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: pypi: EVM
https://packages.ecosyste.ms/registries/pypi.org/packages/EVM
The Extreme Value Machine
3 versions
Latest release: over 6 years ago
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Papers Mentioning EVM 152
10.3390/e22020203
An Analysis of Smart Contracts Security Threats Alongside Existing SolutionsCited by: 18
Author(s): Antonio López Vivar, Alberto Turégano Castedo, Ana Lucila Sandoval Orozco, Luis Javier García Villalba
Software Mentions: 13
Published: over 4 years ago
10.1002/advs.201901850
<i>Mesostigma viride</i> Genome and Transcriptome Provide Insights into the Origin and Evolution of StreptophytaCited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: about 5 years ago
10.1038/s42003-020-01637-2
Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplicationCited by: 23
Author(s): Wenyan Nong, Zhe Qu, Yiqian Li, Tom Barton-Owen, Hon Kit Wong, Ho Yin Yip, Hoi Ting Lee, Satya Narayana, Tobias Baril, Thomas Swale, Jianquan Cao, Ting‐Fung Chan, Hoi Shan Kwan, Sai Ming Ngai, Gianni Panagiotou, Pei‐Yuan Qian, Jian Qiu, Kevin Yuk‐Lap Yip, Normaz Wana Ismail, Siddhartha Pati, Akbar John, Stephen S. Tobe, William G. Bendena, Siu Gin Cheung, Alexander Hayward, Jerome H.L. Hui
Software Mentions: 8
Published: almost 4 years ago
10.7554/eLife.36495
Firefly genomes illuminate parallel origins of bioluminescence in beetlesCited by: 95
Author(s): Timothy R. Fallon, Sarah E. Lower, Ching-Ho Chang, Manabu Bessho-Uehara, Gavin J. Martin, Adam J. Bewick, Megan G Behringer, Humberto Julio Debat, Isaac Wong, John C. Day, Anton Suvorov, Christian J. Silva, Kathrin F. Stanger‐Hall, David W. Hall, Robert J. Schmitz, David R. Nelson, Sara M. Lewis, Shuji Shigenobu, Seth Bybee, Amanda M. Larracuente, Yuichi Oba, Jing‐Ke Weng
Software Mentions: 8
Published: about 6 years ago
10.1111/pbi.13210
The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barleyCited by: 39
Author(s): Miao Liu, Yan Li, Yanling Ma, Qiang Zhao, Jiri Stiller, Qi Feng, Qifeng Tian, Dengcai Liu, Bin Han, Chunji Liu
Software Mentions: 6
Published: over 5 years ago
10.1038/s42003-018-0122-7
Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fishCited by: 44
Author(s): Marianna Pauletto, Tereza Manousaki, Serena Ferraresso, Massimiliano Babbucci, Alexandros Tsakogiannis, Bruno Louro, Nicola Vitulo, Viet Ha Quoc, R. Carraro, Daniela Bertotto, Rafaella Franch, Francesco Maroso, Muhammad Aslam, Anna K. Sonesson, Barbara Simionati, G Malacrida, Alessandro Cestaro, Stefano Caberlotto, Elena Sarropoulou, C. C. Mylonas, Deborah M. Power, Tomaso Patarnello, Adelino V.M. Canário, Costas S. Tsigenopoulos, Luca Bargelloni
Software Mentions: 5
Published: about 6 years ago
10.1007/s00253-016-7588-3
Ploidy influences the functional attributes of de novo lager yeast hybridsCited by: 65
Author(s): Kristoffer Krogerus, Mikko Arvas, Matteo De Chiara, Frederico Magalhães, Laura Mattinen, Merja Oja, Virve Vidgren, Jia-Xing Yue, Gianni Liti, Brian Gibson
Software Mentions: 5
Published: over 8 years ago
10.3390/s18020574
Patch Transporter: Incentivized, Decentralized Software Patch System for WSN and IoT EnvironmentsCited by: 17
Author(s): Jong-Hyup Lee
Software Mentions: 5
Published: over 6 years ago
10.1093/gigascience/giz071
The genome assembly and annotation of yellowhorn (Xanthoceras sorbifolium Bunge)Cited by: 35
Author(s): Liang Qiang, Huayang Li, Shouke Li, Fuling Yuan, Jiantong Sun, Qicheng Duan, Qingyun Li, Rui Zhang, Ya Lin Sang, Nian Wang, Xiangwen Hou, Ke Yang, Jian Ning Liu, Long Yang
Software Mentions: 5
Published: over 5 years ago
10.1186/s13742-016-0134-5
Genome sequence of the olive tree, Olea europaeaCited by: 158
Author(s): Fernando Cruz, Irene Julca, Jèssica Gómez-Garrido, Damian Loska, Marina Marcet‐Houben, Emilio Cano, Beatriz Galán, Leonor Frías, Paolo Ribeca, Sophia Derdak, Marta Gut, Manuel Sánchez-Fernández, José Luis Garcı́a, Pablo Vargas, Tyler Alioto, Toni Gabaldón
Software Mentions: 5
Published: over 8 years ago
10.1038/s41438-021-00487-1
Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit developmentCited by: 34
Author(s): Anzhen Fu, Qing Wang, Jianlou Mu, Lili Ma, Changlong Wen, Xiaoyan Zhao, Lipu Gao, Jian Li, Kai Shi, Yunxiang Wang, Xuechuan Zhang, Xuewen Zhang, Fengling Wang, Donald Grierson, Jinhua Zuo
Software Mentions: 5
Published: almost 4 years ago
10.1155/2019/4767354
GAAP: A Genome Assembly + Annotation PipelineCited by: 5
Author(s): Jinhwa Kong, Sun Huh, Jung-Im Won, Jeehee Yoon, Baeksop Kim, Ki-Yong Kim
Software Mentions: 5
Published: over 5 years ago
10.1111/pbi.12926
Genome and evolution of the shade‐requiring medicinal herb <i>Panax ginseng</i>Cited by: 120
Author(s): Nam Hoon Kim, Murukarthick Jayakodi, Sang Choon Lee, Beom Soon Choi, Woojong Jang, Junki Lee, Hyun Hee Kim, Nomar Espinosa Waminal, Meiyappan Lakshmanan, Binh van Nguyen, Yun Sun Lee, Hyun Seung Park, Hyun Jo Koo, Jee Young Park, Sampath Perumal, Ho Jun Joh, Hana Lee, Jin‐Kyung Kim, In Seo Kim, Kyung‐Hee Kim, Lokanand Koduru, Kyo Bin Kang, Sang Hyun Sung, Yeisoo Yu, Daniel Park, Doil Choi, Eun-Young Seo, Seungill Kim, Young Chang Kim, Dong Yun Hyun, Youn‐Il Park, Chang-Soo Kim, Tae Ho Lee, Hyun Uk Kim, Moon-Soo Soh, Liu Yi, Jun Gyo In, Heui-Soo Kim, Yong Min Kim, Deok Chun Yang, Rod A. Wing, Dong-Yup Lee, Andrew H. Paterson, Tae Jin Yang
Software Mentions: 5
Published: over 6 years ago
10.1186/s12864-020-6495-2
Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic featuresCited by: 8
Author(s): Yang Li, Menggen Dalai, Rongguo Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
Software Mentions: 5
Published: almost 5 years ago
10.1111/pbi.13115
Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseedCited by: 48
Author(s): Jun Zou, Limin Mao, Jie Qiu, Meng Wang, Jia Lu, Dongya Wu, Zhesi He, Meihong Chen, Yifei Shen, Enhui Shen, Yongji Huang, Ruiyuan Li, Dandan Hu, Lei Shi, Kai Wang, Qian Zhu, Chu-Yu Ye, Ian Bancroft, Graham J. King, Jinling Meng
Software Mentions: 5
Published: over 5 years ago
10.1038/s42003-021-01659-4
Amynthas corticis genome reveals molecular mechanisms behind global distributionCited by: 4
Author(s): Xing Wang, Yi Zhang, Yufeng Zhang, Mingming Kang, Yuanbo Li, Samuel W. James, Yang Yang, Yang Bi, Hao Jiang, Yi Zhao, Zhenjun Sun
Software Mentions: 5
Published: almost 4 years ago
10.1111/1755-0998.13257
High quality genome of <i>Erigeron breviscapus</i> provides a reference for herbal plants in AsteraceaeCited by: 19
Author(s): Simei He, Dong Xiao, Guanghui Zhang, Wei Fan, Shengchang Duan, Hong Shi, Dawei Li, Rui Li, Cuizhi Geng, Guangqiang Long, Yan Zhao, Mo Chen, Mi Yan, Jianli Yang, Yingchun Lu, Yanli Zhou, Wei Chen, Yang Dong, Shengchao Yang
Software Mentions: 5
Published: about 4 years ago
10.1002/ece3.5965
Draft genome of the famous ornamental plant <i>Paeonia suffruticosa</i>Cited by: 31
Author(s): Shuzuo Lv, Shu Cheng, Zhanying Wang, Shiming Li, Xin Jin, Lei Lan, Bing Yang, Kun Yu, Xiliang Ni, Ning Li, Xiaogai Hou, Gang Huang, Jie Wang, Yang Dong, Erqiang Wang, Jun Huang, Gengyun Zhang, Zhang Can-jun
Software Mentions: 4
Published: over 4 years ago
10.1111/pbi.13260
The pomegranate (<i>Punica granatum</i>L.) draft genome dissects genetic divergence between soft‐ and hard‐seeded cultivarsCited by: 59
Author(s): Xiang Luo, Haoxian Li, Zhuona Wu, Wen Yao, Peng Zhao, Da Cao, Haiyan Yu, Kaidi Li, Krishna Poudel, Dan Zhao, Fuhong Zhang, Xiaocong Xia, Lina Chen, Qi Wang, Dan Jing, Shangyin Cao
Software Mentions: 4
Published: about 5 years ago
10.1186/gb-2008-9-1-r7
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced AlignmentsCited by: 2,092
Author(s): Brian J. Haas, Steven L. Salzberg, Wei Zhu, Mihaela Pertea, Jonathan Allen, Joshua Orvis, Owen White, C. Robin Buell, Jennifer Wortman
Software Mentions: 4
Published: almost 17 years ago
10.1038/srep46553
Genome sequence of Plasmopara viticola and insight into the pathogenic mechanismCited by: 60
Author(s): Ling Yin, Yunhe An, Junjie Qu, Xinlong Li, Yali Zhang, Ian B. Dry, Huijuan Wu, Jiang Lu
Software Mentions: 4
Published: over 7 years ago
10.1093/gigascience/giy101
The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptationCited by: 56
Author(s): Conghui Liu, Yan Zhang, Yingxue Ren, Hengchao Wang, Shuqu Li, Fan Jiang, Lei Yin, Xi Qiao, Guojie Zhang, Wanqiang Qian, Bo Liu, Wei Fan
Software Mentions: 4
Published: over 6 years ago
10.1186/s13068-018-1060-9
Deciphering lignocellulose deconstruction by the white rot fungus Irpex lacteus based on genomic and transcriptomic analysesCited by: 33
Author(s): Xing Qin, Xiaoyun Su, Huiying Luo, Rui Ma, Bin Yao, Fuying Ma
Software Mentions: 4
Published: over 6 years ago
10.1093/gigascience/giz112
Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)Cited by: 49
Author(s): Yu Xing, Yang Liu, Qing Zhang, Xinghua Nie, Yamin Sun, Zhiyong Zhang, Huchen Li, Kefeng Fang, Guangpeng Wang, Hongwen Huang, Ton Bisseling, Qingqin Cao, Ling Qin
Software Mentions: 4
Published: about 5 years ago
10.1534/g3.119.400413
The Genome Sequence of the Eastern Woodchuck (<i>Marmota monax</i>) – A Preclinical Animal Model for Chronic Hepatitis BCited by: 13
Author(s): Tyler Alioto, Fernando Cruz, Jèssica Gómez-Garrido, Miriam Triyatni, Marta Gut, Leonor Frías, Anna Esteve‐Codina, Stephan Menne, Anna Kiialainen, Nadine Kumpesa, Fabian Birzele, Roland Schmucki, Ivo Gut, Olivia Spleiss
Software Mentions: 4
Published: almost 5 years ago
10.1093/gigascience/giz067
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-CCited by: 52
Author(s): Changming Bai, Lusheng Xin, Umberto Rosani, Biao Wu, Qingchen Wang, Xiaoke Duan, Zhihong Liu, Wang Chongming
Software Mentions: 4
Published: over 5 years ago
10.1007/978-3-030-53288-8_10
Synthesis of Super-Optimized Smart Contracts Using Max-SMTCited by: 12
Author(s): Elvira Albert, Pablo Gordillo, Albert Rubio, Maria Anna Schett
Software Mentions: 4
Published: almost 5 years ago
10.1038/sdata.2018.305
The sequence and de novo assembly of hog deer genomeCited by: 7
Author(s): Wei Wang, Yan Huang, Shiyi Chen, Zhenzhen Li, Jun Yi, Lili Niu, Jia-Po Deng, Weigang Chen, Yunfeng Pu, Xianbo Jia, Yu Qu, Ang Chen, Yan Zhong, Xiaoxi Yu, Shuai Pang, Wanlong Huang, Yue Han, Guangjian Liu, Jianqiu Yu
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12864-015-1660-8
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungusCited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.pone.0121961
SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft GenomeCited by: 34
Author(s): Jeremy R. Shearman, Duangjai Sangsrakru, Nukoon Jomchai, Panthita Ruang-areerate, Chutima Sonthirod, Chaiwat Naktang, Kanikar Theerawattanasuk, Somvong Tragoonrung, Sithichoke Tangphatsornruang
Software Mentions: 3
Published: over 9 years ago
10.1038/s42003-018-0089-4
De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolutionCited by: 19
Author(s): Zhigang Wu, Dongming Fang, Rui Yang, Fei Gao, Xingyu An, Xiaoxuan Zhuo, Yafei Li, Chuandeng Yi, Tao Zhang, Chengzhi Liang, Peng Cui, Zhukuan Cheng, Qiong Luo
Software Mentions: 3
Published: over 6 years ago
10.1038/s42003-020-01172-0
Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expressionCited by: 23
Author(s): Ryoichi Yano, Tohru Ariizumi, Satoko Nonaka, Yoichi Kawazu, Silin Zhong, Lukas A. Mueller, James Giovannoni, Jocelyn K. C. Rose, Hiroshi Ezura
Software Mentions: 3
Published: about 4 years ago
10.1186/s12864-019-6414-6
Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae familyCited by: 26
Author(s): Sivasubramanian Rajarammohan, Kumar Paritosh, Deepak Pental, Jagreet Kaur
Software Mentions: 3
Published: almost 5 years ago
10.1093/gigascience/giz070
Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genomeCited by: 42
Author(s): Quanxin Bi, Yang Zhao, Wei Du, Ying Lu, Gui Liu, Zhimin Zheng, Haiyan Yu, Yubo Cui, Zhi Liu, Tianpeng Cui, Deshi Cui, Xiaojuan Liu, Yingchao Li, Fan Siqi, Xiaoyu Hu, Guanghui Fu, Jian Ding, Chengjiang Ruan, Libing Wang
Software Mentions: 3
Published: over 5 years ago
10.1093/gigascience/giy074
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrubCited by: 18
Author(s): Fei Gao, Xue Wang, Xuming Li, Mingyue Xu, Huayun Li, Merhaba Abla, Han Sun, Shanjun Wei, Jinchao Feng, Yijun Zhou
Software Mentions: 3
Published: over 6 years ago
10.1093/gigascience/giw004
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera)Cited by: 35
Author(s): Lin Wang, Nan Tang, Xinlei Gao, Zhaoxia Chang, Liqin Zhang, Guohui Zhou, Dongyang Guo, Zhen Zeng, Wenjie Li, Ibukun A. Akinyemi, Huanming Yang, Qingfa Wu
Software Mentions: 3
Published: almost 8 years ago
10.1038/s41438-020-00449-z
A chromosome-level reference genome of non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis]Cited by: 41
Author(s): Ying Li, Gao-Feng Liu, Liming Ma, Tongkun Liu, Changwei Zhang, Dong Xiao, Hongkun Zheng, Fei Chen, Xilin Hou
Software Mentions: 3
Published: almost 4 years ago
10.3389/fmicb.2021.682356
Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SHCited by: 3
Author(s): Bei Lü, Guo Wu, Yu Sun, Liang S. Zhang, Xiao Wu, Wei Jiang, Peng Li, Yan Huang, Jin B. Wang, Yong Zhao, Hua Liu, Li Song, Qin Mo, Ai H. Pan, Yan Yang, Xuan Long, Wei Cui, Chao Zhang, Xu Wang, Xue Tang
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-015-1588-z
Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandicaCited by: 87
Author(s): Selene L. Fernández-Valverde, Andrew Calcino, Bernard M. Degnan
Software Mentions: 3
Published: over 9 years ago
10.1186/1471-2164-14-49
Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomesCited by: 54
Author(s): Walter L. Eckalbar, Elizabeth Hutchins, Glenn J. Markov, April N. Allen, Jason J. Corneveaux, Kerstin Lindblad‐Toh, Federica Di Palma, Jessica Alföldi, Matthew J. Huentelman, Kenro Kusumi
Software Mentions: 3
Published: almost 12 years ago
10.3389/fpls.2020.525102
The Eruca sativa Genome and Transcriptome: A Targeted Analysis of Sulfur Metabolism and Glucosinolate Biosynthesis Pre and PostharvestCited by: 11
Author(s): Luke Bell, Martin J. Chadwick, Manik Puranik, Richard Tudor, Lisa Methven, Sue Kennedy, Carol Wagstaff
Software Mentions: 3
Published: about 4 years ago
10.1186/1471-2164-14-498
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functionsCited by: 159
Author(s): Andreas Zimmer, Daniel Lang, Karol Buchta, Stéphane Rombauts, Tomoaki Nishiyama, Mitsuyasu Hasebe, Yves Van de Peer, Stefan A. Rensing, Ralf Reski
Software Mentions: 3
Published: over 11 years ago
10.1093/gbe/evu291
Genomics of Ecological Adaptation in Cactophilic DrosophilaCited by: 47
Author(s): Yolanda Guillén, Núria Rius, Alejandra Delprat, Anna Williford, Francesc Muyas, Marta Puig, Sònia Casillas, Miquel Ràmia, Raquel Egea, Bárbara Negre, Gisela Mir, Jordi Camps, Valentí Moncunill, Francisco J. Ruíz-Ruano, J. Cabrero, Leonardo Gomes de Lima, Guilherme Borges Dias, Jerônimo C. Ruiz, Aurélie Kapusta, Jordi García-Más, Marta Gut, David Torrents, Juan Pedro M. Camacho, Gustavo C. S. Kuhn, Cédric Feschotte, Andrew G. Clark, Esther Betrán, Antonio Barbadilla, Alfredo Ruíz
Software Mentions: 3
Published: almost 10 years ago
10.3390/genes11050483
A High-Quality Genome Sequence of Model Legume Lotus japonicus (MG-20) Provides Insights into the Evolution of Root Nodule SymbiosisCited by: 24
Author(s): Haoxing Li, Jun Fan, Ping Wu, Ke Wang, Yangrong Cao
Software Mentions: 3
Published: over 4 years ago
10.1038/s41438-019-0164-0
Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica speciesCited by: 46
Author(s): Sun DeLing, Chunguo Wang, Xiaoli Zhang, Wenlin Zhang, Hanmin Jiang, Xingwei Yao, Li‐Li Liu, Wen Zhang, Guobao Niu, Xiaozheng Shan
Software Mentions: 3
Published: over 5 years ago
10.1038/s41438-020-0328-y
A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensisCited by: 18
Author(s): Jinghe Xie, Haifeng Zhao, Kunpeng Li, Rui Zhang, Yanling Jiang, Meimei Wang, Xijie Guo, Ben Yu, Hongzhi Kong, Yuannian Jiao, Guiyun Xu
Software Mentions: 3
Published: over 4 years ago
10.1038/s41438-020-00424-8
Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana KoidzCited by: 24
Author(s): Jian Zhang, Huwei Yuan, Yujuan Li, Yanhong Chen, Guoyuan Liu, Meixia Ye, Chunmei Yu, Bolin Lian, Fei Zhong, Yuna Jiang, Junfeng Xu
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13068-019-1466-z
Heterozygous diploid structure of Amorphotheca resinae ZN1 contributes efficient biodetoxification on solid pretreated corn stoverCited by: 21
Author(s): Xia Yi, Qinghai Gao, Lei Zhang, Xia Wang, Yanqing He, Fengxian Hu, Jian Zhang, Gen Zou, Shihui Yang, Zhihua Zhou, Jie Bao
Software Mentions: 3
Published: over 5 years ago
10.1080/21501203.2017.1419995
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymesCited by: 11
Author(s): Wladimir Mardones, Alex Di Génova, María Paz Cortés, Dante Travisany, Alejandro Maass, Jaime Eyzaguirre
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41438-021-00632-w
High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancyCited by: 30
Author(s): Yuhao Gao, Qinsong Yang, Xue Yan, Xinyue Wu, Feng Yang, Jianzhao Li, Jia Wei, Junbei Ni, Mudassar Ahmad, Songling Bai, Yuanwen Teng
Software Mentions: 3
Published: about 3 years ago
10.1186/1471-2164-14-75
Draft genome sequence of the rubber tree Hevea brasiliensisCited by: 214
Author(s): Azimah Abd Rahman, Abhilash O Usharraj, Biswapriya B. Misra, Gincy P. Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Feong Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz, Anton Yuryev, Bjarne Knudsen, Alexandre Dionne‐Laporte, Nokuthula Peace Mchunu, Qingyi Yu, Brennick J. Langston, Tracey Freitas, Aaron G. Young, Rui Chen, Lei Wang, Nazalan Najimudin, Jennifer A. Saito, Maqsudul Alam
Software Mentions: 3
Published: almost 12 years ago
10.1111/pbi.13132
Genome sequencing and <scp>CRISPR</scp>/Cas9 gene editing of an early flowering Mini‐Citrus (<i>Fortunella hindsii</i>)Cited by: 76
Author(s): Chenqiao Zhu, Xiongjie Zheng, Yue Huang, Junli Ye, Peng Chen, Chenglei Zhang, Fei Zhao, Zongzhou Xie, Siqi Zhang, Nan Wang, Hang Li, Lun Wang, Xiaomei Tang, Lijun Chai, Qiang Xu, Xiuxin Deng
Software Mentions: 3
Published: over 5 years ago
10.1002/pld3.232
Draft genomes of two outcrossing wild rice, <i>Oryza rufipogon</i> and <i>O. longistaminata</i> , reveal genomic features associated with mating‐system evolutionCited by: 8
Author(s): Wei Li, Qun‐Jie Zhang, Ting Zhu, Yan Tong, Kui Li, Cong Shi, Yun Zhang, Yun‐Long Liu, Jianjun Jiang, Yuan Liu, Enhua Xia, Hui Huang, Liping Zhang, Dan Zhang, Chao Shi, Wenkai Jiang, Yanjie Zhao, Shu‐Yan Mao, Jun-Ying Jiao, Peng Xu, Lili Yang, Li‐Zhi Gao
Software Mentions: 3
Published: over 4 years ago
10.1038/s41438-021-00612-0
A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesisCited by: 37
Author(s): Jianye Chen, Fangfang Xie, Yanze Cui, Canbin Chen, Wang-jin Lu, Xiaodi Hu, Qian Hua, Jing Zhao, Zhengkai Wu, Gao Da, Zhi-ke Zhang, Wenkai Jiang, Sun Qi-zhong, Guibing Hu, Yonghua Qin
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pbio.2003790
The sea cucumber genome provides insights into morphological evolution and visceral regenerationCited by: 164
Author(s): Xiaojun Zhang, Lina Sun, Jianbo Yuan, Yamin Sun, Yi Gao, Libin Zhang, Shihao Li, Hui Dai, Jean‐François Hamel, Xianhui Qin, Yang Yu, Shilin Liu, Wenchao Lin, Kaimin Guo, Shiwei Jin, Peng Xu, Kenneth B. Storey, Pin Huan, Tao Zhang, Yi Zhou, Jiquan Zhang, Chenggang Lin, Xiaoni Li, Lili Xing, Da Huo, Mingzhe Sun, Lei Wang, Annie Mercier, Fuhua Li, Hongsheng Yang, Jianhai Xiang
Software Mentions: 3
Published: about 7 years ago
10.1371/journal.pbio.2002527
Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombinationCited by: 65
Author(s): Sheng Sun, Vikas Yadav, R. Blake Billmyre, Christina A. Cuomo, Minou Nowrousian, Liuyang Wang, Jean-Luc Souciet, Teun Boekhout, Betina M. Porcel, Patrick Wincker, Joshua A. Granek, Kaustuv Sanyal, Joseph Heitman
Software Mentions: 3
Published: about 7 years ago
10.1038/s41438-021-00505-2
Genome of a citrus rootstock and global DNA demethylation caused by heterograftingCited by: 43
Author(s): Yue Huang, Yuantao Xu, Xiaolin Jiang, Huang Yu, Hui-Hui Jia, Chunming Tan, Gang Hu, Yibo Hu, Muhammad Junaid Rao, Xiuxin Deng, Qiang Xu
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pgen.1004078
Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal FungusCited by: 229
Author(s): Kui Lin, Erik Limpens, Zhonghua Zhang, Sergey Ivanov, Diane G. O. Saunders, Desheng Mu, Erli Pang, Huifen Cao, Hwangho Cha, Tao Lin, Qian Zhou, Yi Shang, Ying Liu, Teena Sharma, Robin van Velzen, N.C.A. de Ruijter, Duur K. Aanen, Joe Win, Sophien Kamoun, Ton Bisseling, René Geurts, Sanwen Huang
Software Mentions: 3
Published: almost 11 years ago
10.1038/s41597-019-0291-3
A de novo genome assembly of the dwarfing pear rootstock Zhongai 1Cited by: 23
Author(s): C. Ou, Fei Wang, Jiahong Wang, Li Song, Yanjie Zhang, Ming Fang, Li Ma, Yanan Zhao, Shuling Jiang
Software Mentions: 3
Published: almost 5 years ago
10.1093/gigascience/giaa114
Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genomeCited by: 14
Author(s): Yan Li, Guangliang Gao, Yu Lin, Silu Hu, Yi Luo, Guosong Wang, Long Jin, Qigui Wang, Jiwen Wang, Qianzi Tang, Mingzhou Li
Software Mentions: 3
Published: about 4 years ago
10.1093/gigascience/giaa001
A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae)Cited by: 8
Author(s): Martin Pippel, David Jebb, Franziska Patzold, Sylke Winkler, Heiko Vogel, Gene Myers, Michael Hiller, Anna K. Hundsdoerfer
Software Mentions: 3
Published: almost 5 years ago
10.1093/gigascience/gix075
The draft genome sequence of a desert tree Populus pruinosaCited by: 43
Author(s): Wenbo Yang, Kun Wang, Jian Zhang, Jianchao Ma, Jianquan Liu, Tao Ma
Software Mentions: 2
Published: over 7 years ago
10.1186/s12859-017-1874-7
An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithmCited by: 2
Author(s): Biswanath Chowdhury, Arnav Garai, Gautam Garai
Software Mentions: 2
Published: about 7 years ago
10.1186/s12915-018-0572-x
Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated lociCited by: 47
Author(s): Xiukun Li, Lian Wu, Jiahong Wang, Jian Sun, Xia Xiu-hong, Xin Geng, Xuhong Wang, Zhenbo Xu, Quan Xu
Software Mentions: 2
Published: about 6 years ago
10.1186/1471-2164-12-540
RNA-Seq improves annotation of protein-coding genes in the cucumber genomeCited by: 170
Author(s): Zhen Li, Zhonghua Zhang, Peiyao Yan, Sanwen Huang, Zhangjun Fei, Kui Lin
Software Mentions: 2
Published: about 13 years ago
10.1186/1471-2164-13-493
Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolinaCited by: 193
Author(s): Serajul Islam, Samiul Haque, Mohammad Moinul Islam, Emdadul Mannan Emdad, Abdul Karimi Halim, Quazi Md. Mosaddeque Hossen, Zakir Hossain, Borhan Ahmed, Sifatur Rahim, Shibley Rahman, Monjurul Alam, Shaobin Hou, Xuehua Wan, Jennifer A. Saito, Maqsudul Alam
Software Mentions: 2
Published: about 12 years ago
10.1186/1471-2164-9-562
Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closureCited by: 86
Author(s): Robert S. Coyne, Mathangi Thiagarajan, Kristie M. Jones, Jennifer Wortman, Luke J. Tallon, Brian J. Haas, Donna Cassidy-Hanley, Emily A. Wiley, Joshua Smith, Kathleen Collins, Suzanne R. Lee, Mary Couvillion, Yifan Liu, Jyoti Garg, Ronald E. Pearlman, Eileen P. Hamilton, Eduardo Orias, Jonathan A. Eisen, Barbara A. Methé
Software Mentions: 2
Published: almost 17 years ago
10.1186/s12864-015-1380-0
The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of AgaricomycotinaCited by: 42
Author(s): Rahul Sharma, Sören Gassel, Sabine Steiger, Xiaojuan Xia, Robert Bauer, Gerhard Sandmann, Marco Thines
Software Mentions: 2
Published: over 9 years ago
10.1186/s12864-020-6683-0
Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organismsCited by: 15
Author(s): Kyle Tretina, Roger Pellé, Joshua Orvis, Hanzel T. Gotia, Olukemi O. Ifeonu, Priti Kumari, Nicholas C. Palmateer, Shaikh B. Iqbal, Lindsay M. Fry, Vishvanath Nene, Claudia Daubenberger, Richard P. Bishop, Joana C. Silva
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2229-14-99
A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotypeCited by: 204
Author(s): Nicola Vitulo, Claudio Forcato, Elisa Corteggiani Carpinelli, Andrea Telatin, Davide Campagna, Michela D’Angelo, Rosanna Zimbello, Massimiliano Corso, Alessandro Vannozzi, Claudio Bonghi, Margherita Lucchin, Giorgio Valle
Software Mentions: 2
Published: over 10 years ago
10.1111/pbi.13498
A chromosome‐level genome assembly provides insights into ascorbic acid accumulation and fruit softening in guava (<i>Psidium guajava</i>)Cited by: 42
Author(s): Feng Chen, Chao Feng, Xinggu Lin, Shenghui Liu, Yingzhi Li, Ming Kang
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pgen.1006433
The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit TreesCited by: 119
Author(s): Jian Huang, Chunmei Zhang, Xing Zhao, Zhangjun Fei, Kangkang Wan, Zhong Zhang, Xiaoming Pang, Xiao Yin, Yang Bai, Xiaoqing Sun, Li‐Zhi Gao, Ruiqiang Li, Jinbo Zhang
Software Mentions: 2
Published: almost 8 years ago
10.1371/journal.pone.0131296
BGD: A Database of Bat GenomesCited by: 3
Author(s): Jian‐an Fang, Xuan Wang, Shuo Mu, Shuyi Zhang, Dong Dong
Software Mentions: 2
Published: over 9 years ago
10.1007/978-3-030-53288-8_8
End-to-End Formal Verification of Ethereum 2.0 Deposit Smart ContractCited by: 14
Author(s): Daejun Park, Yi Zhang, Grigore Roşu
Software Mentions: 2
Published: almost 5 years ago
10.1002/ece3.4965
Draft genome of the river water buffaloCited by: 34
Author(s): Abdul Awal Mintoo, Hailin Zhang, Chunhai Chen, Mohammad Moniruzzaman, Tingxian Deng, Mahbub Anam, Q. M. E. Huque, Xuanmin Guang, Ping Wang, Zhisheng Zhong, Pengfei Han, Asma Khatun, Tabith M. Awal, Qiang Gao, Xianwei Liang
Software Mentions: 2
Published: over 5 years ago
10.1111/eva.12705
Endangered Père David’s deer genome provides insights into population recoveringCited by: 17
Author(s): Lifeng Zhu, Cao Deng, Xiang Zhao, Jingjing Ding, Huasheng Huang, Shilin Zhu, Zhiwen Wang, Siyu Qin, Yulong Ding, Guoqing Lu, Yang Zhang
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2018.01827
The Genome of a Thermo Tolerant, Pathogenic Albino Aspergillus fumigatusCited by: 12
Author(s): Brian Couger, Tyler Weirick, André R.L. Damásio, Fernando Segato, Maria de Lourdes Teixeira de Moraes Polizeli, Ricardo Sérgio Almeida, Gustavo H. Goldman, Rolf A. Prade
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2021.727105
Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low TemperatureCited by: 5
Author(s): Rui Guo, Manman He, Xiaoqing Zhang, Xiuling Ji, Yunlin Wei, Qilin Zhang, Qí Zhāng
Software Mentions: 2
Published: about 3 years ago
10.3389/fpls.2019.01274
Assembly and Annotation of a Draft Genome of the Medicinal Plant Polygonum cuspidatumCited by: 31
Author(s): Yonghong Zhang, Lanlan Zheng, Yan Zheng, Chao Zhou, Ping Huang, Xiao Xiao, Yi‐Fang Zhao, Xiao‐Jiang Hao, Zhubing Hu, Qinhua Chen, Hongliang Li, Xuanbin Wang, Kenji Fukushima, Guodong Wang, Chen Li
Software Mentions: 2
Published: about 5 years ago
10.1534/g3.118.200318
A High Quality Genome for <i>Mus spicilegus</i>, a Close Relative of House Mice with Unique Social and Ecological AdaptationsCited by: 7
Author(s): Matthew Brian Couger, Lena Arévalo, Polly Campbell
Software Mentions: 2
Published: over 6 years ago
10.1534/g3.119.400030
Diploid Genome Assembly of the Wine Grape CarménèreCited by: 65
Author(s): Andrea Minio, Mélanie Massonnet, Rosa Figueroa‐Balderas, Álvaro Castro, Dario Cantu
Software Mentions: 2
Published: over 5 years ago
10.3390/genes12050692
Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus GenomeCited by: 0
Author(s): Gangcai Xie, Xu Zhang, Feng Lv, Mengmeng Sang, Hairong Hu, Jinqiu Wang, Dong Liu
Software Mentions: 2
Published: over 3 years ago
10.1128/genomeA.00397-17
Draft Genome Sequences of the Antarctic Endolithic Fungi <i>Rachicladosporium antarcticum</i> CCFEE 5527 and <i>Rachicladosporium</i> sp. CCFEE 5018Cited by: 16
Author(s): Claudia Coleine, Sawyer Masonjones, Laura Selbmann, Laura Zucconi, Silvano Onofri, Claudia Pacelli, Jason E. Stajich
Software Mentions: 2
Published: over 7 years ago
10.1093/gbe/evaa263
The Iron-Responsive Genome of the Chiton <i>Acanthopleura granulata</i>Cited by: 35
Author(s): Rebecca M. Varney, Daniel I. Speiser, Carmel McDougall, Bernard M. Degnan, Kevin M. Kocot
Software Mentions: 2
Published: almost 4 years ago
10.1093/gigascience/giz108
High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencingCited by: 35
Author(s): Andreas J. Stroehlein, Pasi K. Korhonen, Teik Min Chong, Yan Lue Lim, Kok‐Gan Chan, Bonnie L. Webster, David Rollinson, Paul J. Brindley, Robin B. Gasser, Neil D. Young
Software Mentions: 2
Published: about 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 analysisCited 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
10.1038/s41438-021-00565-4
The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesisCited by: 30
Author(s): Xiaoyang Xu, Yuan Huang, Xiaqing Yu, Shihua Huang, Yuming Sun, Ting Zhang, Qingquan Liu, Haiying Tong, Yongxia Zhang, Yinjie Wang, Chunxiao Liu, Lei Wu, Menglan Hou, Yongheng Yang
Software Mentions: 2
Published: over 3 years ago
10.1038/s41438-019-0227-2
The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolutionCited by: 38
Author(s): Qingsen Zhu, Yang Xu, Yong Yang, Changfei Guan, Qiuyun Zhang, Jingwen Huang, Don Grierson, Kunsong Chen, Bangchu Gong, Yin X
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41438-021-00495-1
The <i>Corylus mandshurica</i> genome provides insights into the evolution of Betulaceae genomes and hazelnut breedingCited 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 speciesCited 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/s41438-021-00519-w
The genome of the warm-season turfgrass African bermudagrass (<i>Cynodon transvaalensis</i>)Cited by: 16
Author(s): Fengchao Cui, Geli Taier, Manli Li, Xiaoxia Dai, Nan Hang, Xunzhong Zhang, Xiangfeng Wang, Kehua Wang
Software Mentions: 2
Published: over 3 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 ripeningCited 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
10.1371/journal.ppat.1002219
Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilusCited by: 340
Author(s): Taisei Kikuchi, James A. Cotton, Johnathan J. Dalzell, Koichi Hasegawa, Natsumi Kanzaki, Paul McVeigh, Takuma Takanashi, Isheng Jason Tsai, Samuel Assefa, Peter J. A. Cock, Thomas D. Otto, Martin Hunt, Adam J. Reid, Alejandro Sánchez-Flores, Kazuko Tsuchihara, Toshiro Yokoi, Mattias C. Larsson, Johji Miwa, Aaron G. Maule, Norio Sahashi, John T. Jones, Matthew Berriman
Software Mentions: 2
Published: about 13 years ago
10.1038/srep12525
Draft genome of the most devastating insect pest of coffee worldwide: the coffee berry borer, Hypothenemus hampeiCited by: 60
Author(s): Fernando E. Vega, Stuart M. Brown, Hao Chen, Eric Shen, Mridul Nair, Javier A. Ceja-Navarro, Eoin L. Brodie, Francisco Infante, Patrick F. Dowd, Arnab Pain
Software Mentions: 2
Published: over 9 years ago
10.1038/srep23122
Insights into Adaptations to a Near-Obligate Nematode Endoparasitic Lifestyle from the Finished Genome of Drechmeria coniosporaCited by: 31
Author(s): Liwen Zhang, Zhengfu Zhou, Qiannan Guo, Like Fokkens, Márton Miskei, István Pócsi, Wei Zhang, Ming Chen, Lei Wang, Yamin Sun, Bruno Giuliano Garisto Donzelli, Donna M. Gibson, David R. Nelson, Jian Luo, Martijn Rep, Huan Liu, Shengnan Yang, Jing Wang, Stuart B. Krasnoff, Yuquan Xu, István Molnár, Min Lin
Software Mentions: 2
Published: over 8 years ago
10.1038/s41598-019-38680-x
Comparative genomics sheds light on the predatory lifestyle of accipitrids and owlsCited by: 13
Author(s): Chuang Zhou, Jiazheng Jin, Changjun Peng, Qinchao Wen, Guannan Wang, Weideng Wei, Xue Jiang, Megan Price, Kai Cui, Meng Yang, Zhaobin Song, Jing Li, Xiuyue Zhang, Zhenxin Fan, Bisong Yue
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-019-52840-z
Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy MothsCited by: 8
Author(s): François Hébert, Luca Freschi, Gwylim S. Blackburn, Catherine Béliveau, Ken Dewar, Brian Boyle, Dawn E. Gundersen‐Rindal, Michael E. Sparks, Michel Cusson, Richard Hamelin, Roger C. Levesque
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41598-021-93257-x
Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomesCited by: 3
Author(s): Weitao Chen, Ming Zou, Yuefei Li, Shuli Zhu, Xinhui Li, Jie Li
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-94545-2
Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)Cited by: 2
Author(s): Tongqing Zhang, Jiawen Yin, Shengkai Tang, Daming Li, Xiankun Gu, Shengyu Zhang, Weiguo Suo, Xiaowei Liu, Yanshan Liu, Qichen Jiang, Muzi Zhao, Yue Yin, Jianlin Pan
Software Mentions: 2
Published: over 3 years ago
10.1007/978-3-030-51517-1_24
Trust Execution Environment and Multi-party Computation for Blockchain e-Health SystemsCited by: 0
Author(s): Feriel Yahmed, M. Abid
Software Mentions: 2
Published: almost 5 years ago