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: find
https://packages.ecosyste.ms/registries/pypi.org/packages/find
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Papers Mentioning find 54
10.1371/journal.pcbi.1006158
Comment on "A comprehensive overview and evaluation of circular RNA detection tools"Cited by: 14
Author(s): Chia-Ying Chen, Trees‐Juen Chuang
Software Mentions: 7
Published: over 5 years ago
10.3390/cancers11060759
Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung CancerCited by: 31
Author(s): Fayez Kheir, Mengmeng Zhao, Michael J. Strong, Yi Yu, Asuka Nanbo, Erik K. Flemington, Gilbert F. Morris, Krzysztof Reiss, Li Li, Zhen Lin
Software Mentions: 7
Published: over 5 years ago
10.1371/journal.pcbi.1005420
A comprehensive overview and evaluation of circular RNA detection toolsCited by: 285
Author(s): Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou
Software Mentions: 6
Published: over 7 years ago
10.1186/s40168-018-0507-3
Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA virusesCited by: 64
Author(s): Marcos Parras-Moltó, Ana Rodríguez-Galet, Patricia Suárez-Rodríguez, Alberto López-Bueno
Software Mentions: 6
Published: over 6 years ago
10.1186/s12864-018-4670-5
Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjectsCited by: 28
Author(s): Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger, Winnie S. Liang
Software Mentions: 6
Published: over 6 years ago
10.1186/s13059-021-02497-7
SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAsCited by: 7
Author(s): Alon Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Inés Lucía Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel, Sebastián Kadener
Software Mentions: 5
Published: about 3 years ago
10.3389/fgene.2019.01347
Emerging Roles of Heat-Induced circRNAs Related to Lactogenesis in Lactating SowsCited by: 11
Author(s): Jiajie Sun, Haojie Zhang, Bao-Yu Hu, Yueqin Xie, Dongyang Wang, Jinzhi Zhang, Ting Chen, Junyi Luo, Songbo Wang, Qinyan Jiang, Qianyun Xi, Zujing Chen, Yongliang Zhang
Software Mentions: 5
Published: almost 5 years ago
10.3389/fgene.2020.591806
Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato LeavesCited by: 11
Author(s): Xuedong Yang, Yahui Liu, Hui Zhang, Jinyu Wang, Gaurav Zinta, Shangbo Xie, Weimin Zhu, Wen-Feng Nie
Software Mentions: 5
Published: about 4 years ago
10.1093/jmcb/mjz094
A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stressCited by: 20
Author(s): Antonella Di Liddo, Camila de Oliveira Freitas Machado, Sandra E. Fischer, Stefanie Ebersberger, Andreas W. Heumüller, Julia E. Weigand, Michaela Müller-McNicoll, Kathi Zarnack
Software Mentions: 5
Published: about 5 years ago
10.3389/fgene.2021.663091
Identification of a Potentially Functional circRNA-miRNA-mRNA Regulatory Network in Melanocytes for Investigating Pathogenesis of VitiligoCited by: 4
Author(s): Lili Li, Zhi Xie, Xiliang Qian, Tai Wang, Minmin Jiang, Jinglin Qin, Chen Wang, Rongqun Wu, Canling Song
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0080156
PD5: A General Purpose Library for Primer Design SoftwareCited by: 6
Author(s): Michael C. Riley, Wayne Aubrey, Michael Young, Amanda Clare
Software Mentions: 5
Published: about 11 years ago
10.3390/cells9091937
Arabidopsis thaliana cbp80, c2h2, and flk Knockout Mutants Accumulate Increased Amounts of Circular RNAsCited by: 7
Author(s): Anna Philips, Katarzyna Nowis, Michał Stelmaszczuk, Jan Podkowiński, Luiza Handschuh, Paulina Jackowiak, Marek Figlerowicz
Software Mentions: 5
Published: over 4 years ago
10.1080/22221751.2020.1738277
Competing endogenous RNA network profiling reveals novel host dependency factors required for MERS-CoV propagationCited by: 50
Author(s): Xi Zhang, Hin Chu, Lei Wen, Huiping Shuai, Dong Yang, Yixin Wang, Yuxin Hou, Zheng Zhu, Shuofeng Yuan, Feifei Yin, Jasper Fuk‐Woo Chan, Kwok‐Yung Yuen
Software Mentions: 5
Published: almost 5 years ago
10.1186/s12864-018-4926-0
CircMarker: a fast and accurate algorithm for circular RNA detectionCited by: 23
Author(s): Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu, Yufeng Wu
Software Mentions: 5
Published: over 6 years ago
10.1186/s12864-019-5960-2
Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FTCited by: 19
Author(s): Matteo Schiavinato, Richard Strasser, Lukas Mach, Juliane C. Dohm, Heinz Himmelbauer
Software Mentions: 5
Published: over 5 years ago
10.3389/fcell.2020.602731
CircRNA hsa_circ_0008500 Acts as a miR-1301-3p Sponge to Promote Osteoblast Mineralization by Upregulating PADI4Cited by: 11
Author(s): Qiaoli Zhai, Yi Zhao, Linping Wang, Yan Dai, Peiqing Zhao, Xinxin Xiang, Kui Liu, Wei Du, Wenxiu Tian, Baoye Yang, Tao Li, Lianqing Wang
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2021.627907
Enrichment of Circular RNA Expression Deregulation at the Transition to Recurrent Spontaneous Seizures in Experimental Temporal Lobe EpilepsyCited by: 13
Author(s): Andreia Gomes‐Duarte, Sebastian Bauer, Morten T. Venø, Braxton A. Norwood, David C. Henshall, Jørgen Kjems, Felix Rosenow, Vamshidhar R. Vangoor, R. Jeroen Pasterkamp
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2019.00603
Genome-Wide Identification of Circular RNAs Revealed the Dominant Intergenic Region Circularization Model in Apostichopus japonicusCited by: 15
Author(s): Xuelin Zhao, Xuemei Duan, Jianping Fu, Yina Shao, Weiwei Zhang, Ming Guo, Chenghua Li
Software Mentions: 4
Published: over 5 years ago
10.1111/jcmm.15370
Genome‐Wide Analysis of circular RNAs and validation of hsa_circ_0006719 as a potential novel diagnostic biomarker in congenital scoliosis patientsCited by: 1
Author(s): Gang Liu, Jianxiong Shen, Chong Chen, Yang Jiao, Zheng Li, Haining Tan, Youxi Lin, Tianhua Rong
Software Mentions: 4
Published: over 4 years ago
10.1111/jcmm.16324
Identification of novel dysregulated circular RNAs in early‐stage breast cancerCited by: 17
Author(s): Arunagiri Kuha Deva Magendhra Rao, Vittal Rangan Arvinden, Deepa P. Ramasamy, Krishna Patel, Balaiah Meenakumari, Priya Ramanathan, Shirley Sundersingh, Velusami Sridevi, Thangarajan Rajkumar, Zdenko Herceg, Harsha Gowda, Samson Mani
Software Mentions: 4
Published: almost 4 years ago
10.3389/fnmol.2017.00091
Identification of the Spinal Expression Profile of Non-coding RNAs Involved in Neuropathic Pain Following Spared Nerve Injury by Sequence AnalysisCited by: 114
Author(s): Jun Zhou, Qingming Xiong, Hongtao Chen, Cheng-xiang Yang, Yu Fan
Software Mentions: 4
Published: over 7 years ago
10.1038/srep38820
Acfs: accurate circRNA identification and quantification from RNA-Seq dataCited by: 67
Author(s): Xintian You, Tim Conrad
Software Mentions: 4
Published: almost 8 years ago
10.18632/oncotarget.22130
Systematic analysis of the expression profile of non-coding RNAs involved in ischemia/reperfusion-induced acute kidney injury in mice using RNA sequencingCited by: 25
Author(s): Jun Zhou, Hongtao Chen, Yu Fan
Software Mentions: 4
Published: about 7 years ago
10.1186/s12864-020-6649-2
Trend analysis of the role of circular RNA in goat skeletal muscle developmentCited by: 17
Author(s): Yinghui Ling, Qi Zheng, Lu Zhu, Lei Xu, Menghua Sui, Yunhai Zhang, Ya Liu, Fugui Fang, Mingxing Chu, Yuehui Ma, Xiaorong Zhang
Software Mentions: 3
Published: over 4 years ago
10.3390/ani11092557
Identification of Circular RNAs in the Anterior Pituitary in Rats Treated with GnRHCited by: 3
Author(s): Haixiang Guo, Bao Yuan, Meng-Ting Su, Yi Zheng, Jinyu Zhang, Dong-Xu Han, Hao-Qi Wang, Yongping Huang, Hao Jiang, Jiabao Zhang
Software Mentions: 3
Published: about 3 years ago
10.1186/s12864-021-07706-y
Morphological changes and functional circRNAs screening of rabbit skeletal muscle developmentCited by: 4
Author(s): Qi Zheng, Cuiyun Zhu, Jing Jing, Yinghui Ling, Shuaiqi Qin, Jiao Wang, Lisha Zha, Ya Liu, Fugui Fang
Software Mentions: 3
Published: over 3 years ago
10.18632/aging.102576
Circular RNA SMO sponges miR-338-3p to promote the growth of glioma by enhancing the expression of SMOCited by: 22
Author(s): Xiong Zhang, Chaoyang Zhou, Luyang Wang, Ronglan Zhu, Liangchen Zhong, Dengfeng Wan, Qiangping Wang
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12911-020-1117-0
A machine learning framework for accurately recognizing circular RNAs for clinical decision-supportingCited by: 1
Author(s): Yidan Wang, Xuanping Zhang, Tao Wang, Jinchun Xing, Zhun Wu, Wei Li, Jiayin Wang
Software Mentions: 3
Published: over 4 years ago
10.26508/lsa.201900398
Noncoding AUG circRNAs constitute an abundant and conserved subclass of circlesCited by: 59
Author(s): Lotte Vw Stagsted, Katrine Mandrup Nielsen, Iben Daugaard, Thomas B. Hansen
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0202375
Genome-wide identification and functional analysis of circRNAs in Zea maysCited by: 28
Author(s): Baihua Tang, Zhiqiang Hao, Yanfeng Zhu, Hua Zhang, Guanglin Li
Software Mentions: 3
Published: almost 6 years ago
10.1002/2211-5463.12512
Circular <scp>RNA</scp> expression profile of spleen in a <i>Clostridium perfringens</i> type C‐induced piglet model of necrotizing enteritisCited by: 13
Author(s): Zunqiang Yan, Tiantuan Jiang, Pengfei Wang, Xiaoyu Huang, Qiaoli Yang, Weibo Sun, Shuangbao Gun
Software Mentions: 3
Published: about 6 years ago
10.3389/fcell.2020.00273
Non-coding RNAs in Nervous System Development and DiseaseCited by: 34
Author(s): Beatrice Salvatori, Silvia Biscarini, Mariangela Morlando
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2019.00731
Identification of Potential Immune-Related circRNA–miRNA–mRNA Regulatory Network in Intestine of Paralichthys olivaceus During Edwardsiella tarda InfectionCited by: 36
Author(s): Yunji Xiu, Guangpeng Jiang, Shun Zhou, Jing Diao, Hongjun Liu, Baofeng Su, Chao Li
Software Mentions: 3
Published: over 5 years ago
10.3389/fgene.2019.00431
Analyses of a Panel of Transcripts Identified From a Small Sample Size and Construction of RNA Networks in Hepatocellular CarcinomaCited by: 13
Author(s): Sheng Zhang, Xiaolin Wang, Ge‐Liang Xu, Shengfang Ge, Chen Liang
Software Mentions: 3
Published: over 5 years ago
10.3389/fnmol.2021.665788
CircRNA-ceRNA Network Revealing the Potential Regulatory Roles of CircRNA in Alzheimer’s Disease Involved the cGMP-PKG Signal PathwayCited by: 20
Author(s): Yuan Zhang, Lili Qian, Yingying Liu, Ying Liu, Wanpeng Yu, Yanfang Zhao
Software Mentions: 3
Published: over 3 years ago
10.3390/genes12010084
Identification of Circular RNAs in Hypothalamus of Gilts during the Onset of PubertyCited by: 5
Author(s): Qingnan Li, Xiangchun Pan, Nian Li, Wentao Gong, Yaosheng Chen, Xiaolong Yuan
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13059-014-0571-3
CIRI: an efficient and unbiased algorithm for de novo circular RNA identificationCited by: 780
Author(s): Yuan Gao, Jinfeng Wang, Fangqing Zhao
Software Mentions: 3
Published: almost 10 years ago
10.1186/s13059-015-0801-3
Spatio-temporal regulation of circular RNA expression during porcine embryonic brain developmentCited by: 382
Author(s): Morten T. Venø, Thomas B. Hansen, Susanne T. Venø, Bettina Hjelm Clausen, Manuela Grebing, Bente Finsen, Ida E. Holm, Jørgen Kjems
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.ppat.1007206
The Epstein Barr virus circRNAomeCited by: 105
Author(s): Nathan Ungerleider, Monica Concha, Zhen Lin, Claire Roberts, Xia Wang, Subing Cao, Melody Baddoo, William C. Moss, Yi Yu, Michael Seddon, Terri Lehman, Scott A. Tibbetts, Rolf Renne, Yan Dong, Erik K. Flemington
Software Mentions: 3
Published: over 6 years ago
10.1186/s12931-018-0962-1
Circular RNAs: a rising star in respiratory diseasesCited by: 60
Author(s): Jian Wang, Mengchan Zhu, Jue Pan, Cuicui Chen, Shijin Xia, Yuanlin Song
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12284-021-00455-2
Analysis of Rice Transcriptome Reveals the LncRNA/CircRNA Regulation in Tissue DevelopmentCited by: 21
Author(s): Run Zhou, Pablo Sanz-Jimenez, Xitong Zhu, Jia-Wu Feng, Lin Shen, Jia‐Ming Song, Lingling Chen
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-021-93781-w
Identification and characterization of a novel Epstein-Barr Virus-encoded circular RNA from LMP-2 GeneCited by: 9
Author(s): Ke-En Tan, Wei Lun Ng, Georgi K. Marinov, Ken Hung-On Yu, Lu Tan, Ee Shan Liau, Sook Yan Goh, Kok Siong Yeo, Kevin Y. Yip, Kwok‐Wai Lo, Alan Soo‐Beng Khoo, Lee Fah Yap, Chee-Kwee Ea, Yat-Yuen Lim
Software Mentions: 3
Published: over 3 years ago
10.7554/eLife.58478
circZNF827 nucleates a transcription inhibitory complex to balance neuronal differentiationCited by: 26
Author(s): Anne Kruse Hollensen, Henriette Sylvain Thomsen, Marta Lloret-Llinares, Andreas Bjerregaard Kamstrup, James C. Jensen, Majbritt Luckmann, Nanna Birkmose, Johan Palmfeldt, Torben Heick Jensen, Thomas B. Hansen, Christian Kroun Damgaard
Software Mentions: 3
Published: about 4 years ago
10.3390/ijms22105182
Canonical and Interior Circular RNAs Function as Competing Endogenous RNAs in Psoriatic SkinCited by: 8
Author(s): Xiaoxin Liu, Jacqueline Frost, Anne M. Bowcock, Weixiong Zhang
Software Mentions: 3
Published: over 3 years ago
10.1186/s12864-021-07645-8
Comprehensive analysis of differentially expressed circRNAs and ceRNA regulatory network in porcine skeletal muscleCited by: 18
Author(s): Meng Li, Na Zhang, Wanfeng Zhang, Wei Hei, Chunbo Cai, Yang Yang, Chang Lu, Pengfei Gao, Xiaohong Guo, Guoqing Cao, Bugao Li
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2020.623584
Comprehensive circRNA Expression Profile and Construction of circRNAs-Related ceRNA Network in a Mouse Model of AutismCited by: 6
Author(s): Ji Wang, Zhijun Yang, Canming Chen, Xu Yang, Hongguang Wang, Bing Liu, Wei Zhang, Yanan Jiang
Software Mentions: 2
Published: almost 4 years ago
10.3390/genes12010100
Systematic Identification and Analysis of Circular RNAs of Japanese Flounder (Paralichthys olivaceus) in Response to Vibrio anguillarum InfectionCited by: 5
Author(s): Xianhui Ning, Li Sun
Software Mentions: 2
Published: almost 4 years ago
10.3389/fvets.2021.615405
Genome-Wide Differential Expression Profiling of Pulmonary circRNAs Associated With Immune Reaction to Pasteurella multocida in GoatsCited by: 6
Author(s): Qiaoling Chen, Zhenxing Zhang, Si Chen, Jie Chen, Yiwen Cheng, Ang Liu, Bin Li, Zhe Chen, Yiying Zheng, Manchuriga Ga, Lijun Du, Yafei Wang
Software Mentions: 2
Published: over 3 years ago
10.1186/s12967-021-03075-y
Development of a two-circular RNA panel as potential prognostic biomarker for gastric cancerCited by: 5
Author(s): Jing Liu, Xiaolei Zhu, Meinan Yan, Hui Li
Software Mentions: 2
Published: about 3 years ago
10.1038/s41598-020-66990-y
Expression profile and bioinformatics analysis of circular RNAs in acute ischemic stroke in a South Chinese Han populationCited by: 30
Author(s): Sheng‐Hua Li, Lan Chen, Chen Xu, Xiang Qiu, Zhenxiu Qin, Jinggui Gao, LI Jin-pin, Jingli Liu
Software Mentions: 2
Published: over 4 years ago
10.3390/genes10060421
Engineering CatM, a LysR-Type Transcriptional Regulator, to Respond Synergistically to Two EffectorsCited by: 9
Author(s): Melissa Tumen-Velasquez, Nicole S. Laniohan, Cory Momany, Ellen L. Neidle
Software Mentions: 2
Published: over 5 years ago
10.3389/fvets.2021.692501
Identification of Differentially Expressed Non-coding RNA Networks With Potential Immunoregulatory Roles During Salmonella Enteritidis Infection in DucksCited by: 5
Author(s): Yu Zhang, Xiaoqian Dong, Li-e Hou, Zhen Cao, Guoqiang Zhu, Wanwipa Vongsangnak, Qi Xu, Guohong Chen
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-019-43030-y
Lack of selective resistance of influenza A virus in presence of host-targeted antiviral, UV-4BCited by: 25
Author(s): Kelly L. Warfield, Kaitlyn Schaaf, Lisa Evans DeWald, Kevin B. Spurgers, Wei Wang, Eric Stavale, Michelle Mendenhall, Meghan H. Shilts, Timothy B. Stockwell, Dale L. Barnard, Urban Ramstedt, Suman Das
Software Mentions: 1
Published: over 5 years ago
10.26508/lsa.201800148
Ribosomal stalling landscapes revealed by high-throughput inverse toeprinting of mRNA librariesCited by: 10
Author(s): Britta Seip, Guénaël Sacheau, Denis Dupuy, C.A. Innis
Software Mentions: 1
Published: about 6 years ago