pypi: gff3 | Projects | Ecosyste.ms: Papers

10.1093/molbev/msaa057

Genome Architecture Facilitates Phenotypic Plasticity in the Honeybee (Apis mellifera)
Cited by: 30
Author(s): Elizabeth J. Duncan, Megan Leask, Peter K. Dearden
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0108010

LncRBase: An Enriched Resource for lncRNA Information
Cited by: 58
Author(s): Sohini Chakraborty, Aritra Deb, Ranjan Kumar Maji, Sudipto Saha, Zhumur Ghosh
Software Mentions: 6
Published: almost 10 years ago

10.1093/database/bax079

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Cited by: 9
Author(s): Leandro Costa do Nascimento, Marcela Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas S. Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-020-02028-w

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Cited by: 34
Author(s): Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue‐Agudo, Pablo Bonilla, Jeremy R.B. Newman, Shunichi Kosugi, Lauren McIntyre, Victoria Moreno‐Manzano, Ana Conesa
Software Mentions: 5
Published: over 4 years ago

10.1534/g3.116.030783

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Cited by: 47
Author(s): Benoît Castandet, Amber M. Hotto, Susan R. Strickler, David B. Stern
Software Mentions: 5
Published: about 8 years ago

10.3389/fcell.2020.580848

Adherent Intestinal Cells From Atlantic Salmon Show Phagocytic Ability and Express Macrophage-Specific Genes
Cited by: 5
Author(s): Youngjin Park, Qirui Zhang, G.F. Wiegertjes, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: almost 4 years ago

10.1534/g3.120.401622

Alternative Splicing During the Chlamydomonas reinhardtii Cell Cycle
Cited by: 10
Author(s): Manishi Pandey, Gary D. Stormo, Susan K. Dutcher
Software Mentions: 5
Published: almost 4 years ago

10.1534/g3.120.401479

Genomic Patterns of Introgression in Interspecific Populations Created by Crossing Wheat with Its Wild Relative
Cited by: 12
Author(s): Moses Nyine, Elina Adhikari, Marshall Clinesmith, Katherine Jordan, Allan K. Fritz, Eduard Akhunov
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-019-6235-7

Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network
Cited by: 5
Author(s): Claire Khosravi, Joanna E. Kowalczyk, Tania Chroumpi, Evy Battaglia, María Victoria Aguilar Pontes, Mao Peng, Ad Wiebenga, Vivian Ng, Anna Lipzen, Guifen He, Diane Bauer, Igor V. Grigoriev, Ronald P. de Vries
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-015-2115-y

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars
Cited by: 36
Author(s): Ryan Ghan, Steven C. Van Sluyter, Uri Hochberg, Asfaw Degu, Daniel Hopper, Richard L. Tillet, Karen Schlauch, Paul A. Haynes, Aaron Fait, Grant R. Cramer
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13059-016-1088-8

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface
Cited by: 214
Author(s): Duane D. McKenna, Erin D. Scully, Yannick Pauchet, Kelli Hoover, Roy Kirsch, Scott M. Geib, Robert F. Mitchell, Robert M. Waterhouse, Seung‐Joon Ahn, Deanna Arsala, Joshua B. Benoit, Heath Blackmon, Tiffany Bledsoe, Julia H. Bowsher, André Busch, Bernarda Calla, Hsu Chao, Anna K. Childers, Christopher P. Childers, Dave J. Clarke, Lorna Cohen, Jeffery P. Demuth, Huyen Dinh, Harshavardhan Doddapaneni, Amanda Dolan, Jian J. Duan, Shannon Dugan, Markus Friedrich, Karl M. Glastad, Michael A. D. Goodisman, Stéphanie Haddad, Yi Han, Daniel Hughes, Panagiotis Ioannidis, J. Spencer Johnston, Jeffery W. Jones, Leslie A. Kuhn, D. R. Lance, Chien Yueh Lee, Sandra L. Lee, Han Lin, Jeremy A. Lynch, Armin P. Moczek, Shwetha C. Murali, Donna M. Muzny, David R. Nelson, Subba Reddy Palli, Kristen A. Panfilio, Dan Pers, Monica F. Poelchau, Honghu Quan, Jiaxin Qu, Anandasankar Ray, Joseph P. Rinehart, Hugh M. Robertson, Richard L. Roehrdanz, Andrew J. Rosendale, Seunggwan Shin, Christian Silva, Alex S. Torson, Iris M. Vargas Jentzsch, John H. Werren, Kim C. Worley, George D. Yocum, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2105-10-67

Quantitative measures for the management and comparison of annotated genomes
Cited by: 132
Author(s): Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell
Software Mentions: 3
Published: over 15 years ago

10.3390/plants10020322

Genome-Wide Characterization of Lectin Receptor Kinases in Saccharum spontaneum L. and Their Responses to Stagonospora tainanensis Infection
Cited by: 10
Author(s): Zhoutao Wang, Hui Ren, Xu Fu, Guang Hong Lu, Wei Cheng, Youxiong Que, Liping Xu
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-015-2239-0

The neurotranscriptome of the Aedes aegypti mosquito
Cited by: 167
Author(s): Benjamin J. Matthews, Carolyn S. McBride, Matthew DeGennaro, Orion Despo, Leslie B. Vosshall
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.118.200308

Whole Genome Sequence of the Parasitoid Wasp Microplitis demolitor That Harbors an Endogenous Virus Mutualist
Cited by: 29
Author(s): Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand
Software Mentions: 3
Published: about 6 years ago

10.1038/s41438-020-00424-8

Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz
Cited by: 24
Author(s): Jian Zhang, Huwei Yuan, Yujuan Li, Yanhong Chen, Guoyuan Liu, Meixia Ye, Chunmei Yu, Bolin Lian, Fei Zhong, Yuna Jiang, Junfeng Xu
Software Mentions: 3
Published: almost 4 years ago

10.3390/genes12030417

Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)
Cited by: 9
Author(s): Fulei Mo, Nian Zhang, Yefeng Qiu, Lingjun Meng, Mozhen Cheng, Jiayin Liu, Lanning Yao, Rui Lv, Yuxin Liu, Yao Zhang, Xiuling Chen, Aoxue Wang
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: almost 5 years ago

10.3389/fgene.2018.00033

Genome-Wide Study of YABBY Genes in Upland Cotton and Their Expression Patterns under Different Stresses
Cited by: 54
Author(s): Zhaoen Yang, Qian Gong, Lingling Wang, Yang Jin, Jianping Xi, Liu Zhi, Wenqiang Qin, Zuoren Yang, Lili Lu, Quanjia Chen
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-14-140

D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements
Cited by: 6
Author(s): Josef Laimer, Clemens J Zuzan, Tobias Ehrenberger, Monika Freudenberger, Simone Gschwandtner, Carina Lebherz, Peter Lackner
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-017-1494-2

ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data
Cited by: 5
Author(s): Sergio González, Bernardo Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernández, Joaquín Dopazo, Norma Paniego
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-9-586

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics
Cited by: 17
Author(s): Ki Won Jung, Jongsun Park, Jaeyoung Choi, Bong Soo Park, Seungill Kim, Kyohun Ahn, Jaehyuk Choi, Doil Choi, Seogchan Kang, Yong Hwan Lee
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12864-017-4346-6

RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar ‘Riesling’
Cited by: 14
Author(s): Zachary N. Harris, László Kovács, Jason P. Londo
Software Mentions: 2
Published: almost 7 years ago

10.3389/fgene.2021.741858

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed
Cited by: 4
Author(s): Pengfei Xu, Yujie Zhu, Yanfeng Zhang, Jianxia Jiang, Liyong Yang, Jianxin Mu, Xiang Yu, Yuqing He
Software Mentions: 2
Published: about 3 years ago

10.3389/fgene.2020.00119

Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing
Cited by: 8
Author(s): Yun-Jing Ou, Qingyun Ren, Shun Fang, Jiguo Wu, Yunxia Jiang, Yi-ran Chen, Yong Zhong, Dedong Wang, Guoxia Zhang
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2020.00565

Micro-Evolution Analysis Reveals Diverged Patterns of Polyol Transporters in Seven Gramineae Crops
Cited by: 9
Author(s): Weilong Kong, Tong Sun, Chenhao Zhang, Yalin Qiang, Yangsheng Li
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2021.622724

Comparison of the Microsatellite Distribution Patterns in the Genomes of Euarchontoglires at the Taxonomic Level
Cited by: 11
Author(s): Xuhao Song, Tingbang Yang, Xinyi Zhang, Ying Yuan, Xianghui Yan, Yong Wei, Jun Zhang, Changyong Zhou
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2021.714305

Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus
Cited by: 7
Author(s): Weimeng Zhang, Dongdong Fang, Xiuzhu Cheng, Jun Cao, Xiao‐Li Tan
Software Mentions: 2
Published: about 3 years ago

10.3390/insects11100691

Comparative Transcriptome Analysis of Two Root-Feeding Grape Phylloxera (D. vitifoliae) Lineages Feeding on a Rootstock and V. vinifera
Cited by: 5
Author(s): Stefania Savoi, Markus W. Eitle, Harald Berger, Manuel Curto, Harald Meimberg, Michaela Griesser, Astrid Forneck
Software Mentions: 2
Published: almost 4 years ago

10.1007/s00122-019-03425-x

Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group)
Cited by: 13
Author(s): Moses Nyine, Brigitte Uwimana, Violet Akech, Allan Brown, Rodomiro Ortíz, Jaroslav Doležel, J. Lorenzen, Rony Swennen
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms19113542

DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing
Cited by: 38
Author(s): Ángela S. Prudencio, Olaf Werner, Pedro J. Martínez-García, F. Dicenta, Rosa M. Ros, Pedro Martínez‐Gómez
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-11-516

Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster
Cited by: 21
Author(s): Ismael A. Vergara, Nansheng Chen
Software Mentions: 1
Published: over 14 years ago

10.3390/ijms21113857

Genome-Wide Characterization of GRAS Family and Their Potential Roles in Cold Tolerance of Cucumber (Cucumis sativus L.)
Cited by: 20
Author(s): Xiaohong Lü, Wenqian Liu, Chenggang Xiang, Xiaojun Li, Qing Wang, Tao Wang, Zixi Liu, Jiali Zhang, Lihong Gao, Wenna Zhang
Software Mentions: 1
Published: over 4 years ago

10.1093/database/baab002

SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
Cited by: 2
Author(s): Roddy Jorquera, Carolina González, Philip Thomas Lanken Conradsen Clausen, Bent Petersen, David S. Holmes
Software Mentions: 1
Published: over 3 years ago

10.3390/plants10020382

Evolutionary Divergence and Biased Expression of NAC Transcription Factors in Hexaploid Bread Wheat (Triticum aestivum L.)
Cited by: 8
Author(s): Jianhui Ma, Meng Yuan, Bo Sun, Daijing Zhang, Jie Zhang, Chunxi Li, Yun Shao, Wei Liu, Lina Jiang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-017-4234-0

Large-scale analysis reveals that the genome features of simple sequence repeats are generally conserved at the family level in insects
Cited by: 31
Author(s): Simin Ding, Shuping Wang, Kang He, Mingxing Jiang, Fei Li
Software Mentions: 1
Published: almost 7 years ago

Ecosyste.ms: Papers

Projects: pypi: gff3

Papers Mentioning gff3 36