Ecosyste.ms: Papers

10.1038/srep32013

Evolutionary and Expression Analysis Provides Evidence for the Plant Glutamate-like Receptors Family is Involved in Woody Growth-related Function
Cited by: 13
Author(s): Jianqing Chen, Yinghui Jing, Xinyue Zhang, Leiting Li, Peng Wang, Shaoling Zhang, Hongsheng Zhou, Juyou Wu
Software Mentions: 2
Published: over 8 years ago

10.1038/srep28594

The rubber tree genome shows expansion of gene family associated with rubber biosynthesis
Cited by: 91
Author(s): Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu‐Chien, Minami Matsui
Software Mentions: 2
Published: over 8 years ago

10.1038/srep32598

Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta)
Cited by: 2
Author(s): Xu Zhang, Zhilin Qu, Bing Su
Software Mentions: 2
Published: about 8 years ago

10.1038/srep40579

Endozoicomonas genomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts
Cited by: 160
Author(s): Matthew J. Neave, Craig Michell, Amy Apprill, Christian R. Voolstra
Software Mentions: 2
Published: almost 8 years ago

10.1038/srep41124

Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)
Cited by: 49
Author(s): Kazuki Mori, Kenta Shirasawa, Hitoshi Nogata, Chiharu Hirata, Kosuke Tashiro, Toshiyuki Habu, Sangwan Kim, Shuichi Himeno, Satoru Kuhara, Hiroyasu Ikegami
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-03445-x

Genome-wide analysis of gene expression and protein secretion of Babesia canis during virulent infection identifies potential pathogenicity factors
Cited by: 26
Author(s): Ramon M. Eichenberger, Chandra Ramakrishnan, Giancarlo Russo, Peter Deplazes, Adrian B. Hehl
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-03923-2

Nitric oxide mediated transcriptional modulation enhances plant adaptive responses to arsenic stress
Cited by: 82
Author(s): Pradyumna Kumar Singh, Yuvraj Indoliya, Abhisekh Singh Chauhan, Surendra Singh, Amit Singh, Sanjay Dwivedi, Rudra Deo Tripathi, Debasis Chakrabarty
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-05312-1

Molecular ecological network analysis reveals the effects of probiotics and florfenicol on intestinal microbiota homeostasis: An example of sea cucumber
Cited by: 44
Author(s): Gang Yang, Mo Peng, Xiangli Tian, Shuanglin Dong
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-07039-5

Transcriptomic signature of the follicular somatic compartment surrounding an oocyte with high developmental competence
Cited by: 22
Author(s): Satoshi Sugimura, Norio Kobayashi, Hiroaki Okae, T. Yamanouchi, Hideo Matsuda, Tatsuhiro Kojima, Akira Yajima, Y. Hashiyada, Masahiro Kaneda, Kei Sato, Kyoichi Imai, Kentaro Tanemura, Takahiro Arima, Robert B. Gilchrist
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-08256-8

Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification
Cited by: 22
Author(s): Jianjian Lv, Bingbo Gao, Ping Liu, Jian Li, Xianliang Meng
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-017-11466-9

Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis
Cited by: 19
Author(s): Lior David, Xavier Grau‐Bové, Amy Guillaumet-Adkins, Marta Gut, Michael E. Sieracki, Iñaki Ruiz‐Trillo
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-13513-x

Involvement of Ubiquitin-Conjugating Enzyme (E2 Gene Family) in Ripening Process and Response to Cold and Heat Stress of Vitis vinifera
Cited by: 16
Author(s): Yingying Gao, Yi Wang, H. P. Xin, Shaohua Li, Zhenchang Liang
Software Mentions: 2
Published: about 7 years ago

10.1186/s40793-017-0274-y

First draft genome sequence of a strain belonging to the Zoogloea genus and its gene expression in situ
Cited by: 7
Author(s): Emilie Muller, Shaman Narayanasamy, Myriam Zeimes, Cédric Christian Laczny, Laura Lebrun, Malte Herold, Nathan D. Hicks, John D. Gillece, James M. Schupp, Paul Keim, Paul Wilmes
Software Mentions: 2
Published: about 7 years ago

10.1007/s00122-019-03311-6

A reference high-density genetic map of greater yam (Dioscorea alata L.)
Cited by: 51
Author(s): Fabien Cormier, Floriane Lawac, Erick Malédon, Marie-Claire Gravillon, Elie Nudol, Pierre Mournet, Hélène Vignes, Gemma Arnau
Software Mentions: 2
Published: almost 6 years ago

10.1007/s00122-019-03503-0

Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype
Cited by: 14
Author(s): Shantel A. Martinez, Oluwayesi Shorinola, Samantha Conselman, Deven R. See, Daniel Z. Skinner, Cristóbal Uauy, Camille M. Steber
Software Mentions: 2
Published: almost 5 years ago

10.7150/thno.51243

Utilization of circulating cell-free DNA profiling to guide first-line chemotherapy in advanced lung squamous cell carcinoma
Cited by: 5
Author(s): Tao Jiang, Liyan Jiang, Xiaorong Dong, Kai Gu, Yueyin Pan, Qianling Shi, Guojun Zhang, Huijuan Wang, Xiaochun Zhang, Nong Yang, Yuping Li, Jianping Xiong, Tienan Yi, Min Peng, Yong Song, Yun Fan, Jiuwei Cui, Gongyan Chen, Wei Tan, Aimin Zang, Qisen Guo, Genming Zhao, Ziping Wang, Jianxing He, Wenxiu Yao, Xiaohong Wu, Kai Chen, Xiaohua Hu, Chunhong Hu, Lu Yue, Da Jiang, Guangfa Wang, Junfeng Liu, Guohua Yang, Junling Li, Henghui Zhang, Lihong Wu, Fang Lü, Dandan Liang, Yang Zhao, Weihong Zhao, Wenmin Xie, Shengxiang Ren, Caicun Zhou
Software Mentions: 2
Published: almost 4 years ago

10.1111/1759-7714.13542

Genomic characteristics and drug screening among organoids derived from <scp>non‐small cell</scp> lung cancer patients
Cited by: 31
Author(s): Jinghua Chen, Xiang‐Peng Chu, Jiatao Zhang, Qiang Nie, Wen‐Fang Tang, Jian Su, Hong‐Hong Yan, Huakun Zheng, Ze-Xin Chen, Xin Chen, Mengmeng Song, Xin Yi, Pan-Song Li, Yanfang Guan, Gang Li, Chu‐Xia Deng, Rafael Rosell, Yi‐Long Wu
Software Mentions: 2
Published: over 4 years ago

10.1038/tp.2015.214

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns
Cited by: 129
Author(s): José Vicente Sánchez-Mut, Holger Heyn, Enrique Vidal, Sebastian Morán, Sergi Sayols, Raúl Delgado-Morales, Matthew D. Schultz, Belén Ansoleaga, Paula Garcia‐Esparcia, Meritxell Pons-Espinal, María Martínez de Lagrán, Joaquín Dopazo, Alberto Rábano, Jesús Ávila, Mara Dierssen, Ira T. Lott, Isidre Ferrer, Joseph R. Ecker, Manel Esteller
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41398-020-00879-2

Mapping PTSD symptoms to brain networks: a machine learning study
Cited by: 23
Author(s): Amin Zandvakili, Jennifer Barredo, Hannah Swearingen, Emily Aiken, Yosef A. Berlow, Benjamin D. Greenberg, Linda L. Carpenter, Noah S. Philip
Software Mentions: 2
Published: over 4 years ago

10.1128/mBio.01630-17

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes
Cited by: 87
Author(s): Margaret I. Steele, Waldan K. Kwong, Marvin Whiteley, Nancy A. Moran
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.00097-18

Phosphotyrosine-Mediated Regulation of Enterohemorrhagic <i>Escherichia coli</i> Virulence
Cited by: 6
Author(s): Colin D. Robertson, Tracy H. Hazen, James B. Kaper, David A. Rasko, Anders Højgaard Hansen
Software Mentions: 2
Published: over 6 years ago

10.1128/mBio.02899-18

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes
Cited by: 30
Author(s): Ankita Kothari, Yu Wei Wu, John-Marc Chandonia, Marimikel Charrier, Lara Rajeev, Andrea M. Rocha, Dominique C. Joyner, Terry C. Hazen, Steven W. Singer, Aindrila Mukhopadhyay
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.00764-19

Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to <i>Cryptococcus</i> Pathogens
Cited by: 32
Author(s): Andrew Ryan Passer, Marco A. Coelho, R. Blake Billmyre, Minou Nowrousian, Moritz Mittelbach, Andrey Yurkov, Anna Floyd Averette, Christina A. Cuomo, Sheng Sun, Joseph Heitman
Software Mentions: 2
Published: over 5 years ago

10.1128/mBio.00254-21

Accessory Genome Dynamics and Structural Variation of <i>Shigella</i> from Persistent Infections
Cited by: 7
Author(s): Rebecca J. Bengtsson, Timothy J. Dallman, Hester Allen, P Malaka De Silva, George E. Stenhouse, Caisey V Pulford, Rebecca J. Bennett, Claire Jenkins, Kate S. Baker
Software Mentions: 2
Published: over 3 years ago

10.1128/mSystems.00102-17

Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2 ^T Using Transcriptomics
Cited by: 9
Author(s): Tom Berben, Cherel Balkema, Dimitry Y. Sorokin, Gerard Muyzer
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSystems.00867-20

Insights into the Metabolism and Evolution of the Genus <i>Acidiphilium</i> , a Typical Acidophile in Acid Mine Drainage
Cited by: 24
Author(s): Liangzhi Li, Zhenghua Liu, Min Zhang, Delong Meng, Xueduan Liu, Pei Wang, Xiu-Tong Li, Zhen Jiang, Shuiping Zhong, Cheng‐Ying Jiang, Huaqun Yin
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12960-020-0463-4

Gender imbalance in executive management positions at the Mexican National Institutes of Health
Cited by: 9
Author(s): Lucero Soledad Rivera-Romano, Cristóbal Fresno, Enrique Hernández‐Lemus, Mireya Martínez-García, Maité Vallejo
Software Mentions: 2
Published: over 4 years ago

10.1038/ismej.2016.192

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system
Cited by: 157
Author(s): Laura A. Sauder, Mads Albertsen, Katja Engel, Jasmin Schwarz, Per Halkjær Nielsen, Michael Wagner, Josh D. Neufeld
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41396-020-00827-4

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification
Cited by: 95
Author(s): Dimitra Sakoula, Hanna Koch, J. Howard Frank, Mike S. M. Jetten, Maartje A. H. J. van Kessel, Sebastian Lücker
Software Mentions: 2
Published: about 4 years ago

10.3390/jof7050384

Differential Expression of Amanitin Biosynthetic Genes and Novel Cyclic Peptides in Amanita molliuscula
Cited by: 3
Author(s): Yunjiao Lüli, Shengwen Zhou, Xuan Li, Zuohong Chen, Zhu‐Liang Yang, Hong Luo
Software Mentions: 2
Published: over 3 years ago

10.1155/2013/678969

Conservation, Divergence, and Genome-Wide Distribution of<i>PAL</i>and<i>POX A</i>Gene Families in Plants
Cited by: 29
Author(s): Hukam C. Rawal, Nisha Singh, Tilak Raj Sharma
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13045-017-0465-4

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets
Cited by: 36
Author(s): Katherine E. Hill, Andrew D. Kelly, Marieke L. Kuijjer, William T. Barry, Ahmed Rattani, Cassandra Garbutt, Haydn Kissick, Katherine A. Janeway, Antonio R. Perez–Atayde, Jeffrey D. Goldsmith, Mark C. Gebhardt, Mohamed S. Arredouani, Greg Cote, Francis J. Hornicek, Edwin Choy, Zhenfeng Duan, John Quackenbush, Benjamin Haibe‐Kains, Dimitrios Spentzos
Software Mentions: 2
Published: over 7 years ago

10.3390/ijerph16142474

Implications of Soil Pollution with Diesel Oil and BP Petroleum with ACTIVE Technology for Soil Health
Cited by: 33
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.40655

Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis
Cited by: 64
Author(s): Leonardo Furci, Ritushree Jain, Joost H. M. Stassen, Oliver Berkowitz, James Whelan, David Roquis, Victoire Baillet, Vincent Colot, Frank Johannes, Jurriaan Ton
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.62474

Integron activity accelerates the evolution of antibiotic resistance
Cited by: 39
Author(s): Célia Souque, José Antonio Escudero, R. Craig MacLean
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.09214

Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma
Cited by: 112
Author(s): Ana Rita Grosso, Ana Paula Leite, Sílvia Carvalho, Maria Margarida Nunes Gaspar de Matos, Filipa Martins, Alexandra C Vítor, Joana Desterro, Maria Carmo‐Fonseca, Sérgio Fernandes de Almeida
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.53886

Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital
Cited by: 68
Author(s): Daniel R. Evans, M. Patrick Griffith, Alexander Sundermann, Kathleen A. Shutt, Melissa Saul, Mustapha M. Mustapha, Jane W. Marsh, Vaughn S. Cooper, Lee H. Harrison, Daria Van Tyne
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.26036

Dynamics of genomic innovation in the unicellular ancestry of animals
Cited by: 113
Author(s): Xavier Grau‐Bové, Guifré Torruella, Stuart P. Donachie, Hiroshi Suga, Guy Leonard, Thomas A. Richards, Iñaki Ruiz‐Trillo
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms160922258

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae
Cited by: 24
Author(s): Monika Szczecińska, Jakub Sawicki
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms161125951

Construction of the High-Density Genetic Linkage Map and Chromosome Map of Large Yellow Croaker (Larimichthys crocea)
Cited by: 26
Author(s): Jingqun Ao, Jia Li, Xinxin You, Yinnan Mu, Yang Ding, Kaiqiong Mao, Chao Bian, Pengfei Mu, Qiong Shi, Xinhua Chen
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms18081734

Genome-Wide Organization and Expression Profiling of the SBP-Box Gene Family in Chinese Jujube (Ziziphus jujuba Mill.)
Cited by: 25
Author(s): Shuang Song, Heng Zhou, Songbai Sheng, Mengshu Cao, Yingyue Li, Xiaoming Pang
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms19020550

Expression of Pluripotency Genes in Chondrocyte-Like Cells Differentiated from Human Induced Pluripotent Stem Cells
Cited by: 5
Author(s): Ewelina Stelcer, Katarzyna Kulcenty, Marcin Ruciński, Karol Jopek, Tomasz Trzeciak, Magdalena Richter, Joanna Wróblewska, Wiktoria Maria Suchorska
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.103650

hsa_circRNA6448-14 promotes carcinogenesis in esophageal squamous cell carcinoma
Cited by: 5
Author(s): Yaowen Zhang, Xiang Yuan, Ning J. Yue, Lidong Wang, Junqi Liu, Ning Dai, Haijun Yang, Ruitai Fan, Fuyou Zhou
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2021.707496

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress
Cited by: 5
Author(s): Jirui Gong, Tianlong Shi, Yuke Li, Han-Cheng Wang, Fēi Li
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-017-4218-0

Analyses of methylomes of upland and lowland switchgrass (Panicum virgatum) ecotypes using MeDIP-seq and BS-seq
Cited by: 7
Author(s): Mollee Dworkin, Shaojun Xie, Malay C. Saha, Jyothi Thimmapuram, Venu Kalavacharla
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2018.01127

QTL Alignment for Seed Yield and Yield Related Traits in Brassica napus
Cited by: 39
Author(s): Nadia Raboanatahiry, Hongbo Chao, Dalin Hou, Shi Pu, Wei Yan, Liang Yu, Baoshan Wang, Maoteng Li
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0170181

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue
Cited by: 12
Author(s): Alejandro Quiroz-Zárate, Benjamin J. Harshfield, Rong Hu, Nicholas W. Knoblauch, Andrew H. Beck, Susan E. Hankinson, Vincent J. Carey, Rulla M. Tamimi, David J. Hunter, John Quackenbush, Aditi Hazra
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2148-10-346

Origin and evolution of a placental-specific microRNA family in the human genome
Cited by: 53
Author(s): Zhixiang Yuan, Xiao Sun, Dong-Ke Jiang, Yan Ding, Zhiyuan Lǚ, Li Gong, Hongde Liu, Jingjing Xie
Software Mentions: 2
Published: about 14 years ago

10.1186/s12864-015-1988-0

Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes
Cited by: 40
Author(s): Mingyong Tang, Zhiwen Chen, Corrinne E. Grover, Yumei Wang, Shuangshuang Li, Guozheng Liu, Zhiying Ma, Jonathan F. Wendel, Jinping Hua
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0090391

Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression
Cited by: 14
Author(s): Avinash M. Veerappa, Megha Murthy N, Sangeetha Vishweswaraiah, Kusuma Lingaiah, Raviraj V. Suresh, Somanna Ajjamada Nachappa, Nelchi Prashali, Sangeetha Nuggehalli Yadav, Manjula Arsikere Srikanta, Dinesh S. Manjegowda, Keshava B. Seshachalam, Nallur B. Ramachandra
Software Mentions: 2
Published: over 10 years ago

10.1186/gb-2010-11-10-r104

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Cited by: 141
Author(s): Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stéphane Terry, David Z. Chen, Joel Rozowsky, Ashutosh Tewari, Naoki Kitabayashi, Benjamin Moss, Mark S. Chee, Francesca Demichelis, Mark A. Rubin, Mark Gerstein
Software Mentions: 2
Published: about 14 years ago

10.1080/21505594.2019.1637699

Comparative genomics identifies potential virulence factors in <i>Clostridium tertium</i> and <i>C. paraputrificum</i>
Cited by: 14
Author(s): Marina Muñoz, Daniel Restrepo-Montoya, Nitin Kumar, Gregorio Iraola, Giovanny Herrera, Dora I. Ríos-Chaparro, Diana Díaz-Arévalo, Manuel A. Patarroyo, Trevor D. Lawley, Juan David Ramírez
Software Mentions: 2
Published: almost 6 years ago

10.1186/gb-2011-12-10-r103

Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer
Cited by: 176
Author(s): Wigard P. Kloosterman, Marlous Hoogstraat, Oscar Paling, Masoumeh Tavakoli-Yaraki, Ivo Renkens, Joost S.P. Vermaat, Markus J. van Roosmalen, Stef van Lieshout, Isaäc J Nijman, Wijnand M. Roessingh, Ruben van ‘t Slot, José van de Belt, Victor Guryev, Marco J. Koudijs, Emile E. Voest, Edwin Cuppen
Software Mentions: 2
Published: almost 14 years ago

10.3390/ijms21010351

Systematic Analysis of the Maize OSCA Genes Revealing ZmOSCA Family Members Involved in Osmotic Stress and ZmOSCA2.4 Confers Enhanced Drought Tolerance in Transgenic Arabidopsis
Cited by: 24
Author(s): Liru Cao, Pengyu Zhang, LU Xin-shi, Guorui Wang, Zhenhua Wang, Qianjin Zhang, Xin Zhang, Xin Wei, Fujian Mei, Wei Li, Tongchao Wang
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-019-5981-x

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits
Cited by: 14
Author(s): Jitao Li, Jianjian Lv, Ping Liu, Ping Chen, Jiajia Wang, Jian Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s13068-016-0440-2

Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition
Cited by: 205
Author(s): Cheng Wang, Dan Dong, Haoshu Wang, Karin Müller, Yong Qin, Hailong Wang, Weixiang Wu
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-019-6389-3

Comprehensive genomic analysis of the DUF4228 gene family in land plants and expression profiling of ATDUF4228 under abiotic stresses
Cited by: 13
Author(s): Qi Yang, Xiaocui Niu, Xiao-Li Tian, Xiujuan Zhang, Jingyu Cong, Ruigang Wang, Guosheng Zhang, G. Li
Software Mentions: 2
Published: almost 5 years ago

10.1186/gb-2013-14-11-r129

Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture
Cited by: 77
Author(s): Stefan Grob, Marc W. Schmid, Nathan W. Luedtke, Thomas Wicker, Ueli Grossniklaus
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pcbi.1002320

Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease
Cited by: 55
Author(s): Christian Frech, Nansheng Chen
Software Mentions: 2
Published: almost 13 years ago

10.1186/gb-2014-15-2-r40

Genome-wide discovery and characterization of maize long non-coding RNAs
Cited by: 385
Author(s): Liang-In Lin, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng‐Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Evans Mulenga, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C.P. Timmermans, Nathan M. Springer, Gary J. Muehlbauer
Software Mentions: 2
Published: almost 11 years ago

10.1186/gb-2013-14-6-r64

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat
Cited by: 45
Author(s): Romain Philippe, Etienne Paux, Isabelle Bertin, Pierre Sourdille, Frédéric Choulet, Christel Laugier, Hana Šimková, Jan Šafář, Arnaud Bellec, Sonia Vautrin, Zeev Frenkel, Federica Cattonaro, Federica Magni, Simone Scalabrin, Mihaela M. Martis, Klaus Mayer, Abraham B. Korol, Hélène Bergès, Jaroslav Doležel, Catherine Feuillet
Software Mentions: 2
Published: over 11 years ago

10.1186/s13059-014-0415-1

Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops
Cited by: 81
Author(s): Ke Cao, Zhijun Zheng, Lirong Wang, Xin Liu, Guoqiang Zhu, Weichao Fang, Shifeng Cheng, Peng Zeng, Chang Wen Chen, Xinwei Wang, Min Xie, Xiao Bo Zhong, Xiaoli Wang, Pei Zhao, Chao Bian, Yuxia Zhu, Jiahui Zhang, MA Guo-sheng, Chengxuan Chen, Yanjun Li, Fengge Hao, Yong Li, Guodong Huang, Yuxiang Li, Haiyan Li, Jian Guo, Xun Xu, Jun Wang
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-014-0408-0

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation
Cited by: 159
Author(s): Shaoke Lou, Heung‐Man Lee, Hao Qin, Jing‐Woei Li, Zhibo Gao, Xin Liu, Landon L. Chan, Vincent K. Lam, Wing‐Yee So, Ying Wang, Si Lok, Jun Wang, Ronald Cw, Stephen Kwok‐Wing Tsui, Juliana C.N. Chan, Ting-Fung Chan, Kevin Y. Yip
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-015-0648-7

Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas
Cited by: 37
Author(s): Anthony Mathelier, Calvin Lefebvre, Allen W. Zhang, David J. Arenillas, Jiarui Ding, Wyeth W. Wasserman, Sohrab P. Shah
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1007244

Ten simple rules to create biological network figures for communication
Cited by: 21
Author(s): G. Elisabeta Marai, Bruno Pinaud, Katja Bühler, Alexander Lex, John H. Morris
Software Mentions: 2
Published: about 5 years ago

10.1186/s13059-015-0849-0

Circlator: automated circularization of genome assemblies using long sequencing reads
Cited by: 715
Author(s): Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13059-016-0948-6

Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations
Cited by: 55
Author(s): Alice M. Walsh, John W. Whitaker, Chaohua Huang, Yauheniya Cherkas, S. Lamberth, Carrie Brodmerkel, Mark Curran, Radu Dobrin
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.568457

The Effect of Xylooligosaccharide, Xylan, and Whole Wheat Bran on the Human Gut Bacteria
Cited by: 8
Author(s): Miao Chen, Shujun Liu, Khandaker Md Sharif Uddin Imam, Lichao Sun, Yulu Wang, Tianyi Gu, Bin Wen, Fengjiao Xin
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-016-1080-3

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes
Cited by: 35
Author(s): Anthony J. Studer, James C. Schnable, S. Weissmann, Allison R. Kolbe, Michael R. McKain, Ying Shao, Asaph B. Cousins, Elizabeth A. Kellogg, Thomas P. Brutnell
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-021-07967-7

A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers
Cited by: 16
Author(s): Zhou Hong, Xuezhu Liao, Yuanjun Ye, Ningnan Zhang, Zhen Yang, Weidong Zhu, Wei Gao, Joel Sharbrough, Luke R. Tembrock, Daping Xu, Zhiqiang Wu
Software Mentions: 2
Published: about 3 years ago

10.1186/s12864-015-1554-9

Identification and distribution of the NBS-LRR gene family in the Cassava genome
Cited by: 125
Author(s): Roberto Lozano, Martha T. Hamblin, Simon Prochnik, Jean‐Luc Jannink
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1002464

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm
Cited by: 47
Author(s): Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei Wang, Cátálin Bárbácioru, Sowmi Utiramerur, Penn Whitley, Joel Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John Bodeau, Robert C. Nutter, Jian Gu, Kelli Bramlett, Jeffrey K. Ichikawa, Fiona Hyland, Asim Siddiqui
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0074132

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh, Ihh and Dhh) in Vertebrates
Cited by: 25
Author(s): Joana Pereira, Warren E. Johnson, Stephen J. O’Brien, Erich D. Jarvis, Guojie Zhang, M. Thomas P. Gilbert, Vı́tor Vasconcelos, Agostinho Antunes
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pcbi.1003833

Ten Simple Rules for Better Figures
Cited by: 85
Author(s): Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne
Software Mentions: 2
Published: about 10 years ago

10.1186/s13059-019-1724-1

Genomics and data science: an application within an umbrella
Cited by: 42
Author(s): Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson, Mark Gerstein
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-324

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae
Cited by: 56
Author(s): Dan Xiong, Yonglin Wang, Jie Ma, Steven J. Klosterman, Shuxiao Xiao, Chengming Tian
Software Mentions: 2
Published: over 10 years ago

10.1186/s12864-017-4249-6

Whole genome sequencing of the monomorphic pathogen Mycobacterium bovis reveals local differentiation of cattle clinical isolates
Cited by: 19
Author(s): Moira Lasserre, Pablo Fresia, Gonzalo Greif, Gregorio Iraola, Miguel Castro-Ramos, Arturo Juambeltz, Álvaro Nuñez, Hugo Naya, Carlos Robello, Luisa Berná
Software Mentions: 2
Published: almost 7 years ago

10.1155/2020/9381506

Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer
Cited by: 11
Author(s): Ruoyu Li, Ziqin Pang, Yongmei Zhou, Nyumah Fallah, Chaohua Hu, Wenxiong Lin, Zhaonian Yuan
Software Mentions: 2
Published: about 4 years ago

10.1186/s12864-018-5336-z

Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants
Cited by: 48
Author(s): Abdullah Shalmani, Xiu-Qing Jing, Yi Shi, Izhar Muhammad, Meng-Ru Zhou, Xiaoli Wei, Qiongqiong Chen, Wenqiang Li, Wenting Liu, Kun-Ming Chen
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2019.00504

Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems
Cited by: 25
Author(s): Hanna Koch, Heike M. Freese, Richard L. Hahnke, Meinhard Simon, Matthias Wietz
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2018.00079

Environmental Metagenomic Assemblies Reveal Seven New Highly Divergent Chlamydial Lineages and Hallmarks of a Conserved Intracellular Lifestyle
Cited by: 32
Author(s): Trestan Pillonel, Claire Bertelli, Gilbert Greub
Software Mentions: 2
Published: almost 7 years ago

10.1155/2019/5604843

Microarray Analysis For Expression Profiles of lncRNAs and circRNAs in Rat Liver after Brain-Dead Donor Liver Transplantation
Cited by: 12
Author(s): Sanyang Chen, Hongbo Fang, Jie Li, Jihua Shi, Jiakai Zhang, Peihao Wen, Zhihui Wang, Yang Han, Shengli Cao, Huapeng Zhang, Hongwei Tang, Wenzhi Guo, Shuijun Zhang
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-15-914

The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV
Cited by: 34
Author(s): Seyed Yahya Anvar, J. Howard Frank, Arjan Pol, Arnoud Schmitz, Ken Kraaijeveld, Johan T. den Dunnen, Huub J. M. Op den Camp
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12870-018-1526-8

Genome-wide characterization and phylogenetic analysis of GSK gene family in three species of cotton: evidence for a role of some GSKs in fiber development and responses to stress
Cited by: 31
Author(s): Lingling Wang, Zhaoen Yang, Bin Zhang, Daoqian Yu, Ji Liu, Qian Gong, Ghulam Qanmber, Yi Li, Lili Lu, Yongjun Lin, Zuoren Yang, Fuguang Li
Software Mentions: 2
Published: almost 6 years ago

10.1093/gbe/evu003

Recombination Shapes Genome Architecture in an Organism from the Archaeal Domain
Cited by: 12
Author(s): David J. Krause, Xavier Didelot, Hinsby Cadillo‐Quiroz, Rachel J. Whitaker
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-4487-2

Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history
Cited by: 30
Author(s): Agnieszka Klonowska, Rémy Melkonian, Lucie Miché, Pierre Tisseyre, Lionel Moulin
Software Mentions: 2
Published: almost 7 years ago

10.1155/2016/7823429

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
Cited by: 19
Author(s): Yiqing Xu, Changwei Bi, Guoxin Wu, Suyun Wei, Xiaogang Dai, Tongming Yin, Ning Ye
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms21072580

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)
Cited by: 4
Author(s): Katarzyna B. Czyż, Michał Książkiewicz, Grzegorz Koczyk, Anna Szczepaniak, Jan Podkowiński, B. Naganowska
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-13-477

In depth comparison of an individual’s DNA and its lymphoblastoid cell line using whole genome sequencing
Cited by: 35
Author(s): Dorothee Nickles, Lohith Madireddy, Shan Yang, Pouya Khankhanian, Steve Lincoln, Stephen L. Hauser, Jorge R. Oksenberg, Sergio E. Baranzini
Software Mentions: 2
Published: about 12 years ago

10.3390/ijms21083015

Genome-Scale Analysis of Homologous Genes among Subgenomes of Bread Wheat (Triticum aestivum L.)
Cited by: 10
Author(s): Cai'e Zhou, Zhaonian Dong, Ting Zhang, Jianhui Wu, Shizhou Yu, Qingdong Zeng, Dejun Han, Wei Tong
Software Mentions: 2
Published: over 4 years ago

10.1155/2014/396727

Gender-Specific DNA Methylome Analysis of a Han Chinese Longevity Population
Cited by: 9
Author(s): Liang Sun, Jie Lin, Hongwu Du, Chengping Hu, Zezhi Huang, Zhen Lv, Chenguang Zheng, Xiaoyi Shi, Yan Zhang, Ze Yang
Software Mentions: 2
Published: almost 11 years ago

10.1093/gbe/evx041

Cross-Species Genome-Wide Identification of Evolutionary Conserved MicroProteins
Cited by: 22
Author(s): Daniel Straub, Stephan Wenkel
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.01291

Disentangling the Drivers of Diversity and Distribution of Fungal Community Composition in Wastewater Treatment Plants Across Spatial Scales
Cited by: 33
Author(s): Haihan Zhang, Ji Feng, Shengnan Chen, Baoqin Li, Raju Sekar, Zhenfang Zhao, Jingyu Jia, Yue Wang, Peng-Liang Kang
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evy036

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa
Cited by: 33
Author(s): Germain Chevignon, Bret M. Boyd, Jayce W. Brandt, Kerry M. Oliver, Michael R. Strand
Software Mentions: 2
Published: almost 7 years ago

10.1186/s12859-018-2219-x

mySyntenyPortal: an application package to construct websites for synteny block analysis
Cited by: 6
Author(s): Jongin Lee, Daehwan Lee, Mikang Sim, Daehong Kwon, Ju‐Yeon Kim, Yun Woong Ko, Jaebum Kim
Software Mentions: 2
Published: over 6 years ago

10.1051/parasite/2020034

Genome-wide microsatellite characteristics of five human <i>Plasmodium species</i>, focusing on <i>Plasmodium malariae</i> and <i>P. ovale curtisi</i>
Cited by: 5
Author(s): Vivek Bhakta Mathema, Supatchara Nakeesathit, Nicholas J. White, Arjen M. Dondorp, Mallika Imwong
Software Mentions: 2
Published: almost 5 years ago

10.1093/gbe/evz072

Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship
Cited by: 20
Author(s): Trestan Pillonel, Claire Bertelli, Sébastien Aeby, Marie de Barsy, Nicolas Jacquier, Carole Kebbi-Beghdadi, Linda Mueller, Manon Vouga, Gilbert Greub
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0195974

Genome-wide analysis of basic helix-loop-helix superfamily members in peach
Cited by: 34
Author(s): Chunhua Zhang, Ruchao Feng, Ruijuan Ma, Zhijun Shen, Zeyu Cai, Zhizhong Song, Bin Peng, Mingliang Yu
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2021.662966

Effects of Gallic Acid on Fermentation Parameters, Protein Fraction, and Bacterial Community of Whole Plant Soybean Silage
Cited by: 19
Author(s): Cheng Wang, Mingyang Zheng, Shuo Wu, Xuan Zhou, Xiaoyang Chen, Liangfa Ge, Qing Zhang
Software Mentions: 2
Published: over 3 years ago

10.1523/ENEURO.0101-20.2020

Resolving the Connectome, Spectrally-Specific Functional Connectivity Networks and Their Distinct Contributions to Behavior
Cited by: 7
Author(s): Robert Becker, Alexis Hervais-Adelman
Software Mentions: 2
Published: over 4 years ago