Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: CAFE

https://packages.ecosyste.ms/registries/bioconductor.org/packages/CAFE

Chromosmal Aberrations Finder in Expression data
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Latest release: about 1 year ago
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Papers Mentioning CAFE 251

10.1093/gbe/evz260
The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations
Cited by: 2
Author(s): Mosè Manni, Felipe A. Simão, Hugh M. Robertson, Marco A. Gabaglio, Robert M. Waterhouse, Bernhard Misof, Oliver Niehuis, Nikolaus U. Szucsich, Evgeny M. Zdobnov
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.gpb.2019.01.007
The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium
Cited by: 11
Author(s): Hongmei Luo, Jun Qian, Zhichao Xu, Wanjing Liu, Lei Xu, Ying Liu, Jiang Xu, Jianhong Zhang, Xiaolan Xu, Chang Liu, Li He, Jianqin Li, Chao Sun, Francis Martin, Jingyuan Song, Shilin Chen
Software Mentions: 2
Published: over 4 years ago
10.1080/21501203.2018.1478333
Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi
Cited by: 33
Author(s): Weiwei Zhang, Xiaoling Zhang, Kuan Li, Chengshu Wang, Lei Cai, Wen-Ying Zhuang, Meichun Xiang, Xingzhong Liu
Software Mentions: 2
Published: over 6 years ago
10.1093/gigascience/gix008
Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history
Cited by: 34
Author(s): Xiaofeng Dong, Stuart D. Armstrong, Dong Xia, Benjamin L. Makepeace, Alistair C. Darby, Tatsuhiko Kadowaki
Software Mentions: 2
Published: over 7 years ago
10.1093/gigascience/giy068
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant
Cited by: 38
Author(s): Aixiang Dong, Haibo Xin, Zi-Jing Li, Hui Liu, Yuze Sun, Shuai Nie, Zhengnan Zhao, Rongfeng Cui, Rengang Zhang, Quanzheng Yun, Xinning Wang, Fatemeh Maghuly, Ilga Porth, Richen Cong, Jian‐Feng Mao
Software Mentions: 2
Published: over 6 years ago
10.1093/gigascience/giy127
Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism
Cited by: 27
Author(s): Xiaofeng Dong, Kittipong Chaisiri, Dong Xia, Stuart D. Armstrong, Yongxiang Fang, Martin J. Donnelly, Tatsuhiko Kadowaki, John McGarry, Alistair C. Darby, Benjamin L. Makepeace
Software Mentions: 2
Published: about 6 years ago
10.1186/s12864-019-5818-7
Genome sequencing provides insights into the evolution and antioxidant activity of Chinese bayberry
Cited by: 21
Author(s): Haiyan Ren, Haiyan Yu, Shuwen Zhang, Liang SenMiao, Xiaodong Zheng, Shujian Zhang, Yulin Pu, Hongkun Zheng, Xin Qi
Software Mentions: 2
Published: over 5 years ago
10.1093/gigascience/giy143
The genome of an underwater architect, the caddisfly<i>Stenopsyche tienmushanensis</i>Hwang (Insecta: Trichoptera)
Cited by: 37
Author(s): Shiqi Luo, Min Tang, Paul B. Frandsen, Russell J. Stewart, Xin Zhou
Software Mentions: 2
Published: almost 6 years ago
10.1093/gigascience/giz085
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China
Cited by: 39
Author(s): Jing Yang, Hafiz Muhammad Wariss, Lidan Tao, Rengang Zhang, Quanzheng Yun, Peter M. Hollingsworth, Zhiling Dao, Gongwen Luo, Huijun Guo, Yongpeng Ma, Weibang Sun
Software Mentions: 2
Published: over 5 years ago
10.1093/gigascience/giz128
Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis
Cited by: 22
Author(s): Sihan Lu, Jie Yang, Xuelei Dai, Feiang Xie, Jinwu He, Zhiwei Dong, Junlai Mao, Guichun Liu, Zhou Chang, Ruoping Zhao, Wenting Wan, Ru Zhang, Yuan Li, Wen Wang, Xueyan Li
Software Mentions: 2
Published: about 5 years ago
10.7717/peerj.4873
MIPhy: identify and quantify rapidly evolving members of large gene families
Cited by: 10
Author(s): David M. Curran, John S. Gilleard, James D. Wasmuth
Software Mentions: 2
Published: over 6 years ago
10.1038/s41438-021-00501-6
The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes
Cited by: 23
Author(s): Jie Zheng, Lyndel W. Meinhardt, Ricardo Goenaga, Dapeng Zhang, Yanbin Yin
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-021-00495-1
The <i>Corylus mandshurica</i> genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding
Cited by: 15
Author(s): Ying Liu, Pengchuan Sun, Zhiqiang Lu, Jinyuan Chen, Zhenyue Wang, Xin Du, Zeyu Zheng, Ying Wu, Hongbo Hu, Yang Jiao, Junsheng Ma, Jianquan Liu, Yongzhi Yang
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-020-00382-1
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species
Cited by: 15
Author(s): Xin Yi, Xiaqing Yu, Jie Chen, Min Zhang, Shaowei Liu, Hong Zhu, Meng Li, Yifan Duan, Lin Chen, Lei Wu, Zhu Shun, Zhuo Sun, Xinhong Liu, Xianrong Wang
Software Mentions: 2
Published: about 4 years ago
10.1038/s41438-021-00559-2
The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis
Cited by: 22
Author(s): Da-Xia Chen, Yuan Pan, Yu Wang, Yanze Cui, Yingjun Zhang, Rangyu Mo, Xiaoli Wu, Jun Tan, Jian Zhang, Lianan Guo, Zhao Xiao, Wenkai Jiang, Tsieh Sun, Xiaodi Hu, Longyun Li
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-021-00627-7
Haplotype-resolved genome of diploid ginger (<i>Zingiber officinale</i>) and its unique gingerol biosynthetic pathway
Cited by: 46
Author(s): Honglei Li, Lin Wu, Zhaoming Dong, Yi Jiang, Sanjie Jiang, Haitao Xing, Qiang Li, Guocheng Liu, Shuming Tian, Zhangyan Wu, Bin Wu, Zhexin Li, Ping Zhao, Yan Zhang, Jianmin Tang, Jiabao Xu, Ke Huang, Xia Liu, Wenlin Zhang, Qinhong Liao, Yun Ren, Xianjin Huang, Qingzhi Li, Chengyong Li, Yi Wang, Baskaran Xavier-Ravi, Honghai Li, Yang Liu, Tao Wan, Qinhu Liu, Yong Zou, Jianbo Jian, Qingyou Xia, Yiqing Liu
Software Mentions: 2
Published: over 3 years ago
10.1111/pbi.13310
Deciphering the high‐quality genome sequence of coriander that causes controversial feelings
Cited by: 51
Author(s): Xiaoming Song, Jinpeng Wang, Nan Li, Jigao Yu, Fanbo Meng, Chendan Wei, Chao Liu, Wei Chen, Fulei Nie, Zhikang Zhang, Ke Gong, Xinyu Li, Jingjing Hu, Qing Yang, Yuxian Li, Chunjin Li, Shuyan Feng, He Guo, Jiaqing Yuan, Qiaoying Pei, Tong Yu, Xi Kang, Wei Zhao, Tianyu Lei, Pengchuan Sun, Li Wang, Weina Ge, Di Guo, Xiaoyang Duan, Shaoqi Shen, Chunlin Cui, Ying Yu, Yangqin Xie, Zhang Jin, Yayi Hou, Jinyu Wang, Xiuqing Li, Andrew H. Paterson, Xiyin Wang
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41438-019-0215-6
The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis
Cited by: 84
Author(s): Feng-chao Jiang, Junhuan Zhang, Sen Wang, Yang Li, Yingfeng Luo, Shenghan Gao, Meiling Zhang, Shizhou Wu, Songnian Hu, Hui Sun, Yuzhu Wang
Software Mentions: 2
Published: about 5 years ago
10.1038/s41438-021-00481-7
Genome sequence and evolution of <i>Betula platyphylla</i>
Cited by: 46
Author(s): Su Chen, Yucheng Wang, Lili Yu, Tao Zheng, Sui Wang, Zhen Yue, Jing Jiang, Sapna Kumari, Chunfang Zheng, Haibao Tang, Jun Li, Yuqi Li, Jiongjiong Chen, Wenbo Zhang, Hanhui Kuang, Jon S. Robertson, Patrick Xuechun Zhao, Huiyu Li, Shengqiang Shu, Yordan S. Yordanov, Hongyan Huang, David Goodstein, Ying Gai, Qi Qi, Min Jiang, Chunyan Xu, SongBo Wang, Guanzheng Qu, Andrew H. Paterson, David Sankoff, Hairong Wei, Guifeng Liu, Chuanping Yang
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41438-019-0202-y
A high-quality Actinidia chinensis (kiwifruit) genome
Cited by: 89
Author(s): Haolin Wu, Tao Ma, Minghui Kang, Fandi Ai, Junlin Zhang, Guanyong Dong, Jianquan Liu
Software Mentions: 2
Published: about 5 years ago
10.1038/s41438-020-00458-y
Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis
Cited by: 22
Author(s): Hui Huang, Juan Boo Liang, Qian Tan, Lin-Feng Ou, Xin Li, Caihong Zhong, Ian Max Møller, WU Xian-jin, Song-Quan Song
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41438-020-00423-9
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening
Cited by: 18
Author(s): Lili Ma, Qing Wang, Jianlou Mu, Anzhen Fu, Changlong Wen, Xiaoyan Zhao, Lipu Gao, Jian Li, Kai Shi, Yunxiang Wang, Xuewen Zhang, Xuechuan Zhang, Zhangjun Fei, Donald Grierson, Jinhua Zuo
Software Mentions: 2
Published: almost 4 years ago
10.1038/s41438-020-00391-0
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant
Cited by: 75
Author(s): Qingzhen Wei, Jinglei Wang, Wuhong Wang, Tianhua Hu, Hongbo Hu, Chonglai Bao
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.ppat.1002290
Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica
Cited by: 338
Author(s): Alga Zuccaro, Urs Lahrmann, Ulrich Güldener, Gregor Langen, Stefanie Pfiffi, Dagmar Biedenkopf, Philip Wong, Birgit Samans, Carolin Grimm, Magdalena Basiewicz, Claude Murat, Francis Martin, Karl‐Heinz Kogel
Software Mentions: 2
Published: about 13 years ago
10.1098/rspb.2020.3168
Evidence for reduced immune gene diversity and activity during the evolution of termites
Cited by: 7
Author(s): Shulin He, Thorben Sieksmeyer, Yanli Che, M. Alejandra Esparza Mora, Petr Stiblík, Ronald Banasiak, Mark C. Harrison, Jan Šobotník, Zongqing Wang, Paul R. Johnston, Dino P. McMahon
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-018-5253-1
Alignment-free genome comparison enables accurate geographic sourcing of white oak DNA
Cited by: 4
Author(s): Kujin Tang, Jie Ren, Richard Cronn, David L. Erickson, Brook G. Milligan, Meaghan Parker-Forney, John L. Spouge, Fengzhu Sun
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-018-20154-1
A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)
Cited by: 187
Author(s): Sean D. Schoville, Yolanda H. Chen, Martin Andersson, Joshua B. Benoit, Anita Bhandari, Julia H. Bowsher, Kristian Brevik, Kaat Cappelle, Mei Ju M. Chen, Anna K. Childers, Christopher P. Childers, Olivier Christiaens, Justin Clements, Elise M. Didion, Elena N. Elpidina, Patamarerk Engsontia, Markus Friedrich, Inmaculada García-Robles, Richard A. Gibbs, Chandan Goswami, Alessandro Grapputo, Kristina Gruden, Marcin Grynberg, Bernard Henrissat, Emily C. Jennings, Jeffery W. Jones, Megha Kalsi, Sher Afzal Khan, Abhishek Kumar, Fēi Li, Vincent Lombard, Xingzhou Ma, Alexander Martynov, Nicholas J. Miller, Robert F. Mitchell, Monica Muñoz-Torres, Anna Muszewska, Brenda Oppert, Subba Reddy Palli, Kristen A. Panfilio, Yannick Pauchet, Lindsey C. Perkin, Marko Petek, Monica Poelchau, Éric Record, Joseph P. Rinehart, Hugh M. Robertson, Andrew J. Rosendale, Victor M. Ruiz-Arroyo, Guy Smagghe, Zsofia Szendrei, Gregg W.C. Thomas, Alex S. Torson, Iris M. Vargas Jentzsch, Matthew T. Weirauch, Ashley D. Yates, George D. Yocum, June‐Sun Yoon, Stephen Richards
Software Mentions: 2
Published: almost 7 years ago
10.1038/s41598-020-79194-1
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae)
Cited by: 11
Author(s): Ivan M. De‐la‐Cruz, Asis Hallab, Ulises Olivares-Pinto, Rosalinda Tapia‐López, Sabina Velázquez-Márquez, Daniel Piñero, Ken Oyama, Björn Usadel, Juan Núñez–Farfán
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0160336
Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation
Cited by: 100
Author(s): Lianfu Chen, Yuhua Gong, Yingli Cai, Wei Liu, Yan Zhou, Yang Xiao, Zhangyi Xu, Liang Yin, Xiaoyu Lei, Jinjie Wang, Mengpei Guo, Xiaolong Ma
Software Mentions: 2
Published: over 8 years ago
10.3390/jof7080679
Genomic and Experimental Investigations of Auriscalpium and Strobilurus Fungi Reveal New Insights into Pinecone Decomposition
Cited by: 1
Author(s): Pan-Meng Wang, Jianping Xu, Gang Wu, Liu TieZhi, Zhu L. Yang
Software Mentions: 2
Published: about 3 years ago
10.1155/2017/1707231
Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire
Cited by: 3
Author(s): Ousman Mahmud, Jessica C. Kissinger
Software Mentions: 2
Published: almost 8 years ago
10.1093/jhered/esab009
Limited Evidence for Parallel Evolution Among Desert-Adapted <i>Peromyscus</i> Deer Mice
Cited by: 10
Author(s): Jocelyn P. Colella, Anna Tigano, Olga Dudchenko, Arina D. Omer, Ruqayya Khan, Ivan D. Bochkov, E Aiden, Matthew D. MacManes
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-020-6629-6
Genome of the webworm Hyphantria cunea unveils genetic adaptations supporting its rapid invasion and spread
Cited by: 13
Author(s): Qi Chen, Hanbo Zhao, Ming Wen, Jiaxin Li, Haifeng Zhou, Jiatong Wang, Yuxin Zhou, Yulin Liu, Lixin Du, Hui Kang, Jian Zhang, Rui Cao, Xiaoming Xu, Jing‐Jiang Zhou, Bingzhong Ren, Yinliang Wang
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-021-07480-x
Key metabolism pathways and regulatory mechanisms of high polysaccharide yielding in Hericium erinaceus
Cited by: 7
Author(s): Ming Gong, Henan Zhang, Di Wu, Zhong Zhang, Jinsong Zhang, Dapeng Bao, Yan Yang
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-019-6256-2
Comparative genomics applied to Mucor species with different lifestyles
Cited by: 21
Author(s): Annie Lebreton, Erwan Corre, Jean‐Luc Jany, Loraine Brillet-Guéguen, Carlos Pèrez-Arques, Victoriano Garre, Misharl Monsoor, Robert Debuchy, Christophe Le Meur, Emmanuel Coton, Georges Barbier, Laurence Meslet‐Cladière
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13020-020-00365-3
Genomic analyses reveal evolutionary and geologic context for the plateau fungus Ophiocordyceps sinensis
Cited by: 6
Author(s): Jie Liu, Liyun Guo, Zongwei Li, Zhe Zhou, Zhen Li, Qian Li, Xiaochen Bo, Shengqi Wang, Junli Wang, Shuang‐Cheng Ma, Jian Zheng, Ying Yang
Software Mentions: 2
Published: about 4 years ago
10.1038/s42003-020-1091-1
Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms
Cited by: 25
Author(s): Yongxin Li, Akihito Omori, Rachel L. Flores, Sheri Satterfield, Christine Nguyen, Tomomi Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi, Jason Cheok Kuan Leong, Adrian Reich, Hao Meng, Wenting Wan, Yang Dong, Yaondong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka, Yui Uchida, Xueyan Li, Tomoko Shibata, Takahiro Bino, Kota Ogawa, Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary M. Wessel, Hidetoshi Saiga, R. Andrew Cameron, Brian T. Livingston, Cynthia A. Bradham, Wen Wang, Naoki Irie
Software Mentions: 2
Published: over 4 years ago
10.1038/s42003-020-0890-8
SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation
Cited by: 16
Author(s): Wei Li, Kui Li, Ying Huang, Cong Shi, Wushu Hu, Yun Zhang, Qun‐Jie Zhang, Enhua Xia, Ge-Ran Hutang, Xun-Ge Zhu, Yunlong Liu, Yuan Liu, Yan Tong, Ting Zhu, Hui Huang, Dan Zhang, Yuan Zhao, Wenkai Jiang, Jie Yuan, Yongchao Niu, Chengwen Gao, Li‐Zhi Gao
Software Mentions: 2
Published: over 4 years ago
10.1093/database/bav127
ncRNA orthologies in the vertebrate lineage
Cited by: 17
Author(s): Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato, Leo I. Gordon, Simon White, Paul Flicek, Javier Herrero
Software Mentions: 2
Published: almost 9 years ago
10.1186/1471-2105-11-43
Discovering local patterns of co - evolution: computational aspects and biological examples
Cited by: 8
Author(s): Tamir Tuller, Yifat Felder, Martin Kupiec
Software Mentions: 2
Published: almost 15 years ago
10.1186/s12864-016-2710-6
Genome sequence and comparative analysis of clavicipitaceous insect-pathogenic fungus Aschersonia badia with Metarhizium spp.
Cited by: 12
Author(s): Yamini Agrawal, Tarun Jairaj Narwani, S. Subramanian
Software Mentions: 2
Published: over 8 years ago
10.1111/eva.12609
The mycoparasitic fungus <i>Clonostachys rosea</i> responds with both common and specific gene expression during interspecific interactions with fungal prey
Cited by: 77
Author(s): Kristiina Nygren, Mukesh Dubey, Antonio Zapparata, Mudassir Iqbal, Georgios Tzelepis, Mikael Brandström Durling, Dan Funck Jensen, Magnus Karlsson
Software Mentions: 2
Published: over 6 years ago
10.1111/eva.13134
Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in <i>Clonostachys</i> subgenus <i>Bionectria</i> (Fungi, Ascomycota, Hypocreales)
Cited by: 15
Author(s): Martin Broberg, Mukesh Dubey, Mudassir Iqbal, Mikael Gudmundssson, Katarina Ihrmark, Hans-Josef Schroers, Dan Funck Jensen, Mikael Brandström Durling, Magnus Karlsson
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2019.01340
High-Quality Genome Assembly of Eriocheir japonica sinensis Reveals Its Unique Genome Evolution
Cited by: 29
Author(s): Boping Tang, Zhongkai Wang, Qiu-Ning Liu, Huabin Zhang, Senhao Jiang, Xinzheng Li, Zhengfei Wang, Yue Sun, Zhongli Sha, Hui Jiang, Xugan Wu, Yandong Ren, Haorong Li, Fujun Xuan, Baoming Ge, Wei Jiang, Shusheng She, Hongying Sun, Qiang Qiu, Wen Wang, Qun Wang, Gao‐Feng Qiu, Dai-Zhen Zhang, Yongxin Li
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12915-015-0223-4
The Sinocyclocheilus cavefish genome provides insights into cave adaptation
Cited by: 185
Author(s): Jing Yang, Xiaoli Chen, Jie Bai, Dongming Fang, Ying Qiu, Weixing Jiang, Hui Yuan, Chao Bian, Lu Jiang, Shiyang He, Xiaofu Pan, Yaolei Zhang, Xiaoai Wang, Xinxin You, Yongsi Wang, Yu Sun, Danqing Mao, Yong Liu, Guangyi Fan, He Zhang, Xiaoyong Chen, Xinhui Zhang, Liang Zheng, Jintu Wang, Lei Cheng, Jieming Chen, Zhiqiang Ruan, Jia Li, Hui Yu, Chao Peng, Xingyu Ma, Junmin Xu, Yu He, Zhengfeng Xu, Pao Xu, Jian Wang, Huanming Yang, Jun Wang, Tony Whitten, Xun Xu, Qiong Shi
Software Mentions: 2
Published: almost 9 years ago
10.3389/fgene.2020.621301
The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensis
Cited by: 1
Author(s): Ajit Kumar Patra, Oksung Chung, Ji Yong Yoo, Sang Ho Baek, Tae Won Jung, Min-Seop Kim, Moon Geun Yoon, Yali Yang, Jeong-Hyeon Choi
Software Mentions: 2
Published: almost 4 years ago
10.3389/fgene.2020.00664
The Chromosome-Level Genome Assembly and Comprehensive Transcriptomes of the Razor Clam (Sinonovacula constricta)
Cited by: 15
Author(s): Yan Dong, Qifan Zeng, Jianfeng Ren, Hanhan Yao, Liyuan Lv, Lin He, Wenbin Ruan, Qinggang Xue, Zhenmin Bao, Shi Wang, Lin Zhang
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2148-9-148
Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses
Cited by: 81
Author(s): Jeri Lynn Parrent, Timothy Y. James, Rimvydas Vasaitis, Andrew Taylor
Software Mentions: 2
Published: almost 16 years ago
10.1186/s12864-021-07861-2
Comparative and functional genomics of the ABC transporter superfamily across arthropods
Cited by: 11
Author(s): Shane Denecke, Ivan Rankić, Olympia Driva, Megha Kalsi, Hằng Ngọc Bảo Lương, Benjamin Buer, Ralf Nauen, Sven Geibel, John Vontas
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2018.00711
Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer
Cited by: 8
Author(s): Kujin Tang, Yang Lu, Fengzhu Sun
Software Mentions: 2
Published: over 6 years ago
10.1186/s12864-021-07442-3
Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri
Cited by: 5
Author(s): Hao‐Sen Li, Yu‐Hao Huang, Meilan Chen, Renbin Zhan, Bo-Yuan Qiu, Patrick De Clercq, Gerald Heckel
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2021.694136
Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici
Cited by: 3
Author(s): Joung‐Ho Lee, Muhammad Irfan Siddique, Jae-Hoon Kwon, Byoung‐Cheorl Kang
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.523593
Chilling Stress Triggers VvAgo1-Mediated miRNA-Like RNA Biogenesis in Volvariella volvacea
Cited by: 7
Author(s): Ming Gong, Ying Wang, Jinsong Zhang, Yan Zhao, Jianing Wan, Junjun Shang, Runqiang Yang, Ying‐Ying Wu, Yán Li, Qian Tan, Dapeng Bao
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2020.00687
Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21
Cited by: 17
Author(s): Limin Liang, Xinqing Zheng, Wenfang Fan, Duo Chen, Zhen Huang, Jiangtao Peng, Jinmao Zhu, Weiqi Tang, Youqiang Chen, Ting Xue
Software Mentions: 2
Published: over 4 years ago
10.1186/s12915-021-00998-2
The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance
Cited by: 1
Author(s): Tengcheng Que, Huifeng Wang, Weifei Yang, Jianbao Wu, Chenyang Hou, Surui Pei, Qunying Wu, Liu Ming Li, Shilu Wei, Xing Xie, Hongli Huang, Panyu Chen, Yiming Huang, Aiqiong Wu, Meihong He, Dengpan Nong, Wei Xiao, Junyi Wu, Ru Nong, Ning Huang, Qingniao Zhou, Yue Lin, tingxi lu, Yongjie Wei, Shousheng Li, Jianglong Yao, Yanli Zhong, Huayong Qin, Luohao Tan, Ying-Jiao Li, Weidong Li, Tao Liu, Sanyang Liu, Yifan Yu, Hong Qiu, Yonghua Jiang, You-Cheng Li, Zhijin Liu, Cheng Huang, Yanling Hu
Software Mentions: 2
Published: over 3 years ago
10.1186/s12870-021-02858-1
The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality
Cited by: 25
Author(s): I. S. E. Bally, Aureliano Bombarely, Alan H. Chambers, Yuval Cohen, Natalie Dillon, David J. Innes, María A. Islas-Osuna, David N. Kuhn, Lukas A. Mueller, Ron Ophir, Aditi Rambani, Amir Sherman, Haidong Yan
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2164-15-718
Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins
Cited by: 72
Author(s): Sean K. McKenzie, Peter R. Oxley, Daniel J. C. Kronauer
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12864-019-6281-1
Genomic insights into mite phylogeny, fitness, development, and reproduction
Cited by: 22
Author(s): Yanxuan Zhang, Xia Chen, Jieping Wang, Zhiqiang Zhang, Hui Wei, Haiyan Yu, Hongkun Zheng, Yong Chen, Lisheng Zhang, Jian Lin, Li Sun, Dongyuan Liu, Juan Tang, Lei Yan, Xuming Li, Min Liu
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12915-021-01033-0
The genome of a wild Medicago species provides insights into the tolerant mechanisms of legume forage to environmental stress
Cited by: 29
Author(s): Tianzuo Wang, Lifei Ren, Caihong Li, Di Zhang, Xiuxiu Zhang, Gang Zhou, Gao Da, Rujin Chen, Yuhui Chen, Zhaolan Wang, Fengling Shi, Andrew Farmer, Yansu Li, Min Zhou, Nevin D. Young, Wenhao Zhang
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-017-4118-3
Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche
Cited by: 12
Author(s): Bo Wang, Xiaofei Liang, Mark L. Gleason, Rong Zhang
Software Mentions: 2
Published: about 7 years ago
10.1186/s13059-014-0557-1
Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species
Cited by: 74
Author(s): Shengbin Li, Bo Li, Cheng Cheng, Zijun Xiong, Qingbo Liu, Jianghua Lai, Hannah V. Carey, Qiong Zhang, Hao Zheng, Shuguang Wei, Hongbo Zhang, Liao Chang, Shiping Liu, Shanxin Zhang, Bing Yu, Xiaofan Zeng, Yong Hou, Wei Nie, Youmin Guo, Teng Chen, Jiuqiang Han, Jian Wang, Jun Wang, Chen Chen, Jiankang Liu, Peter J. Stambrook, Ming Xu, Guojie Zhang, M. Thomas P. Gilbert, Huanming Yang, Erich D. Jarvis, Jun Yu, Jiaqi Yan
Software Mentions: 2
Published: almost 10 years ago
10.1186/gb-2009-10-5-r48
Co-evolutionary networks of genes and cellular processes across fungal species
Cited by: 17
Author(s): Tamir Tuller, Martin Kupiec, Eytan Ruppin
Software Mentions: 1
Published: almost 16 years ago
10.3390/ani11020584
Genetic Adaptations in Mudskipper and Tetrapod Give Insights into Their Convergent Water-to-Land Transition
Cited by: 0
Author(s): Ju‐Wan Kim, Chul Lee, DongAhn Yoo, Heebal Kim
Software Mentions: 1
Published: over 3 years ago
10.1016/j.appet.2013.07.011
The skinny on cocaine: Insights into eating behavior and body weight in cocaine-dependent men
Cited by: 74
Author(s): Karen D. Ersche, Jan Štochl, Jeremy Woodward, Paul C. Fletcher
Software Mentions: 1
Published: almost 11 years ago
10.5194/acp-18-5967-2018
Assessment and economic valuation of air pollution impacts on human health over Europe and the United States as calculated by a multi-model ensemble in the framework of AQMEII3
Cited by: 57
Author(s): Ulaş İm, Jørgen Brandt, Camilla Geels, Kaj Hansen, J. H. Christensen, Mikael Skou Andersen, Efisio Solazzo, Ioannis Kioutsioukis, Ümmügülsüm Alyüz, Alessandra Balzarini, Rocío Baró, Roberto Bellasio, Roberto Bianconi, Johannes Bieser, Augustin Colette, Gabriele Curci, Aidan Farrow, Johannes Flemming, Andrea Fraser, Pedro Jiménez‐Guerrero, Nutthida Kitwiroon, Ching-Ping Liang, Uarporn Nopmongcol, Guido Pirovano, Luca Pozzoli, Marje Prank, Rebecca Rose, Ranjeet S. Sokhi, Paolo Tuccella, Alper Ünal, Marta G. Vivanco, Jason West, Greg Yarwood, Christian Hogrefe, Stefano Galmarini
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2105-12-426
A Bayesian model for gene family evolution
Cited by: 24
Author(s): Liang Liu, Lili Yu, Venugopal Kalavacharla, Zhanji Liu
Software Mentions: 1
Published: about 13 years ago
10.1186/s12859-016-1302-4
muBLASTP: database-indexed protein sequence search on multicore CPUs
Cited by: 11
Author(s): Jing Zhang, Sanchit Misra, Hao Wang, Wu-chun Feng
Software Mentions: 1
Published: about 8 years ago
10.1186/1471-2105-13-S15-S5
Computational workflow for analysis of gain and loss of genes in distantly related genomes
Cited by: 7
Author(s): Andrey A. Ptitsyn, Leonid L. Moroz
Software Mentions: 1
Published: about 12 years ago
10.1186/s12915-018-0520-9
Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum
Cited by: 51
Author(s): Amelia R.I. Lindsey, Yogeshwar D. Kelkar, Xin Wu, Dan Sun, Ellen O. Martinson, Zhichao Yan, Paul F. Rugman‐Jones, Daniel Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, Harshavardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Gōngyín Yè, Richard A. Gibbs, Stephen Richards, Soojin V. Yi, Richard Stouthamer, John H. Werren
Software Mentions: 1
Published: over 6 years ago
10.1186/1471-2148-10-51
Functional evolution of the trace amine associated receptors in mammals and the loss of TAAR1 in dogs
Cited by: 31
Author(s): Eric J. Vallender, Zhihua Xie, Susan V. Westmoreland, Gregory M. Miller
Software Mentions: 1
Published: almost 15 years ago
10.1186/s12862-020-01650-3
Expansions and contractions in gene families of independently-evolved blood-feeding insects
Cited by: 9
Author(s): Lucas Freitas, Mariana F. Nery
Software Mentions: 1
Published: over 4 years ago
10.1186/s12862-015-0315-3
Amino acid transporter expansions associated with the evolution of obligate endosymbiosis in sap-feeding insects (Hemiptera: sternorrhyncha)
Cited by: 22
Author(s): Romain A. Dahan, Rebecca P. Duncan, Alex C. C. Wilson, Liliana M. Dávalos
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2148-10-318
The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina
Cited by: 4
Author(s): Aminael Sánchez-Rodríguez, Cindy Martens, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
Software Mentions: 1
Published: about 14 years ago
10.1186/s12862-017-0925-z
Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life
Cited by: 41
Author(s): Chao Tong, Fei Tian, Cunfang Zhang, Kai Zhao
Software Mentions: 1
Published: over 7 years ago
10.1186/s12864-016-2409-8
The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions
Cited by: 15
Author(s): Su Mei Yew, Chai Ling Chan, Chee Sian Kuan, Yue Fen Toh, Yun Fong Ngeow, Shiang Ling Na, Kok Wei Lee, Chee-Choong Hoh, Wai-Yan Yee, Kee Peng Ng
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12864-019-5590-8
Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects
Cited by: 10
Author(s): Charikleia Karageorgiou, Víctor Gámez-Visairas, Rosa Tarrı́o, Francisco Rodríguez‐Trelles
Software Mentions: 1
Published: over 5 years ago
10.1186/s12864-020-6642-9
Comparative transcriptomic analysis of deep- and shallow-water barnacle species (Cirripedia, Poecilasmatidae) provides insights into deep-sea adaptation of sessile crustaceans
Cited by: 14
Author(s): Zhibin Gan, Jianbo Yuan, Xinming Liu, Dong Dong, Fuhua Li, Xinzheng Li
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-019-5825-8
Lignocellulose degradation in isopods: new insights into the adaptation to terrestrial life
Cited by: 22
Author(s): Marius Bredon, Benjamin Herran, Baptiste Lheraud, Joanne Bertaux, Pierre Grève, Bouziane Moumen, Didier Bouchon
Software Mentions: 1
Published: over 5 years ago
10.1186/s12864-021-07852-3
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids
Cited by: 8
Author(s): Weixiong Zhang, Guoqiang Zhang, Peng Zeng, Yongqiang Zhang, Haiyuan Hu, Zhong‐Jian Liu, Jing Cai
Software Mentions: 1
Published: over 3 years ago
10.1186/1471-2164-13-218
Large-scale analysis of microRNA evolution
Cited by: 53
Author(s): José Afonso Guerra-Assunção, Anton J. Enright
Software Mentions: 1
Published: almost 13 years ago
10.1186/s12864-019-6278-9
Massive expansion and diversity of nicotinic acetylcholine receptors in lophotrochozoans
Cited by: 28
Author(s): Yu Jiao, Yanyan Cao, Zhe Zheng, Ming Liu, Ximing Guo
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12864-015-1771-2
Trends in genome dynamics among major orders of insects revealed through variations in protein families
Cited by: 5
Author(s): Nadav Rappoport, Michal Linial
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-015-2187-8
Multicopy gene family evolution on primate Y chromosomes
Cited by: 18
Author(s): Ana‐Hermina Ghenu, Benjamin M. Bolker, Don J. Melnick, Ben Evans
Software Mentions: 1
Published: over 8 years ago
10.1186/s12864-017-3590-0
Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors
Cited by: 2
Author(s): Sara J. Oppenheim, Jeffrey Rosenfeld, Rob DeSalle
Software Mentions: 1
Published: over 7 years ago
10.1136/bmjopen-2016-015099
A review of rate control in atrial fibrillation, and the rationale and protocol for the RATE-AF trial
Cited by: 33
Author(s): Dipak Kotecha, Melanie Calvert, Jonathan J Deeks, Michael Griffith, Paulus Kirchhof, Gregory Y.H. Lip, Samir Mehta, Gemma Slinn, Mary Stanbury, Richard P. Steeds, Jonathan N. Townend
Software Mentions: 1
Published: over 7 years ago
10.1093/bioinformatics/btaa1086
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
Cited by: 3
Author(s): Anna Abramova, Adriana Osińska, Haveela Kunche, Emil Burman, Johan Bengtsson‐Palme
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13068-018-1201-1
Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway
Cited by: 37
Author(s): Chunrong Zhong, Maozhen Han, Shaojun Yu, Pengshuo Yang, Hongjun Li, Kang Ning
Software Mentions: 1
Published: over 6 years ago
10.3390/ma12233829
2-D Selector Simulation Studies on Grain Selection for Single Crystal Superalloy of CM247LC
Cited by: 2
Author(s): Hang Zhang, Xintao Zhu, Fu Wang, Dexin Ma
Software Mentions: 1
Published: about 5 years ago
10.3390/ma14113055
Material Databases and Validation in Modelling the Structure of Castings Using the Cellular Automaton Method
Cited by: 0
Author(s): Jakub Hajkowski, Robert Sika, Michał Rogalewicz, Paweł Popielarski, Waldemar Matysiak, Stanisław Legutko
Software Mentions: 1
Published: over 3 years ago
10.7717/peerj.8914
First de novo whole genome sequencing and assembly of the bar-headed goose
Cited by: 5
Author(s): Wen Wang, Fang Wang, Rongkai Hao, Aizhen Wang, Kirill Sharshov, Alexey Druzyaka, Zhuoma Lancuo, Yuetong Shi, Shuo Feng
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pgen.1003909
Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi
Cited by: 89
Author(s): Tejashwari Meerupati, Karl-Magnus Andersson, Eva Friman, Dharmendra Kumar, Anders Tunlid, Dag Ahrén
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pgen.0030197
Gene Family Evolution across 12 Drosophila Genomes
Cited by: 315
Author(s): Matthew W. Hahn, Mira V. Han, Sang-Gook Han
Software Mentions: 1
Published: about 17 years ago
10.1371/journal.pgen.1009724
Cholecystokinin-like peptide mediates satiety by inhibiting sugar attraction
Cited by: 7
Author(s): Di Guo, Yijie Zhang, Su Zhang, Jian Li, Chao Guo, Yufeng Pan, Ning Zhang, Chenxi Liu, Ya-Long Jia, Chenyu Li, Jun‐Yu Ma, Dick R. Nässel, Cong‐Fen Gao, Shun‐Fan Wu
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0209644
Subjective ratings and emotional recognition of children’s facial expressions from the CAFE set
Cited by: 12
Author(s): Marília Prada, Margarida Garrido, Cláudia Camilo, David L. Rodrigues
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0002944
The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes
Cited by: 241
Author(s): Luiz Gustavo Guedes Corrêa, Diego Mauricio Riaño-Pachón, Carlos G. Schrago, Renato Vicentini, Bernd Mueller‐Roeber, Michel Vincentz
Software Mentions: 1
Published: over 16 years ago
10.1371/journal.pone.0099480
Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions
Cited by: 5
Author(s): Ryan M. Ames, Daniel Money, Simon C. Lovell
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0196303
Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses
Cited by: 39
Author(s): Xiaofei Liang, Bo Wang, Qiuyue Dong, Lingnan Li, Jeffrey A. Rollins, Rong Zhang
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0036146
The Genome of Ganderma lucidum Provide Insights into Triterpense Biosynthesis and Wood Degradation
Cited by: 75
Author(s): Dongbo Liu, Jing Gong, Wenkui Dai, Xincong Kang, Zhuo Huang, Hongmei Zhang, Wei Liu, Le Liu, Junping Ma, Xia Zhi-lan, Yuxin Chen, Yuewen Chen, Depeng Wang, Peixiang Ni, An‐Yuan Guo, Xingyao Xiong
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0008345
Molecular Evolution of Drosophila Cuticular Protein Genes
Cited by: 48
Author(s): Robert S. Cornman
Software Mentions: 1
Published: almost 15 years ago
10.1038/s42003-021-02602-3
A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest
Cited by: 12
Author(s): Daniel Powell, Ewald Große-Wilde, Paal Krokene, Amit Roy, Amrita Chakraborty, Christer Löfstedt, Heiko Vogel, Martin N. Andersson, Fredrik Schlyter
Software Mentions: 1
Published: about 3 years ago