Ecosyste.ms: Papers

10.1128/mBio.00636-18

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis
Cited by: 14
Author(s): Yan Wang, Matt Stata, Wei Wang, Jason E. Stajich, Merlin M. White, Jean‐Marc Moncalvo
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2019.00378

Evolution of Complex Thallus Alga: Genome Sequencing of Saccharina japonica
Cited by: 16
Author(s): Tao Liu, Xumin Wang, Guoliang Wang, Shangang Jia, Guiming Liu, Guangle Shan, Changliang Shan, Jing Zhang, Yahui Yu, Ting Xue, Jun Yu
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.718266

High-Quality de novo Chromosome-Level Genome Assembly of a Single Bombyx mori With BmNPV Resistance by a Combination of PacBio Long-Read Sequencing, Illumina Short-Read Sequencing, and Hi-C Sequencing
Cited by: 5
Author(s): Min Tang, Suqun He, Xun Gong, Ping Lu, Rehab Taha, Keping Chen
Software Mentions: 1
Published: about 3 years ago

10.1007/s00580-012-1423-8

An ethnoveterinary study of medicinal plants in treatment of diseases and syndromes of herd dog in southern regions of Ilam province, Iran
Cited by: 43
Author(s): Mahmoud Bahmani, Zohre Eftekhari
Software Mentions: 1
Published: almost 13 years ago

10.1093/gigascience/giz101

A chromosome-level draft genome of the grain aphid Sitobion miscanthi
Cited by: 37
Author(s): Xin Jiang, Qian Zhang, Yuchuan Qin, Hong Yin, Siyu Zhang, Qian Li, Yong Zhang, Jia Fan
Software Mentions: 1
Published: over 5 years ago

10.1186/s12966-020-00949-0

Cultural adaptation of ‘Healthy Dads, Healthy Kids’ for Hispanic families: applying the ecological validity model
Cited by: 14
Author(s): Teresia M. O’Connor, Oriana Pérez, Alicia Beltran, Isabel Colón García, Elva M. Arredondo, Ruben Parra Cardona, Natasha Cabrera, Debbe Thompson, Tom Baranowski, Philip J. Morgan
Software Mentions: 1
Published: over 4 years ago

10.1155/2016/9471696

Noninvasive Free Flap Monitoring Using Eulerian Video Magnification
Cited by: 9
Author(s): Yuan Fang Liu, Christopher Vuong, Paul C. Walker, Nathaniel R. Peterson, Jared C. Inman, Pedro A. Andrade Filho, Steve Choon-Sung Lee
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12915-021-01031-2

Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification
Cited by: 31
Author(s): Na Guo, Shenyun Wang, Lei Gao, Yongming Liu, Xin Wang, Enhui Lai, Mengmeng Duan, Guixiang Wang, Jingjing Li, Meng Yang, Ming Zong, Shuo Han, Yanzheng Pei, Theo Borm, Honghe Sun, Liming Miao, Di Liu, Fangwei Yu, Wei Zhang, Heliang Ji, Chaohui Zhu, Yong Xu, Guusje Bonnema, Jianbin Li, Zhangjun Fei, Fan Liu
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pntd.0000716

New Assembly, Reannotation and Analysis of the Entamoeba histolytica Genome Reveal New Genomic Features and Protein Content Information
Cited by: 94
Author(s): Hernán Lorenzi, Daniela Puiu, Jason R. Miller, Lauren Brinkac, Paolo Amedeo, Neil Hall, Elisabet Caler
Software Mentions: 1
Published: over 14 years ago

10.1093/gigascience/giaa013

Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family
Cited by: 28
Author(s): Xuezhi Ding, Wen‐Li Mei, Qiang Lin, Hao Wang, Jun Wang, Shi-Qing Peng, Hui‐Liang Li, Jiahong Zhu, Wei Li, Pei Wang, Huiqin Chen, Wei Dong, Dong Guo, Cai-Hong Cai, Sheng‐Zhuo Huang, Peng Cui, Hao‐Fu Dai
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pntd.0003348

Genome Update of the Dimorphic Human Pathogenic Fungi Causing Paracoccidioidomycosis
Cited by: 35
Author(s): José F. Muñoz, Juan Esteban Gallo, Elizabeth Misas, Margaret Priest, Alma Imamović, Sarah Young, Qiandong Zeng, Oliver Clay, Juan G. McEwen, Christina A. Cuomo
Software Mentions: 1
Published: almost 10 years ago

10.1093/gigascience/giaa130

Chromosome-level draft genome of a diploid plum (<i>Prunus salicina</i>)
Cited by: 37
Author(s): Chaoyang Liu, Chao Feng, Weizhuo Peng, Jingjing Hao, Juntao Wang, Jianjun Pan, Yehua He
Software Mentions: 1
Published: almost 4 years ago

10.1038/srep41457

De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species
Cited by: 72
Author(s): Wirulda Pootakham, Chutima Sonthirod, Chaiwat Naktang, Panthita Ruang-areerate, Thippawan Yoocha, Duangjai Sangsrakru, Kanikar Theerawattanasuk, Ratchanee Rattanawong, Napawan Lekawipat, Sithichoke Tangphatsornruang
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-14-926

Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production
Cited by: 78
Author(s): Christian Bogen, Arwa Al-Dilaimi, Andreas Albersmeier, Julian Wichmann, Michael Grundmann, Oliver Rupp, Kyle J. Lauersen, Olga Blifernez-Klassen, Joern Kalinowski, Alexander Goesmann, Jan H. Mussgnug, Olaf Kruse
Software Mentions: 1
Published: almost 11 years ago

10.7554/eLife.45017

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions
Cited by: 45
Author(s): Alessandro W. Rossoni, Dana C. Price, Mark Seger, Dagmar Lyska, Peter J. Lammers, Debashish Bhattacharya, Andreas P.M. Weber
Software Mentions: 1
Published: over 5 years ago

10.1128/mBio.00868-15

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii
Cited by: 89
Author(s): Rhys A. Farrer, Christopher A. Desjardins, Sharadha Sakthikumar, Sharvari Gujja, Sakina Saif, Qiandong Zeng, Yuan Chen, Kerstin Voelz, Joseph Heitman, Robin C. May, Matthew C. Fisher, Christina A. Cuomo
Software Mentions: 1
Published: about 9 years ago

10.1038/s41598-020-73744-3

Facial erythema detects diabetic neuropathy using the fusion of machine learning, random matrix theory and self organized criticality
Cited by: 3
Author(s): Esmaeil S. Nadimi, Tomáš Majtner, Knud Bonnet Yderstræde, Victoria Blanes-Vidal
Software Mentions: 1
Published: about 4 years ago

10.1038/s41438-021-00498-y

De novo assembly of a new Olea europaea genome accession using nanopore sequencing
Cited by: 35
Author(s): Guodong Rao, Jianguo Zhang, Xiaoxia Liu, Chun-Fu Lin, Huaigen Xin, Li Xue, Chenhe Wang
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1004094

Nannochloropsis Genomes Reveal Evolution of Microalgal Oleaginous Traits
Cited by: 205
Author(s): Dongmei Wang, Kang Ning, Jing Li, Jian-Qiang Hu, Danxiang Han, Hui Wang, Xiaowei Zeng, Xiaoyan Jing, Qian Zhou, Xiaoquan Su, Xingzhi Chang, Anhui Wang, Wei Wang, Jun Jia, Li Wei, Xin Yi, Yinghe Qiao, Ranran Huang, Jie Chen, Bo Han, Kang-Sup Yoon, Russell T. Hill, Yonathan Zohar, Feng Chen, Qiang Hu, Jian Xu
Software Mentions: 1
Published: almost 11 years ago

10.3390/plants10081620

Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms
Cited by: 4
Author(s): Xiaolong Yuan, Chengsheng Zhang, Fanyu Kong, Zhongfeng Zhang, Fenglong Wang
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.9114

A de novo assembly of the sweet cherry (<i>Prunus avium</i> cv. Tieton) genome using linked-read sequencing technology
Cited by: 8
Author(s): J. Wang, Weizhen Liu, Dong Zhu, Xiang Zhou, Po Hong, Hongjun Zhao, Yue Tan, Xin Chen, Xiaojuan Zong, Li Xu, Lisi Zhang, Hairong Wei, Qingzhong Li
Software Mentions: 1
Published: over 4 years ago

10.1093/femspd/ftw080

Annotated draft genome sequences of three species of<i>Cryptosporidium</i>:<i>Cryptosporidium meleagridis</i>isolate UKMEL1,<i>C. baileyi</i>isolate TAMU-09Q1 and<i>C. hominis</i>isolates TU502_2012 and UKH1
Cited by: 32
Author(s): Olukemi O. Ifeonu, Marcus C. Chibucos, Joshua Orvis, Qi Su, Kristin Elwin, Feng Guo, Haili Zhang, Lihua Xiao, Mingfei Sun, Rachel M. Chalmers, Claire M. Fraser, Guangxi Zhu, Jessica C. Kissinger, Giovanni Widmer, Joana C. Silva
Software Mentions: 1
Published: about 8 years ago

10.1186/s12905-020-01131-1

Female university students’ preferences for different types of sexual relationships: implications for gender-based violence prevention programs and policies
Cited by: 7
Author(s): Laura Ruiz-Eugenio, Sandra Racionero-Plaza, Elena Duque, Lídia Puigvert
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-020-06891-6

Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera
Cited by: 4
Author(s): Changqing Liu, Xiaoli Shi, Fan Wu, Mingdong Ren, Guang Gao, Qinglong L. Wu
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-87419-0

The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago
Cited by: 11
Author(s): Nathalie Raharimalala, Stéphane Rombauts, A.A. McCarthy, Andréa Garavito, Simón Orozco-Arias, Laurence Bellanger, Alexa Yadira Morales-Correa, Solène Froger, Stéphane Michaux, Victoria Berry, Sylviane Métairon, Coralie Fournier, Maud Lepelley, Lukas A. Mueller, Emmanuel Couturon, Perla Hamon, J. J. R. Rakotomalala, Patrick Descombes, Romain Guyot, Dominique Crouzillat
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-15-312

An improved genome release (version Mt4.0) for the model legume Medicago truncatula
Cited by: 336
Author(s): Haibao Tang, Vivek Krishnakumar, Shelby L. Bidwell, Benjamin D. Rosen, Agnes P. Chan, Shiguo Zhou, Laurent Gentzbittel, Kevin L. Childs, Mark Yandell, Heidrun Gundlach, Klaus Mayer, David C. Schwartz, Christopher D. Town
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-021-07616-z

Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications
Cited by: 5
Author(s): Chao Yang, Xuejuan Li, Qingxiong Wang, Hao Yuan, Yuan Huang, Hong Xiao
Software Mentions: 1
Published: over 3 years ago

10.1186/1746-4269-5-37

Animals to heal animals: ethnoveterinary practices in semiarid region, Northeastern Brazil
Cited by: 58
Author(s): Maine V A Confessor, Lívia Emanuelle Tavares Mendonça, José da Silva Mourão, Rômulo Romeu Nóbrega Alves
Software Mentions: 1
Published: almost 15 years ago

10.1186/s12915-019-0716-7

Extracting physiological information in experimental biology via Eulerian video magnification
Cited by: 20
Author(s): Henrik Lauridsen, Selina Grace Gonzales, Daniela Hedwig, Kathryn L. Perrin, Catherine J. Williams, Peter H. Wrege, Mads F. Bertelsen, Michael Pedersen, Jonathan T. Butcher
Software Mentions: 1
Published: almost 5 years ago

10.1038/sdata.2018.234

First draft genome sequence of the rock bream in the family Oplegnathidae
Cited by: 4
Author(s): Younhee Shin, Myunghee Jung, Ga-Hee Shin, Hojin Jung, Su‐Jin Baek, Gi Yong Lee, Byeong-Chul Kang, Jae-Young Shim, Jiman Hong, Jung Youn Park, Cheul Min An, Young‐Ok Kim, Jae Koo Noh, Juwon Kim, Bo‐Hye Nam, Chan-Il Park
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-019-5980-y

Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)
Cited by: 11
Author(s): Sabyasachi Mukherjee, Zexi Cai, Anupama Mukherjee, Imsusosang Longkumer, Moonmoon Mech, Kezhavituo Vüpru, K. Khate, C. Rajkhowa, Abhijit Mitra, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
Software Mentions: 1
Published: over 5 years ago

10.1038/s41597-019-0067-9

Draft genome of the big-headed turtle Platysternon megacephalum
Cited by: 13
Author(s): Dainan Cao, Meng Wang, Guiqin Yan, Shunsheng Gong
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2164-15-788

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa,the causative agent of loiasis
Cited by: 24
Author(s): Luke J. Tallon, Xinyue Liu, Sasisekhar Bennuru, Marcus C. Chibucos, Alvaro Godinez, Sandra Ott, Xüna Zhao, Lisa Sadzewicz, Claire M. Fraser, Thomas B. Nutman, Julie C. Dunning Hotopp
Software Mentions: 1
Published: about 10 years ago

10.1128/genomeA.00885-15

Genome Sequence and Annotation of <i>Trichoderma parareesei</i> , the Ancestor of the Cellulase Producer <i>Trichoderma reesei</i>
Cited by: 28
Author(s): Dongqing Yang, Kyle R. Pomraning, Alexey G. Kopchinskiy, Razieh Karimi Aghcheh, Lea Atanasova, Komal Chenthamara, Scott E. Baker, Ruifu Zhang, Qirong Shen, Michael Freitag, Christian P. Kubicek, Irina S. Druzhinina
Software Mentions: 1
Published: about 9 years ago

10.1038/s41597-020-0370-5

A chromosome-level reference genome of the hornbeam, Carpinus fangiana
Cited by: 6
Author(s): Xiaoyue Yang, Zefu Wang, Lei Zhang, Guoqian Hao, Jianquan Liu, Yongzhi Yang
Software Mentions: 1
Published: almost 5 years ago

10.1534/genetics.117.300573

Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen <i>Trichophyton rubrum</i>
Cited by: 47
Author(s): Gabriela Félix Persinoti, Diego Martínez, Wenjun Li, Aylin Döğen, R. Blake Billmyre, Anna Floyd Averette, Jonathan M. Goldberg, Terrance Shea, Sarah Young, Qiandong Zeng, Brian G. Oliver, Richard Barton, Banu Metin, Süleyha Hilmioğlu Polat, Macit İlkit, Yvonne Gräser, Nilce Maria Martinez-Rossi, Theodore C. White, Joseph Heitman, Christina A. Cuomo
Software Mentions: 1
Published: over 6 years ago

10.1186/gb-2013-14-7-r77

The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation
Cited by: 89
Author(s): Gretchen Ehrenkaufer, Gareth D. Weedall, Daryl R. Williams, Hernán Lorenzi, Elisabet Caler, Neil Hall, Upinder Singh
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13059-017-1341-9

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication
Cited by: 207
Author(s): Seungill Kim, Jieun Park, Seon-In Yeom, Yongmin Kim, Eun-Young Seo, Ki-Tae Kim, Myung-Shin Kim, Je Min Lee, Kwang Ho Cheong, Hosub Shin, Saet-Byul Kim, Koeun Han, Jundae Lee, Minkyu Park, Hyunah Lee, Hyeyoung Lee, Youngsill Lee, Soohyun Oh, Juhyun Lee, Eun‐Hye Choi, Eunbi Choi, So Eui Lee, Jongbum Jeon, Hyunbin Kim, Gobong Choi, Hyeunjeong Song, Junki Lee, Sang-Choon Lee, Jae-Hoon Kwon, Hea-Young Lee, Namjin Koo, Young Jun Hong, Ryan W. Kim, Won-Hee Kang, Jin Hoe Huh, Byoung−Cheorl Kang, Tae-Jin Yang, Yong-Hwan Lee, Jeffrey L. Bennetzen, Doil Choi
Software Mentions: 1
Published: about 7 years ago

10.1186/s13059-020-01959-8

The genome evolution and domestication of tropical fruit mango
Cited by: 86
Author(s): Peng Wang, Yingfeng Luo, Jianfeng Huang, Shenghan Gao, Guopeng Zhu, Dang Zhiguo, Jiangtao Gai, Meng Yang, Min Zhu, Huangkai Zhang, Xiuxu Ye, Aiping Gao, Xinyu Tan, Sen Wang, Shizhou Wu, Edgar B. Cahoon, Beibei Bai, Zhao Zhong, Qian Li, June Wei, Huarui Chen, Ruibang Luo, Deyong Gong, Kexuan Tang, Bing Zhang, Ni ZhangGuang, Guodi Huang, Songnian Hu, Yeyuan Chen
Software Mentions: 1
Published: over 4 years ago

10.1093/g3journal/jkab180

<i>De novo</i> genome assembly of the land snail <i>Candidula unifasciata</i> (Mollusca: Gastropoda)
Cited by: 7
Author(s): Luis J. Chueca, Tilman Schell, Markus Pfenninger
Software Mentions: 1
Published: over 3 years ago

10.1093/gbe/evz251

A High-quality Draft Genome Assembly of the Black-necked Crane (Grus nigricollis) Based on Nanopore Sequencing
Cited by: 2
Author(s): Chuang Zhou, Haoran Yu, Geng Yang, Wei Liu, Shuai Zheng, Nan Yang, Meng Yang, Liang Dou, Megan Price, Jianghong Ran, Bisong Yue, Yongjie Wu
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41597-020-0400-3

The sequence and de novo assembly of the wild yak genome
Cited by: 15
Author(s): Yanbin Liu, Jiayu Luo, Jiajia Dou, Biao Yan, Qingmiao Ren, Bolin Tang, Kun Wang, Qiang Qiu
Software Mentions: 1
Published: over 4 years ago

10.1093/gbe/evab026

Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte <i>Laburnicola rhizohalophila</i>: A Model for Investigating Root-Fungus Symbiosis
Cited by: 4
Author(s): Xinghua He, Zhuang Youxiang
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.115.017731

RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus <i>Zymoseptoria</i> Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements
Cited by: 99
Author(s): Jonathan Grandaubert, Amitava Bhattacharyya, Eva H. Stukenbrock
Software Mentions: 1
Published: over 9 years ago

10.3389/fmicb.2020.599150

Genome Assembly and Transcriptome Analysis of the Fungus Coniella diplodiella During Infection on Grapevine (Vitis vinifera L.)
Cited by: 4
Author(s): Ruitao Liu, Yiming Wang, Peng Li, Lina Sun, Jianfu Jiang, Xiucai Fan, Chonghuai Liu, Ying Zhang
Software Mentions: 1
Published: almost 4 years ago

10.1093/gigascience/gix016

The genome sequence of the wisent (Bison bonasus)
Cited by: 22
Author(s): Kun Wang, Lizhong Wang, Johannes A. Lenstra, Jianbo Jian, Yongzhi Yang, Quanjun Hu, Deyong Lai, Qiang Qiu, Tao Ma, Zheng Du, Richard J. Abbott, Jianquan Liu
Software Mentions: 1
Published: over 7 years ago

10.1155/2019/5287287

Effective Vaccine Management: The Case of a Rural District in Ghana
Cited by: 10
Author(s): Eric Osei, Mohammed Ibrahim, Gregory Kofi Amenuvegbe
Software Mentions: 1
Published: about 5 years ago

10.1093/gigascience/gix102

Draft genome of the reindeer (Rangifer tarandus)
Cited by: 37
Author(s): Zhipeng Li, Qisheng Wang, Hengxing Ba, Lei Chen, Yongzhi Yang, Kun Wang, Qiang Qiu, Wen Wang, Guangyu Li
Software Mentions: 1
Published: about 7 years ago

10.1093/gigascience/giy006

Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus
Cited by: 17
Author(s): Yuan-Ming Wu, Lingling Jiang, Xiang-Sheng Chen
Software Mentions: 1
Published: over 6 years ago

10.1093/gigascience/giy038

The draft genome sequence of forest musk deer (Moschus berezovskii)
Cited by: 25
Author(s): Zhenxin Fan, Wujiao Li, Jiazheng Jin, Kai Cui, Chaochao Yan, Changjun Peng, Zhongyu Jian, Ping Bu, Megan Price, Xiuyue Zhang, Yongmei Shen, Jing Li, Wenbao Qi, Bisong Yue
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2021.705839

Physiological, Genomic and Transcriptomic Analyses Reveal the Adaptation Mechanisms of Acidiella bohemica to Extreme Acid Mine Drainage Environments
Cited by: 9
Author(s): Shu-ning Ou, Jie-Liang Liang, Xiaomin Jiang, Bin Liao, Pu Jia, Wen‐Sheng Shu, Jintian Li
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2018.00643

First Draft Genome for Red Sea Bream of Family Sparidae
Cited by: 20
Author(s): Ga-Hee Shin, Younhee Shin, Myunghee Jung, Jiman Hong, Sang‐Min Lee, Sathiyamoorthy Subramaniyam, Eun-Soo Noh, Eun-Ha Shin, Eun-Hee Park, Jung Youn Park, Young‐Ok Kim, Kwang-Min Choi, Bo‐Hye Nam, Chan-Il Park
Software Mentions: 1
Published: almost 6 years ago