Ecosyste.ms: Papers

10.3389/fbioe.2014.00088

Discovery of Protein–lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
Cited by: 55
Author(s): Junhao Li, Shun Liu, Ling‐Ling Zheng, Jie Wu, Wenju Sun, Zelin Wang, Hui Zhou, Liang‐Hu Qu, Jianhua Yang
Software Mentions: 3
Published: almost 10 years ago

10.3389/fgene.2019.00561

Genome-Wide Identification and Homoeologous Expression Analysis of PP2C Genes in Wheat (Triticum aestivum L.)
Cited by: 44
Author(s): Xiao‐Lan Yu, Jiapeng Han, Efan Wang, Jie Xiao, Rui Hu, Guangxiao Yang, Guoqing He
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2021.671650

A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)
Cited by: 7
Author(s): Weidong Ding, Xinhui Zhang, Xiaomeng Zhao, Jing Wu, Zhen Cao, Jia Li, Yu Huang, Xinxin You, Min Wang, Qiong Shi, Xuwen Bing
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-773

Maize protein phosphatase gene family: identification and molecular characterization
Cited by: 53
Author(s): Kaifa Wei, Si Pan
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12859-019-2624-9

Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions
Cited by: 4
Author(s): Norbert Bokros, S. Popescu, George V. Popescu
Software Mentions: 3
Published: over 5 years ago

10.3389/fgene.2020.00652

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes
Cited by: 25
Author(s): Bin Zeng, Ting Chen, Junyi Luo, Mei-Ying Xie, Limin Wei, Qianyun Xi, Jiajie Sun, Yongliang Zhang
Software Mentions: 3
Published: over 4 years ago

10.1038/s42003-021-02559-3

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing
Cited by: 63
Author(s): Caroline Belser, Franc-Christophe Baurens, Benjamin Noël, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D’Hont, Jean‐Marc Aury
Software Mentions: 3
Published: about 3 years ago

10.3389/fgene.2020.598183

Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the R2R3-MYB Gene Family in Capsicum annuum L.
Cited by: 19
Author(s): Jin Wang, Yi Liu, Bi‐Yu Tang, Xiang Dai, Lingling Xie, Liping Feng, Xuexiao Zou
Software Mentions: 3
Published: almost 4 years ago

10.3389/fmicb.2017.01009

Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes
Cited by: 8
Author(s): Tam Tran, Sophie Mangenot, Ghislaine Magdelenat, Emilie Payen, Zoé Rouy, Hassiba Belahbib, Barry M. Grail, D. Barrie Johnson, Violaine Bonnefoy, Emmanuel Talla
Software Mentions: 3
Published: over 7 years ago

10.1016/j.celrep.2019.05.014

Breakage-Fusion-Bridge Events Trigger Complex Genome Rearrangements and Amplifications in Developmentally Arrested T Cell Lymphomas
Cited by: 13
Author(s): Joy J. Bianchi, Valentine Murigneux, Marie Bedora-Faure, Chloé Lescale, Ludovic Deriano
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-1293-y

Genome-wide survey and expression analysis of F-box genes in chickpea
Cited by: 59
Author(s): Shefali Gupta, Vanika Garg, Chandra Kant, Sabhyata Bhatia
Software Mentions: 3
Published: almost 10 years ago

10.18632/aging.101461

The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese
Cited by: 20
Author(s): Xin Zhao, Xiaomin Liu, Aiping Zhang, Huashuai Chen, Qing Huo, Weiyang Li, Rui Ye, Zhihua Chen, Liping Liang, Alison Liu, Juan Shen, Xin Jin, Wenwen Li, Marianne Nygaard, Xiao Liu, Yong Hou, Ting Ni, Lars Bolund, William K. Gottschalk, Wei Tao, Jun Gu, Xiao-Li Tian, Huanming Yang, Jian Wang, Xun Xu, Michael W. Lutz, Junxia Min, Yi Zeng, Chao Nie
Software Mentions: 3
Published: over 6 years ago

10.3390/cells8101253

Genome-Wide Mapping Defines a Role for C/EBPβ and c-Jun in Non-Canonical Cyclic AMP Signalling
Cited by: 5
Author(s): Jolanta Wiejak, Boy van Basten, Graham Hamilton, Stephen J. Yarwood
Software Mentions: 3
Published: about 5 years ago

10.3389/fninf.2018.00052

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit
Cited by: 49
Author(s): Kaibin Xu, Yong Liu, Yafeng Zhan, Jiaji Ren, Tianzi Jiang
Software Mentions: 3
Published: about 6 years ago

10.1186/s13104-016-2069-4

Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus
Cited by: 4
Author(s): Matteo Buti, Daniel J. Sargent, Khethani Mhelembe, Pietro Delfino, K. R. Tobutt, Riccardo Velasco
Software Mentions: 3
Published: over 8 years ago

10.1186/s12870-019-2121-3

Twelve complete chloroplast genomes of wild peanuts: great genetic resources and a better understanding of Arachis phylogeny
Cited by: 14
Author(s): Juan Wang, Yuan Li, Chunjuan Li, Yan Cheng, Xiaobo Zhao, Cuiling Yuan, Quanxi Sun, Chengren Shi, Shiguang Shan
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-019-2122-2

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties
Cited by: 29
Author(s): Heshan Du, Jingjing Yang, Bin Chen, Xiaofen Zhang, Jian Zhang, Kun Yang, Sansheng Geng, Changlong Wen
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12864-016-3336-4

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance
Cited by: 53
Author(s): William T. Molin, Alice A. Wright, Amy Lawton‐Rauh, Christopher Saski
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-018-1386-2

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time
Cited by: 23
Author(s): Gilad Gabay, Yardena Dahan, Yacov Izhaki, Adi Faigenboim, Giora Ben-Ari, Yonatan Elkind, Moshe A. Flaishman
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0185439

Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification
Cited by: 36
Author(s): Hailing Zhang, Yong Cao, Chaoqun Shang, Jikai Li, JianLi Wang, Zhenying Wu, Lichao Ma, Tianxiong Qi, Chunxiang Fu, Zetao Bai, HU Bao-zhong
Software Mentions: 3
Published: about 7 years ago

10.1186/s12866-020-01737-3

Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
Cited by: 7
Author(s): Jiaokun Li, Tianyuan Gu, Liangzhi Li, Xueling Wu, Li Shen, Runlan Yu, Yuandong Liu, Guanzhou Qiu, Weimin Zeng
Software Mentions: 3
Published: over 4 years ago

10.3390/biology9090295

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing
Cited by: 33
Author(s): Girum Fitihamlak Ejigu, Jaehee Jung
Software Mentions: 3
Published: about 4 years ago

10.3389/fnins.2017.00358

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study
Cited by: 7
Author(s): Edgar Guevara, Wyston C. Pierre, Camille Tessier, Luis Akakpo, Irène Londono, Frédéric Lesage, Gregory A. Lodygensky
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-331

Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells
Cited by: 40
Author(s): Suhn Kyong Rhie, Dennis J. Hazelett, Simon Coetzee, Chunli Yan, Houtan Noushmehr
Software Mentions: 3
Published: over 10 years ago

10.3389/fonc.2021.669270

A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer
Cited by: 11
Author(s): Peide Huang, Fengyu Li, Zongchao Mo, Chunyu Geng, Wen Fang, Chunyan Zhang, Jia Guo, Song Wu, Lin Li, Nils Brünner, Jan Stenvang
Software Mentions: 3
Published: over 3 years ago

10.1186/s12866-020-02024-x

High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis
Cited by: 15
Author(s): Yunfeng Luo, Zhongke Wang, Ya-Ling He, Guifang Li, Xinhua Lv, Zhuang Li
Software Mentions: 3
Published: about 4 years ago

10.1186/s12920-017-0245-6

Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer
Cited by: 17
Author(s): Shirley Pepke, Greg Ver Steeg
Software Mentions: 3
Published: over 7 years ago

10.3389/fonc.2018.00183

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line
Cited by: 8
Author(s): Anne Steininger, Grit Ebert, B Becker, Chalid Assaf, Markus Möbs, Christian A. Schmidt, Piotr Grabarczyk, Lars Riff Jensen, Grzegorz K. Przybylski, Matthias Port, Andreas W. Kuß, Reinhard Ullmann
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0165089

Chromosomal Instability Estimation Based on Next Generation Sequencing and Single Cell Genome Wide Copy Number Variation Analysis
Cited by: 29
Author(s): Stephanie Greene, Angel E. Dago, Laura Leitz, Yipeng Wang, Jerry Lee, Shannon L. Werner, Steven Gendreau, Premal H. Patel, Shidong Jia, Liangxuan Zhang, Eric Tucker, Michael Malchiodi, Ryon P. Graf, Ryan Dittamore, Dena Marrinucci, Mark Landers
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0189334

aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
Cited by: 3
Author(s): Victor Renault, Jörg Tost, Fabien Pichon, Shu‐Fang Wang‐Renault, Éric Letouzé, Sandrine Imbeaud, Jessica Zucman‐Rossi, Jean‐François Deleuze, Alexandre How‐Kit
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-016-2736-9

Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family
Cited by: 42
Author(s): Fengya Zheng, Haiyang Wu, Rongzhi Zhang, Shiming Li, Weiming He, Fuk‐Ling Wong, Genying Li, Shancen Zhao, Hon‐Ming Lam
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-015-1959-5

Development of ListeriaBase and comparative analysis of Listeria monocytogenes
Cited by: 8
Author(s): Mui Fern Tan, Cheuk Chuen Siow, Avirup Dutta, Naresh V.R. Mutha, Wei Yee Wee, Hamed Heydari, Shi Tan, Mia Yang Ang, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: about 9 years ago

10.1128/JVI.02083-19

Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain
Cited by: 11
Author(s): Syun suke Kadoya, Syun-ichi Urayama, Takuro Nunoura, Miho Hirai, Yoshihiro Takaki, Masaaki Kitajima, Toyoko Nakagomi, Osamu Nakagomi, Satoshi Okabe, Osamu Nishimura, Daisuke Sano
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0141613

Gene Expression Profiles in Rice Developing Ovules Provided Evidence for the Role of Sporophytic Tissue in Female Gametophyte Development
Cited by: 15
Author(s): Ya Fang Wu, Liyu Yang, Aqin Cao, Jianbo Wang
Software Mentions: 3
Published: about 9 years ago

10.1186/s12967-021-02845-y

Identification of an immune classification for cervical cancer and integrative analysis of multiomics data
Cited by: 7
Author(s): Xintong Lyu, Guang Li, Qiao Qiao
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.20739

Biomarkers identified for prostate cancer patients through genome-scale screening
Cited by: 10
Author(s): Lei‐Yun Wang, Jiajia Cui, Tao Zhu, Wei Shao, Yi Zhao, Qianqian Wang, Yupeng Zhang, Ji-Chu Wu, Le Zhang
Software Mentions: 3
Published: about 7 years ago

10.18632/oncotarget.13937

Conditionally reprogrammed normal and primary tumor prostate epithelial cells: a novel patient-derived cell model for studies of human prostate cancer
Cited by: 50
Author(s): Olga Timofeeva, Nancy Palechor-Ceron, Guanglei Li, Hang Yuan, Ewa Krawczyk, Xiaogang Zhong, Geng Li, Geeta Upadhyay, Aleksandra Dakić, Songtao Yu, Shuang Fang, Sujata Maiti Choudhury, Xueping Zhang, Andrew Ju, Myeong-Seon Lee, Dong Han, Youngmi Ji, Yong Hou, Yun‐Ling Zheng, Chris Albanese, Johng S. Rhim, Richard Schlegel, Anatoly Dritschilo, Xuefeng Li
Software Mentions: 3
Published: almost 8 years ago

10.18632/oncotarget.26225

Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival
Cited by: 10
Author(s): Hanna Engqvist, Toshima Z. Parris, Elisabeth Werner Rönnerman, Elin Söderberg, Jana Biermann, Claudia Mateoiu, Karin Sundfeldt, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 3
Published: about 6 years ago

10.1523/ENEURO.0205-16.2016

Graph Theoretic and Motif Analyses of the Hippocampal Neuron Type Potential Connectome
Cited by: 24
Author(s): Colin Rees, Diek W. Wheeler, D. R. Hamilton, Charise M. White, Alexander O. Komendantov, Giorgio A. Ascoli
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0201854

Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice
Cited by: 21
Author(s): Xiang Li, Hang Yu, Yamin Jiao, Muhammad Qasim Shahid, Jinwen Wu, Xiangdong Liu
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0010433

The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments
Cited by: 259
Author(s): Paul Janssen, Rob Van Houdt, Hugo Moors, Pieter Monsieurs, Nicolas Morin, Arlette Michaux, Mohammed Abderrafi Benotmane, Natalie Leys, Tatiana Vallaeys, Alla Lapidus, Sébastien Monchy, Claudine Médigue, Safiyh Taghavi, S. McCorkle, John J. Dunn, Daniël van der Lelie, Max Mergeay
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0010795

Identification of Novel Pathogenicity Loci in Clostridium perfringens Strains That Cause Avian Necrotic Enteritis
Cited by: 90
Author(s): Dion Lepp, Bryan Roxas, Valeria R. Parreira, Pradeep Reddy Marri, Everett L. Rosey, Joshua Gong, J. Glenn Songer, Gayatri Vedantam, John F. Prescott
Software Mentions: 3
Published: over 14 years ago

10.3390/ijms22169002

Insights into the Host Specificity of a New Oomycete Root Pathogen, Pythium brassicum P1: Whole Genome Sequencing and Comparative Analysis Reveals Contracted Regulation of Metabolism, Protein Families, and Distinct Pathogenicity Repertoire
Cited by: 2
Author(s): Mojtaba Mohammadi, Eric A. Smith, M. E. Stanghellini, Rakesh Kaundal
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-019-6416-4

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line
Cited by: 10
Author(s): Shumin Zhou, Jinpeng Zhang, Hongyu Han, Jing Zhang, Huihui Ma, Zhi Zhang, Yuqing Lu, Weihua Liu, Xinming Yang, Xiuquan Li, Lihui Li
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22147401

Analysis of Immune Associated Co-Expression Networks Reveals Immune-Related Long Non-Coding RNAs during MI in the Presence and Absence of HDC
Cited by: 2
Author(s): Zhiwei Zhang, Saidan Ding, Xiangdong Yang, Junbo Ge
Software Mentions: 3
Published: over 3 years ago

10.1186/s12951-021-01047-4

An atherosclerotic plaque-targeted single-chain antibody for MR/NIR-II imaging of atherosclerosis and anti-atherosclerosis therapy
Cited by: 15
Author(s): Liwei Zhang, Sheng Xue, Feng Ren, Si-Yang Huang, Ruizhi Zhou, Yu Wang, Chunxiao Zhou, Zhen Li
Software Mentions: 3
Published: about 3 years ago

10.1080/20002297.2020.1773067

A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing
Cited by: 14
Author(s): Roland Wirth, Gergely Maróti, Róbert Mihók, Donát Simon-Fiala, Márk Antal, Bernadett Pap, Anett Demcsák, János Minárovits, Kornél L. Kovács
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2164-14-617

Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
Cited by: 99
Author(s): Janja Zajc, Yongfeng Liu, Wenkui Dai, Zhenyu Yang, Jingzhi Hu, Cene Gostinčar, Nina Gunde‐Cimerman
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0240916

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors
Cited by: 5
Author(s): Luisa M. Arias-Giraldo, Marina Muñoz, Carolina Hernández, Giovanny Herrera, Natalia Velásquez-Ortiz, Omar Cantillo-Barraza, Plutarco Urbano, Juan David Ramírez
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms22042060

Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome
Cited by: 13
Author(s): Ghausia Begum, Ammar Albanna, Asma Bankapur, Nasna Nassir, Richa Tambi, Bakhrom K. Berdiev, Hosneara Akter, Noushad Karuvantevida, Barbara Kellam, Deena Alhashmi, Wilson W L Sung, Bhooma Thiruvahindrapuram, Alawi A. Alsheikh‐Ali, Stephen W. Scherer, Mohammed Uddin
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms21103660

Genome-Wide Dissection of the CRF Gene Family in Brassica napus Indicates that BnaCRF8s Specifically Regulate Root Architecture and Phosphate Homeostasis against Phosphate Fluctuation in Plants
Cited by: 7
Author(s): Sheliang Wang, Hao Zhang, Lei Shi, Fangsen Xu, Guangda Ding
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-017-1653-5

ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins
Cited by: 20
Author(s): Bertjan Broeksema, Magdalena Całusińska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms21020483

Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes
Cited by: 25
Author(s): Wei Liu, Yingli Cai, Qianqian Zhang, Shu Fang, Lianfu Chen, Xiaolong Ma, Yinbing Bian
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22094326

Delineating the Tnt1 Insertion Landscape of the Model Legume Medicago truncatula cv. R108 at the Hi-C Resolution Using a Chromosome-Length Genome Assembly
Cited by: 10
Author(s): Parwinder Kaur, Christopher Lui, Olga Dudchenko, Raja Sekhar Nandety, Bhavna Hurgobin, Melanie Pham, E Aiden, Jiangqi Wen, Kirankumar S. Mysore
Software Mentions: 3
Published: over 3 years ago

10.3390/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-021-89146-y

Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes
Cited by: 3
Author(s): Chris Smith
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms20184593

Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry (Fragaria vesca)
Cited by: 16
Author(s): Hong Chen, Huihui Li, Xiaoyan Lu, Longzheng Chen, Jing Liu, Hongmiao Wu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pntd.0001512

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing
Cited by: 85
Author(s): Adriano C. Coelho, Sébastien Boisvert, Avinaba Mukherjee, Philippe Leprohon, Jacques Corbeil, Marc Ouellette
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0196588

FusionHub: A unified web platform for annotation and visualization of gene fusion events in human cancer
Cited by: 42
Author(s): Priyabrata Panigrahi, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22094919

Genome-Wide Identification and Expression Profiling of the WOX Gene Family in Citrus sinensis and Functional Analysis of a CsWUS Member
Cited by: 9
Author(s): Faiza Shafique Khan, Ren‐Fang Zeng, Zhi-Meng Gan, Jin‐Zhi Zhang, Chun-Gen Hu
Software Mentions: 3
Published: over 3 years ago

10.1155/2018/5206758

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in<i>Brassica rapa</i>
Cited by: 8
Author(s): Nadeem Khan, Chunmei Hu, Waleed Amjad Khan, Emal Naseri, Koeun Han, Hansong Dong, Xilin Hou
Software Mentions: 3
Published: about 6 years ago

10.1186/s12864-017-3852-x

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida
Cited by: 97
Author(s): Anna Faddeeva-Vakhrusheva, Ken Kraaijeveld, Martijn F.L. Derks, Seyed Yahya Anvar, Valeria Agamennone, Wouter Suring, Andries A. Kampfraath, Jacintha Ellers, Giang Le Ngoc, Cornelis A.M. van Gestel, Janine Mariën, Sandra Smit, Nico M. van Straalen, Dick Roelofs
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-54720-y

Statistical characteristics of amino acid covariance as possible descriptors of viral genomic complexity
Cited by: 7
Author(s): C. K. Sruthi, Meher K. Prakash
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-53469-8

Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)
Cited by: 6
Author(s): Xinhua Wang, Haiyang Liu, Maolin Pang, Bishi Fu, Xin Yu, Shunping He, Jingou Tong
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pntd.0008935

Dual RNAseq analyses at soma and germline levels reveal evolutionary innovations in the elephantiasis-agent Brugia malayi, and adaptation of its Wolbachia endosymbionts
Cited by: 3
Author(s): Germain Chevignon, Vincent Foray, Mercedes M. Pérez‐Jiménez, Silvia Libro, Matthew Chung, Jeremy M. Foster, Frédéric Landmann
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-52139-z

8-OxoG in GC-rich Sp1 binding sites enhances gene transcription in adipose tissue of juvenile mice
Cited by: 6
Author(s): Jong Woo Park, Young In Han, Sung Woo Kim, Tae Min Kim, Su Cheong Yeom, Jaeku Kang, Joonghoon Park
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-54446-x

High throughput barcoding method for genome-scale phasing
Cited by: 13
Author(s): David Redin, Tobias Frick, Hooman Aghelpasand, Max Käller, Erik Borgström, Remi‐André Olsen, Afshin Ahmadian
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-019-39286-z

Comprehensive identification of the full-length transcripts and alternative splicing related to the secondary metabolism pathways in the tea plant (Camellia sinensis)
Cited by: 41
Author(s): Dahe Qiao, Chun Yang, Juan Chen, Yan Guo, Yán Li, Suzhen Niu, Kemei Cao, Zhengwu Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2967-9

Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection
Cited by: 44
Author(s): Stanford Kwenda, Paul R. J. Birch, Lucy N. Moleleki
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-36059-y

Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Cited by: 22
Author(s): Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey Hicks, James R. Davie, Mojgan Rastegar
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-6404-8

EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis
Cited by: 0
Author(s): Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao‐Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung‐Yen Lin
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1006508

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Cited by: 88
Author(s): Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Yingying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell, Jukka Corander
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pgen.1008646

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages
Cited by: 26
Author(s): Yufeng Fang, Marco A. Coelho, Haidong Shu, Klaas Schotanus, Bhagya C. Thimmappa, Vikas Yadav, H Chen, Ewa Malc, Jeremy Wang, Piotr A. Mieczkowski, Brent Kronmiller, Brett M. Tyler, Kaustuv Sanyal, Suomeng Dong, Minou Nowrousian, Joseph Heitman
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-019-50624-z

Diversity, Co-occurrence and Implications of Fungal Communities in Wastewater Treatment Plants
Cited by: 66
Author(s): Hailemariam Abrha Assress, Ramganesh Selvarajan, Hlengilizwe Nyoni, Khayalethu Ntushelo, Bhekie B. Mamba, Titus A.M. Msagati
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-28299-9

Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Cited by: 38
Author(s): Jun Han, Meijun Chen, Yihan Wang, Boxuan Gong, Tianwei Zhuang, Lingyu Liang, Hong Qiao
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-30583-7

The landscape of the A-to-I RNA editome from 462 human genomes
Cited by: 14
Author(s): Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-017-4169-5

CGDV: a webtool for circular visualization of genomics and transcriptomics data
Cited by: 3
Author(s): Vineet Jha, Gulzar Singh, Sanjiv Kumar, Amol D. Sonawane, Abhay Jere, Krishanpal Anamika
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-23334-1

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
Cited by: 32
Author(s): Jinfang Zhang, Lijuan Wei, Jun Jiang, Annaliese S. Mason, Haojie Li, Cheng Cui, Linna Chai, Beibei Zheng, Yongqing Zhu, Qing Xia, Long Jiang, Donghui Fu
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-31770-2

Characterisation and functional predictions of canine long non-coding RNAs
Cited by: 24
Author(s): Céline Le Béguec, Valentin Wucher, Laëtitia Lagoutte, Édouard Cadieu, Nadine Botherel, Benoît. Hédan, Clotilde De Brito, Anne-Sophie Guillory, Catherine André, Thomas Derrien, Christophe Hitte
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-20862-8

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Cited by: 79
Author(s): Nan Li, Yuezhu Wang, Chunping You, Jianke Ren, Chen Wan-yi, Huajun Zheng, Zhenmin Liu
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-017-17203-6

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication
Cited by: 15
Author(s): Xinnian Xia, Lin Lin Luan, Gengsheng Qin, Yu Li, Zhi Wei Wang, Wan Chen Dong, Youjian Song, Yongli Qiao, Xian Sheng Zhang, Long Yang
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-018-21560-1

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
Cited by: 40
Author(s): Sarika Jaiswal, Tushar J. Antala, M. K. Mandavia, Meenu Chopra, Rahul Singh Jasrotia, R. S. Tomar, Jashminkumar Kheni, U. B. Angadi, Mir Asif Iquebal, B. A. Golakia, Anil Rai, Dinesh Kumar
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pcbi.1008980

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Cited by: 1
Author(s): Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-22237-5

Gene expression models based on a reference laboratory strain are poor predictors of Mycobacterium tuberculosis complex transcriptional diversity
Cited by: 13
Author(s): Álvaro Chiner‐Oms, Fernando Gónzález-Candelas, Iñaki Comas
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-33744-w

Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube
Cited by: 42
Author(s): Zhijun Zhong, Xingang Li
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-020-69389-x

A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
Cited by: 22
Author(s): Honghao Lv, Yong Wang, Fengqing Han, Jialei Ji, Zhiyuan Fang, Mu Zhuang, Zhansheng Li, Yangyong Zhang, Limei Yang
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2164-15-249

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis
Cited by: 73
Author(s): Karlheinz Mann, Daniel J. Jackson
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-017-3499-7

Visualization of consensus genome structure without using a reference genome
Cited by: 3
Author(s): Isao Tada, Yasuhiro Tanizawa, Masanori Arita
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-09680-6

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation
Cited by: 10
Author(s): Qi You, Xin Yi, Kang Zhang, Chunchao Wang, Xuelian Ma, Xueyan Zhang, Wenying Xu, Fuguang Li, Zhen Su
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-03528-9

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations
Cited by: 8
Author(s): Yufang Guo, Wei Kuang Lin, Qiuxia Chen, Verónica Vallejo, Ryan M. Warner
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-018-2425-6

Tigmint: correcting assembly errors using linked reads from large molecules
Cited by: 86
Author(s): Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Ben Vandervalk, Sarah Yeo, Zhen‐Zhen Xue, Hamid Mohamadi, Jöerg Bohlmann, Steven J.M. Jones, İnanç Birol
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-017-15363-z

LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets
Cited by: 45
Author(s): Zhixu Ni, Georgia Angelidou, Ralf Hoffmann, Maria Fedorova
Software Mentions: 3
Published: about 7 years ago

10.1038/srep28851

Systems view of adipogenesis via novel omics-driven and tissue-specific activity scoring of network functional modules
Cited by: 17
Author(s): Isar Nassiri, Rosario Lombardo, Mario Lauria, Melissa J. Morine, Petros Moyseos, Vijayalakshmi Varma, Greg T. Nolen, Bridgett Knox, Daniel T. Sloper, Jim Kaput, Corrado Priami
Software Mentions: 3
Published: over 8 years ago

10.1038/srep32417

Authentication and characterisation of a new oesophageal adenocarcinoma cell line: MFD-1
Cited by: 20
Author(s): Edwin Garcia, Annette Hayden, Charles N. Birts, Edward Britton, Andrew Cowie, Karen Pickard, Massimiliano Mellone, C Choh, Mathieu Derouet, Patrick J. Duriez, Fergus Noble, Michael J. White, John Primrose, Jonathan C. Strefford, Matthew Rose-Zerilli, Gareth J. Thomas, Yeng Ang, Andrew D Sharrocks, Rebecca C. Fitzgerald, Tim Underwood
Software Mentions: 3
Published: about 8 years ago

10.1038/srep25107

Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns
Cited by: 27
Author(s): Weike Duan, Zhinan Huang, Xiaoming Song, Tongkun Liu, Hailong Liu, Xilin Hou, Ying Liu
Software Mentions: 3
Published: over 8 years ago

10.3390/plants10091874

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)
Cited by: 3
Author(s): Zhihua Xie, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, Shutian Tao
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pbio.2003769

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis
Cited by: 88
Author(s): Eleni Gentekaki, Bruce A. Curtis, Courtney W. Stairs, Vladimír Klimeš, Marek Eliáš, Dayana E. Salas‐Leiva, Emily K. Herman, Laura Eme, María Cecilia Arias, Bernard Henrissat, Frédérique Hilliou, Mary J. Klute, Hiroshi Suga, Shehre-Banoo Malik, Arthur W. Pightling, Martin Kolísko, Richard A. Rachubinski, Alexander Schlacht, Darren M. Soanes, Anastasios D. Tsaousis, John M. Archibald, Steven Ball, Joel B. Dacks, C. Graham Clark, Mark van der Giezen, Andrew J. Roger
Software Mentions: 3
Published: about 7 years ago

10.1038/srep02962

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
Cited by: 17
Author(s): Jianliang Li, Joseph Mazar, Cuncong Zhong, Geoffrey J. Faulkner, Subramaniam S. Govindarajan, Zhan Zhang, Marcel E. Dinger, Gavin Meredith, Christopher M. Adams, Shaojie Zhang, John S. Mattick, Animesh Ray, Ranjan J. Perera
Software Mentions: 3
Published: about 11 years ago

10.1038/srep20957

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Cited by: 9
Author(s): Sandra Steyaert, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, Carolina Frankl-Vilches, Annemie Van der Linden, Wim Van Criekinge, Wim Vanden Berghe, Tim De Meyer
Software Mentions: 3
Published: almost 9 years ago