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
1 version
Latest release: about 1 year ago
16,003 downloads total
Papers Mentioning CAFE 251
10.1038/s42003-021-02197-9
Insights into the genomic evolution of insects from cricket genomesCited by: 35
Author(s): Guillem Ylla, Taro Nakamura, Takehiko Itoh, Rei Kajitani, Atsushi Toyoda, Sayuri Tomonari, Toshikazu Bando, Yoshiyasu Ishimaru, Takahito Watanabe, Masao Fuketa, Yuji Matsuoka, Austen A. Barnett, Sumihare Noji, Taro Mito, Cassandra G. Extavour
Software Mentions: 1
Published: over 3 years ago
10.1038/s42003-020-01541-9
Whole-genome sequencing reveals sex determination and liver high-fat storage mechanisms of yellowstripe goby (Mugilogobius chulae)Cited by: 9
Author(s): Lei Cai, Guocheng Liu, Yuanzheng Wei, Yabing Zhu, Jianjun Li, Zhimin Miao, Meili Chen, Zhen Yue, Lujun Yu, Dong Zhou, Huixin Ye, Wenjing Sun, Haitao Ren
Software Mentions: 1
Published: almost 4 years ago
10.1007/s40572-018-0175-2
Choices Behind Numbers: a Review of the Major Air Pollution Health Impact Assessments in EuropeCited by: 15
Author(s): Ebba Malmqvist, Anna Oudin, Mathilde Pascal, Sylvia Médina
Software Mentions: 1
Published: almost 7 years ago
10.1093/dnares/dsaa031
The genome of walking catfish <i>Clarias magur</i> (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishesCited by: 16
Author(s): Basdeo Kushwaha, Manmohan Pandey, Paramananda Das, Chaitanya Joshi, N. S. Nagpure, Ravindra Kumar, Dinesh Kumar, Suyash Agarwal, Shreya Srivastava, Mahender Singh, Lakshman Sahoo, P. Jayasankar, Prem Kumar Meher, Tejas Shah, Ankit T. Hinsu, Namrata Patel, Prakash G. Koringa, Satyajit Das, Siddhi Patnaik, Amrita Bit, Mir Asif Iquebal, Sarika Jaiswal, J. K. Jena
Software Mentions: 1
Published: almost 4 years ago
10.1093/dnares/dsaa016
Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the NepetoideaeCited by: 18
Author(s): Nolan Bornowski, John Hamilton, Pan Liao, Joshua C. Wood, Natalia Dudareva, C. Robin Buell
Software Mentions: 1
Published: over 4 years ago
10.3390/e22010104
Complexity of Cardiotocographic Signals as A Predictor of LaborCited by: 4
Author(s): João Monteiro-Santos, Teresa Henriques, Inês Nunes, Célia Amorim-Costa, João Bernardes, Cristina Costa-Santos
Software Mentions: 1
Published: almost 5 years ago
10.1186/1476-069X-6-24
Parameter and model uncertainty in a life-table model for fine particles (PM2.5): a statistical modeling studyCited by: 17
Author(s): Marko Tainio, Jouni T. Tuomisto, Otto Hänninen, Juhani Ruuskanen, Matti Jantunen, Juha Pekkanen
Software Mentions: 1
Published: about 17 years ago
10.1186/1476-069X-9-58
Estimation of incidence and social cost of colon cancer due to nitrate in drinking water in the EU: a tentative cost-benefit assessmentCited by: 61
Author(s): Hans van Grinsven, Ari Rabl, Theo M. de Kok
Software Mentions: 1
Published: about 14 years ago
10.1017/S2045796021000263
Enhancing the capabilities of forcibly displaced people: a human development approach to conflict- and displacement-related stressorsCited by: 11
Author(s): Ross White, Catharina van der Boor
Software Mentions: 1
Published: almost 4 years ago
10.3389/fgene.2021.735690
Chromosome-Level Genome Assembly and Annotation of the Fiber Flax (Linum usitatissimum) GenomeCited by: 12
Author(s): Rula Sa, Liuxi Yi, Siqin Bateer, Ming An, Haizhu Bao, Xiaoling Song, Shuyan Wang, Zhiwei Li, Zheng Zhang, Hanipa Hazaisi, Jingjing Guo, Shaofeng Su, Jinhuan Li, Xiaoqing Zhao, Zhanyuan Lu
Software Mentions: 1
Published: about 3 years ago
10.3389/fgene.2021.707546
Chromosome Genome Assembly and Annotation of the Capitulum mitella With PacBio and Hi-C Sequencing DataCited by: 0
Author(s): Duo Chen, Xinqing Zheng, Zhen Huang, Youqiang Chen, Ting Xue, Ké Li, Xiaozhen Rao, Gang Lin
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2020.00812
The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome DuplicationCited by: 10
Author(s): Qiao Yang, Hao Bi, Wenjie Yang, Ting Li, Jiebei Jiang, Lei Zhang, Jianquan Liu, Quanjun Hu
Software Mentions: 1
Published: over 4 years ago
10.3389/fgene.2020.533611
Draft Genome of the European Mouflon (Ovis orientalis musimon)Cited by: 2
Author(s): Rui Su, Xuguang Qiao, Yun Gao, Xiaokai Li, Wei Jiang, Wei Chen, Yixing Fan, Bingwu Zheng, Yanjun Zhang, Zhihong Liu, Ruijun Wang, Zhiying Wang, Zhixin Wang, Wenting Wan, Yang Dong, Jinquan Li
Software Mentions: 1
Published: about 4 years ago
10.3389/fgene.2018.00392
Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering BirdCited by: 26
Author(s): Shubham K. Jaiswal, Ankit Gupta, Rituja Saxena, Vishnu P. K. Prasoodanan, Ashok Sharma, Parul Mittal, Anirban Roy, Aaron B. A. Shafer, Nagarjun Vijay, Vineet K. Sharma
Software Mentions: 1
Published: about 6 years ago
10.3389/fmicb.2021.663217
Sequencing and Comparative Genomic Analysis of a Highly Metal-Tolerant Penicillium janthinellum P1 Provide Insights Into Its Metal ToleranceCited by: 11
Author(s): Bin-Bin Chi, Yitong Lu, Ping-Chuan Yin, Hongyan Liu, Huiying Chen, Yang ShaoHua
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2021.652802
Phylogenomics of Plant-Associated Botryosphaeriaceae SpeciesCited by: 19
Author(s): Jadran F. García, Daniel P. Lawrence, Abraham Morales‐Cruz, Renaud Travadon, Andrea Minio, Rufina Hernández-Martínez, Philippe E. Rolshausen, Kendra Baumgartner, Dario Cantu
Software Mentions: 1
Published: over 3 years ago
10.3389/fmicb.2017.01924
Comparative Genomics of Sibling Species of Fonsecaea Associated with Human ChromoblastomycosisCited by: 23
Author(s): Vânia A. Vicente, Vinícius Almir Weiss, Amanda Bombassaro, Leandro Ferreira Moreno, Flávia F. Costa, Roberto Tadeu Raittz, Aniele Carolina Ribas Leão, Renata Rodrigues Gomes, Anamélia Lorenzetti Bocca, Gheniffer Fornari, Raffael Júnio Araújo de Castro, Jiufeng Sun, Helisson Faoro, Michelle Z. Tadra-Sfeir, Valter A. Baura, Eduardo Balsanelli, Sandro Rogério de Almeida, Suelen Silvana dos Santos, Marcus de Melo Teixeira, Maria Sueli Soares Felipe, Mariana Machado Fidelis do Nascimento, Fábio O. Pedrosa, Maria Steffens, Derlene Attili‐Angelis, Mohammad Javad Najafzadeh, Flávio Queiroz‐Telles, Emanuel Maltempi de Souza, Sybren de Hoog
Software Mentions: 1
Published: about 7 years ago
10.3389/fmicb.2018.01841
Comparative Genomic Studies of Salmonella Heidelberg Isolated From Chicken- and Turkey-Associated Farm Environmental SamplesCited by: 21
Author(s): Loïc Deblais, Benjamin J. Lorentz, Joy Scaria, K. V. Nagaraja, Muhammad Imran Nisar, Dale Lauer, Shauna Voss, Gireesh Rajashekara
Software Mentions: 1
Published: over 6 years ago
10.3389/fnana.2017.00064
Midbrain-Hindbrain Boundary Morphogenesis: At the Intersection of Wnt and Fgf SignalingCited by: 44
Author(s): Holly C. Gibbs, Ana C. Chang-Gonzalez, Wonmuk Hwang, Alvin T. Yeh, Arne C. Lekven
Software Mentions: 1
Published: over 7 years ago
10.3389/fpsyg.2014.01532
The Child Affective Facial Expression (CAFE) set: validity and reliability from untrained adultsCited by: 169
Author(s): Vanessa LoBue, Cat Thrasher
Software Mentions: 1
Published: almost 10 years ago
10.3389/fpsyg.2020.01283
Beyond Screen Time: A Synergistic Approach to a More Comprehensive Assessment of Family Media Exposure During Early ChildhoodCited by: 63
Author(s): Rachel Barr, Heather L. Kirkorian, Jenny Radesky, Sarah M. Coyne, Deborah L. Nichols, Olivia A. Blanchfield, Sylvia N. Rusnak, Laura Stockdale, Andrew Ribner, Joke Durnez, Mollie Epstein, Mikael Heimann, Felix‐Sebastian Koch, Annette Sundqvist, Ulrika Birberg Thornberg, Carolin Konrad, Michaela Slussareff, Adriana G. Bus, Francesca Bellagamba, Caroline Fitzpatrick
Software Mentions: 1
Published: over 4 years ago
10.3389/fpsyg.2021.666245
The Child Emotion Facial Expression Set: A Database for Emotion Recognition in ChildrenCited by: 13
Author(s): Juliana Gioia Negrão, Ana Alexandra Caldas Osório, Rinaldo Focaccia Siciliano, Vivian Renne Gerber Lederman, Elisa Harumi Kozasa, Maria Eloísa Famá D’Antino, Anderson Tamborim, Vítor Santos, David Leonardo Barsand de Leucas, Paulo Sergio Camargo, Daniel C. Mograbi, Tatiana Pontrelli Mecca, José Salomão Schwartzman
Software Mentions: 1
Published: over 3 years ago
10.3389/fpsyg.2021.589664
How Infant and Toddlers’ Media Use Is Related to Sleeping Habits in Everyday Life in ItalyCited by: 10
Author(s): Francesca Bellagamba, Fabio Presaghi, M Di Marco, Emilia D’Abundo, Olivia A. Blanchfield, Rachel Barr
Software Mentions: 1
Published: over 3 years ago
10.3389/fpsyg.2020.599245
The Child Affective Facial Expression Set Short Versions (CAFE-Ss): Development and Validation of Two Subsets of Children’s Emotional Faces With VariabilityCited by: 0
Author(s): Yang Yang, Vanessa LoBue
Software Mentions: 1
Published: almost 4 years ago
10.1534/g3.116.038638
A New Reference Genome Assembly for the Microcrustacean <i>Daphnia pulex</i>Cited by: 90
Author(s): Zhiqiang Ye, Sen Xu, Ken Spitze, Jana Asselman, Xiaoqian Jiang, Matthew S. Ackerman, Jacqueline Lopez, Brent W. Harker, R. Taylor Raborn, W. Kelley Thomas, Jordan Ramsdell, Michael E. Pfrender, Michael Lynch
Software Mentions: 1
Published: over 7 years ago
10.1534/g3.117.300078
The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in PinaceaeCited by: 79
Author(s): David B. Neale, Patrick E. McGuire, Nicholas C. Wheeler, Kristian Stevens, Marc W. Crepeau, Charis Cardeno, Aleksey V. Zimin, Daniela Puiu, Geo Pertea, U. Uzay Sezen, Claudio Casola, Tomasz E. Koralewski, R. Paul, Daniel González-Ibeas, Sumaira Zaman, Richard Cronn, Mark Yandell, Carson Holt, Charles H. Langley, James A. Yorke, Steven L. Salzberg, Jill L. Wegrzyn
Software Mentions: 1
Published: about 7 years ago
10.1534/g3.120.401532
Construction of Pseudomolecules for the Chinese Chestnut (<i>Castanea mollissima</i>) GenomeCited by: 20
Author(s): Jinping Wang, Shengke Tian, Xiaofen Sun, Xin-Chao Cheng, Naibin Duan, Jihan Tao, Shen GuangNing
Software Mentions: 1
Published: about 4 years ago
10.3390/genes11101149
Genome-Wide Analysis of Chemosensory Protein Genes (CSPs) Family in Fig Wasps (Hymenoptera, Chalcidoidea)Cited by: 2
Author(s): Zhao-Zhe Xin, Dawei Huang, Dan Zhao, Jiaxing Li, Xianqin Wei, Jin‐Hua Xiao
Software Mentions: 1
Published: about 4 years ago
10.1186/gb-2007-8-7-r141
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolutionCited by: 149
Author(s): Matthew W. Hahn
Software Mentions: 1
Published: almost 18 years ago
10.1186/s13059-015-0711-4
Kiwi genome provides insights into evolution of a nocturnal lifestyleCited by: 67
Author(s): Diana Le Duc, Gabriel Renaud, Arunkumar Krishnan, Markus Sällman Almén, Leon Huynen, Sonja J. Prohaska, Matthias Ongyerth, Bárbara Domingues Bitarello, Helgi B. Schiöth, Michael Hofreiter, Peter F. Stadler, Kay Prüfer, David M. Lambert, Janet Kelso, Torsten Schöneberg
Software Mentions: 1
Published: over 9 years ago
10.1093/gbe/evu292
Insights on the Evolution of Mycoparasitism from the Genome of Clonostachys roseaCited by: 118
Author(s): Magnus Karlsson, Mikael Brandström Durling, Jaeyoung Choi, Chatchai Kosawang, Gerald Lackner, Georgios Tzelepis, Kristiina Nygren, Mukesh Dubey, Nathalie N. Kamou, Anthony Levasseur, Antonio Zapparata, Jinhui Wang, Daniel Buchvaldt Amby, Birgit Jensen, Sabrina Sarrocco, Emmanuel Panteris, Anastasia L. Lagopodi, Stefanie Pöggeler, Giovanni Vannacci, David B. Collinge, Dirk Hoffmeister, Bernard Henrissat, Yong-Hwan Lee, Dan Funck Jensen
Software Mentions: 1
Published: almost 10 years ago
10.1093/gbe/evw018
Duplication and Diversification of Dipteran Argonaute Genes, and the Evolutionary Divergence of Piwi and AubergineCited by: 97
Author(s): Samuel H. Lewis, Heli Salmela, Darren J. Obbard
Software Mentions: 1
Published: almost 9 years ago
10.1093/gbe/evv204
The Distant Siblings—A Phylogenomic Roadmap Illuminates the Origins of Extant Diversity in Fungal Aromatic Polyketide BiosynthesisCited by: 25
Author(s): Grzegorz Koczyk, Adam Dawidziuk, Delfina Popiel
Software Mentions: 1
Published: about 9 years ago
10.1093/gbe/evy274
Genome Sequence of<i>Jaltomata</i>Addresses Rapid Reproductive Trait Evolution and Enhances Comparative Genomics in the Hyper-Diverse SolanaceaeCited by: 14
Author(s): Meng Wu, Jamie L. Kostyun, Leonie C. Moyle
Software Mentions: 1
Published: almost 6 years ago
10.1016/j.gpb.2020.06.002
Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid BiosynthesisCited by: 43
Author(s): Zhichao Xu, Ranran Gao, Xiangdong Pu, Rong Xu, Jiyong Wang, Shu-Jian Zheng, Yan Zeng, Jun Chen, Chunnian He, Jingyuan Song
Software Mentions: 1
Published: over 4 years ago
10.1186/2047-217X-3-27
Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environmentCited by: 67
Author(s): Li Cai, Yong Zhang, Jianwen Li, Lesheng Kong, Haofu Hu, Hailin Pan, Luohao Xu, Yuan Deng, Qiye Li, Lijun Jin, Hao Yu, Yan Chen, Binghang Liu, L. Yang, Shiping Liu, Yan Zhang, Yongshan Lang, Jinquan Xia, Weiming He, Qiong Shi, Sankar Subramanian, Craig D. Millar, Stephen Meader, Chris M. Rands, Matthew K. Fujita, Matthew J. Greenwold, Todd A. Castoe, David D. Pollock, Wanjun Gu, Kiwoong Nam, Hans Ellegren, Simon Y. W. Ho, David W. Burt, Chris P. Ponting, Erich D. Jarvis, M. Thomas P. Gilbert, Huanming Yang, Jian Wang, David M. Lambert, Jun Wang, Guojie Zhang
Software Mentions: 1
Published: almost 10 years ago
10.1093/gigascience/giy119
The genome of common long-arm octopus Octopus minorCited by: 39
Author(s): Bomi Kim, Seunghyun Kang, Do-Hwan Ahn, Seung-Hyun Jung, Hwanseok Rhee, Jong Su Yoo, Jong-Eun Lee, Seungjae Lee, Young Hwan Han, Kyoung‐Bin Ryu, Sung–Jin Cho, Hyun Park, Hye Suck An
Software Mentions: 1
Published: about 6 years ago
10.1093/gigascience/giaa139
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environmentsCited by: 5
Author(s): Xiang Zeng, Yaolei Zhang, Lingfeng Meng, Guangyi Fan, Jie Bai, Jian Wei Chen, Yue Song, Inge Seim, Congyan Wang, Zenghua Shao, Nanxi Liu, Haorong Lu, Xiugen Fu, Liping Wang, Xin Liu, Shanshan Liu, Zongze Shao
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41438-019-0235-2
The genome sequence of celery (Apium graveolens L.), an important leaf vegetable crop rich in apigenin in the Apiaceae familyCited by: 59
Author(s): Mengyao Li, Kai Feng, Xilin Hou, Qian Jiang, Zhihong Xu, Guang-Long Wang, Jie-Xia Liu, Rui Wang, Ai‐Sheng Xiong
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41438-020-0240-5
A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicineCited by: 55
Author(s): Minghui Kang, Haolin Wu, Qiao Yang, Li Huang, Quanjun Hu, Tao Ma, Zaiyun Li, Jianquan Liu
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41438-020-0271-y
Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceusCited by: 23
Author(s): Shufen Li, Jin Wang, Ran Dong, Hongwei Zhu, Liping Lan, Yulan Zhang, Ning Li, Chuan‐Liang Deng, Wu‐Jun Gao
Software Mentions: 1
Published: over 4 years ago
10.1038/s41438-020-0295-3
A high-quality reference genome of wild Cannabis sativaCited by: 57
Author(s): Shan Gao, Baishi Wang, Shanshan Xie, Xiaoyu Xu, Jin Zhang, Pei Li, Yifan Yu, Weifei Yang, Ying Zhang
Software Mentions: 1
Published: over 4 years ago
10.1038/s41597-020-0424-8
First draft genome for the sand-hopper Trinorchestia longiramusCited by: 8
Author(s): Ajit Kumar Patra, Oksung Chung, Ji Yong Yoo, Min-Seop Kim, Moon Geun Yoon, Jeong Hyeon Choi, Yali Yang
Software Mentions: 1
Published: over 4 years ago
10.1038/srep21902
The genome of the miiuy croaker reveals well-developed innate immune and sensory systemsCited by: 65
Author(s): Tianjun Xu, Guoliang Xu, Rongbo Che, Rixin Wang, Yanjin Wang, Jingrui Li, Shanchen Wang, Chen Shu, Yuena Sun, Tianxing Liu, Jiang Liu, Aishuai Wang, Jingjing Han, Qing Chu, Qiong Yang
Software Mentions: 1
Published: over 8 years ago
10.1038/srep31586
Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genusCited by: 47
Author(s): Wei Wu, Yulan Yang, Weiming He, Mathieu Rouard, Weiming Li, Meng Xu, Nicolás Roux, Xue‐Jun Ge
Software Mentions: 1
Published: over 8 years ago
10.1038/srep32961
Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the gooseCited by: 33
Author(s): Guangliang Gao, Xianzhi Zhao, Li Qin, Chuan He, Wenjing Zhao, Shuyun Liu, Jinmei Ding, Weixing Ye, Jun Wang, Ye Chen, Haiwei Wang, Jing Li, Yi Luo, Jian Su, Yong Huang, Zuohua Liu, Ronghua Dai, Yixiang Shi, He Meng, Qigui Wang
Software Mentions: 1
Published: about 8 years ago
10.1038/s41598-017-00132-9
Comparative genomics reveals contraction in olfactory receptor genes in batsCited by: 15
Author(s): Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J. Rossiter
Software Mentions: 1
Published: over 7 years ago
10.1128/mBio.02452-18
Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen <i>Phytophthora ramorum</i>Cited by: 49
Author(s): Angela Dale, Nicolas Feau, Sydney E. Everhart, Braham Dhillon, Barbara Wong, Julie Sheppard, Guillaume J. Bilodeau, Avneet Brar, Javier F. Tabima, Danyu Shen, C. M. Brasier, Brett M. Tyler, Niklaus J. Grünwald, Richard Hamelin
Software Mentions: 1
Published: over 5 years ago
10.1016/j.isci.2020.101267
Insights into the Evolution of Neoteny from the Genome of the Asian Icefish Protosalanx chinensisCited by: 6
Author(s): Jie Zhang, Jiwei Qi, Fanglei Shi, Huijuan Pan, Meng Li, Ran Tian, Yuepan Geng, Huaying Li, Yujie Qu, Jinping Chen, Inge Seim, Ming Li
Software Mentions: 1
Published: over 4 years ago
10.3390/nu13093076
Dietary Protein Requirement Threshold and Micronutrients Profile in Healthy Older Women Based on Relative Skeletal Muscle MassCited by: 4
Author(s): Praval Khanal, Lingxiao He, Hans Degens, Georgina K. Stebbings, Gladys Onambélé-Pearson, Alun G. Williams, Martine Thomis, Christopher I. Morse
Software Mentions: 1
Published: about 3 years ago