matthew R. Graham, Prashant P. Sharma, Ernesto Ortíz, L.D. Possani
Software Mentions: 4
Published: about 5 years ago

10.1186/s13756-018-0356-7

Dynamics of colistin and tobramycin resistance among Enterobacter cloacae during prolonged use of selective decontamination of the digestive tract
Cited by: 5
Author(s): Mirjam J. D. Dautzenberg, Jumamurat R. Bayjanov, Maurine A. Leverstein–van Hall, Anouk E. Muller, L. B. S. Gelinck, C. L. Jansen, Eliane M. S. Leyten, Thomas Ruys, Jelle Scharringa, R. E. van der Starre, Ad C. Fluit, Marc J. M. Bonten
Software Mentions: 3
Published: over 6 years ago

10.1186/s12917-017-1093-5

Whole genome sequencing of an ExPEC that caused fatal pneumonia at a pig farm in Changchun, China
Cited by: 9
Author(s): Lingcong Kong, Xulin Guo, Zi Wang, Yunhang Gao, Boyin Jia, Shuming Liu, Huiqin Ma
Software Mentions: 3
Published: over 7 years ago

10.1186/s13068-021-01958-2

Zymomonas diversity and potential for biofuel production
Cited by: 8
Author(s): Magdalena M. Felczak, Robert M. Bowers, Tanja Woyke, Michaela A. TerAvest
Software Mentions: 3
Published: over 3 years ago

10.1186/s13068-019-1569-6

Genome expansion by allopolyploidization in the fungal strain Coniochaeta 2T2.1 and its exceptional lignocellulolytic machinery
Cited by: 11
Author(s): Stephen J. Mondo, Diego Javier Jiménez, Ronald E. Hector, Anna Lipzen, Mi Yan, Kurt LaButti, Kerrie Barry, Jan Dirk van Elsas, Igor V. Grigoriev, Nancy N. Nichols
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2019.00345

Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family
Cited by: 23
Author(s): Jacob S. Stai, Akhilesh Yadav, Carole Sinou, Anne Bruneau, Jeff J. Doyle, David Fernández-Baca, Steven B. Cannon
Software Mentions: 3
Published: over 5 years ago

10.3390/genes10090649

Origin and Evolution of Deleterious Mutations in Horses
Cited by: 29
Author(s): Ludovic Orlando, Pablo Librado
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-11543-z

Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans
Cited by: 13
Author(s): Misty M. Attwood, Arunkumar Krishnan, Markus Sällman Almén, Helgi B. Schiöth
Software Mentions: 3
Published: about 7 years ago

10.1128/mSphereDirect.00011-19

Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions
Cited by: 27
Author(s): Ruben Props, Pieter Monsieurs, Peter Vandamme, Natalie Leys, Vincent J. Denef, Nico Boon
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1005366

Genome composition and phylogeny of microbes predict their co-occurrence in the environment
Cited by: 42
Author(s): Olga K. Kamneva
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2014.00370

A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution
Cited by: 69
Author(s): Eva Heinz, Trevor Lithgow
Software Mentions: 2
Published: over 10 years ago

10.1186/s12859-019-2670-3

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
Cited by: 17
Author(s): Yongzhi Yang, Ying Liu, Chunming Qiao, Yongshuai Sun, Zhiqiang Lu
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.120.401405

Two New <i>Aspergillus flavus</i> Reference Genomes Reveal a Large Insertion Potentially Contributing to Isolate Stress Tolerance and Aflatoxin Production
Cited by: 13
Author(s): Jake C. Fountain, Josh Clevenger, Brian Nadon, Ramey C Youngblood, Walid Korani, Perng‐Kuang Chang, Dakota Starr, Hui Wang, R. Benjamin Isett, H. Richard Johnston, Raegan Wiggins, Gaurav Agarwal, Ye Chu, Robert C. Kemerait, Manish K. Pandey, Deepak Bhatnagar, Peggy Ozias‐Akins, Rajeev K. Varshney, Brian E. Scheffler, Justin N. Vaughn, Bao‐Zhu Guo
Software Mentions: 2
Published: about 4 years ago

10.1093/gbe/evv097

Evolution of the Translocation and Assembly Module (TAM)
Cited by: 58
Author(s): Eva Heinz, Joel Selkrig, Matthew J. Belousoff, Trevor Lithgow
Software Mentions: 2
Published: over 9 years ago

10.1093/gbe/evv194

The Genome and Methylome of a Beetle with Complex Social Behavior,<i>Nicrophorus vespilloides</i>(Coleoptera: Silphidae)
Cited by: 79
Author(s): Christopher B. Cunningham, Lexiang Ji, R. Axel W. Wiberg, Jennifer Shelton, Elizabeth C. McKinney, Darren J. Parker, Richard B. Meagher, Kyle M. Benowitz, Eileen M. Roy-Zokan, Michael G. Ritchie, Susan J. Brown, Robert J. Schmitz, Allen J. Moore
Software Mentions: 2
Published: about 9 years ago

10.1186/s43008-019-0011-9

Genome sequencing and comparison of five Tilletia species to identify candidate genes for the detection of regulated species infecting wheat
Cited by: 20
Author(s): Hai D. T. Nguyen, Tahera Sultana, Prasad Kesanakurti, Sarah Hambleton
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1002290

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica
Cited by: 338
Author(s): Alga Zuccaro, Urs Lahrmann, Ulrich Güldener, Gregor Langen, Stefanie Pfiffi, Dagmar Biedenkopf, Philip Wong, Birgit Samans, Carolin Grimm, Magdalena Basiewicz, Claude Murat, Francis Martin, Karl‐Heinz Kogel
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.ppat.1006670

Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles
Cited by: 55
Author(s): Eva-Maria Niehaus, Hee-Kyoung Kim, Martin Münsterkötter, Slavica Janevska, Birgit Arndt, Svetlana A. Kalinina, Petra M. Houterman, Il-Pyung Ahn, I. Alberti, Stefano Tonti, Da-Woon Kim, Christian M. K. Sieber, Hans‐Ulrich Humpf, Sung-Hwan Yun, Ulrich Güldener, Bettina Tudzynski
Software Mentions: 2
Published: about 7 years ago

10.1038/s41396-019-0362-7

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems
Cited by: 25
Author(s): Vera Bischoff, Boyke Bunk, Jan P. Meier‐Kolthoff, Cathrin Spröer, Anja Poehlein, Marco Dogs, Mary Nguyen, Jörn Petersen, Rolf Daniel, Jörg Overmann, Markus Göker, Meinhard Simon, Thorsten Brinkhoff, Cristina Moraru
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0013409

Genome-Wide Comparative Gene Family Classification
Cited by: 27
Author(s): Christian Frech, Nansheng Chen
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0009474

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions
Cited by: 90
Author(s): Benjamin Schuster-Böckler, Donald F. Conrad, Alex Bateman
Software Mentions: 1
Published: over 14 years ago

10.7554/eLife.45199

Natural selection and repeated patterns of molecular evolution following allopatric divergence
Cited by: 14
Author(s): Yibo Dong, Shichao Chen, Shifeng Cheng, Wenbin Zhou, Qing Ma, Zhiduan Chen, Chengxin Fu, Xin Liu, Yunpeng Zhao, Pamela S. Soltis, Gane Ka‐Shu Wong, Douglas E. Soltis, Qiu-Yun Jenny Xiang
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2018.03058

Genomic and Genetic Insights Into a Cosmopolitan Fungus, Paecilomyces variotii (Eurotiales)
Cited by: 33
Author(s): Andrew S. Urquhart, Stephen J. Mondo, Miia Mäkelä, James K. Hane, Ad Wiebenga, Guifen He, Sirma Mihaltcheva, Jasmyn Pangilinan, Anna Lipzen, Kerrie Barry, Ronald P. de Vries, Igor V. Grigoriev, Alexander Idnurm
Software Mentions: 1
Published: almost 6 years ago

10.1186/1472-6785-14-16

Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution
Cited by: 20
Author(s): Eric Alsop, Eric S. Boyd, Jason Raymond
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pcbi.1004120

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
Cited by: 285
Author(s): Susan Dina Ghiassian, Jörg Menche, Albert Laszló Barabási
Software Mentions: 1
Published: over 9 years ago

10.1186/s12862-017-1053-5

Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria
Cited by: 20
Author(s): Robin Koch, Anne Kupczok, Karina Stucken, Judith Ilhan, Katrin Hammerschmidt, Tal Dagan
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0140398

De Novo Assembly and Genome Analyses of the Marine-Derived Scopulariopsis brevicaulis Strain LF580 Unravels Life-Style Traits and Anticancerous Scopularide Biosynthetic Gene Cluster
Cited by: 29
Author(s): Abhishek Kumar, Bernard Henrissat, Mikko Arvas, Muhammad Fahad Syed, Nils Thieme, J. Philipp Benz, Jens Laurids Sørensen, Éric Record, Stefanie Pöggeler, Frank Kempken
Software Mentions: 1
Published: about 9 years ago

Ecosyste.ms: Papers

Projects: pypi: mcl

Papers Mentioning mcl 37