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: toolkit
https://packages.ecosyste.ms/registries/pypi.org/packages/toolkit
toolkit for script and utils
3 versions
Latest release: about 9 years ago
284 downloads last month
Papers Mentioning toolkit 33
10.1038/s41598-017-09064-w
Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switchingCited by: 27
Author(s): Douglas C. Wu, Alan M. Lambowitz
Software Mentions: 8
Published: over 7 years ago
10.1371/journal.pgen.1004900
An Intracellular Transcriptomic Atlas of the Giant Coenocyte Caulerpa taxifoliaCited by: 41
Author(s): Aashish Ranjan, Brad T. Townsley, Yasunori Ichihashi, Neelima Sinha, Daniel H. Chitwood
Software Mentions: 7
Published: almost 10 years ago
10.1371/journal.pone.0080822
Bacterial Endosymbiosis in a Chordate Host: Long-Term Co-Evolution and Conservation of Secondary MetabolismCited by: 50
Author(s): Jason C. Kwan, Eric W. Schmidt
Software Mentions: 5
Published: almost 11 years ago
10.3389/fdata.2021.582468
Named Data Networking for Genomics Data Management and Integrated WorkflowsCited by: 3
Author(s): Cameron Ogle, David Reddick, Coleman B. McKnight, Tyler D. Biggs, Rini Pauly, Stephen P. Ficklin, F. Alex Feltus, Susmit Shannigrahi
Software Mentions: 4
Published: almost 4 years ago
10.1002/ece3.3063
Regulation of gene expression is associated with tolerance of the Arctic copepod <i>Calanus glacialis</i> to <scp>CO</scp> <sub>2</sub> ‐acidified sea waterCited by: 40
Author(s): Allison Bailey, Pierre De Wit, Peter Thor, Howard I. Browman, Reidun M. Bjelland, Steven Shema, David M. Fields, Jeffrey A. Runge, Cameron Thompson, Haakon Hop
Software Mentions: 4
Published: over 7 years ago
10.1038/srep15968
Dengue virus infection alters post-transcriptional modification of microRNAs in the mosquito vector Aedes aegyptiCited by: 32
Author(s): Kayvan Etebari, Solomon Osei-Amo, Simon P. Blomberg, Sassan Asgari
Software Mentions: 4
Published: about 9 years ago
10.1186/s12915-019-0659-z
Biological and RNA regulatory function of MOV10 in mammalian germ cellsCited by: 18
Author(s): Kaiqiang Fu, Suwen Tian, Huanhuan Tan, Caifeng Wang, Hanben Wang, Min Wang, Yuan‐Yuan Wang, Zhen Chen, Yanfeng Wang, Qiuling Yue, Qiushi Xu, Shuya Zhang, Haixin Li, Jie Xie, Mingyan Lin, Mengcheng Luo, Feng Chen, Lan Ye, Ke Zheng
Software Mentions: 4
Published: over 5 years ago
10.1038/srep18470
Genome-wide analysis of microRNAs identifies the lipid metabolism pathway to be a defining factor in adipose tissue from different sheepCited by: 37
Author(s): Xiangyang Miao, Qingmiao Luo, Xiaoqiong Qin, Yuntao Guo
Software Mentions: 3
Published: almost 9 years ago
10.1038/s41598-019-41189-y
Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcasCited by: 11
Author(s): Mo Yang, Hongyu Lu, Feiqun Xue, Lanqing Ma
Software Mentions: 3
Published: over 5 years ago
10.18632/oncotarget.14248
Mutations acquired by hepatocellular carcinoma recurrence give rise to an aggressive phenotypeCited by: 12
Author(s): Ji-Hye Choi, Min Jae Kim, Yong Keun Park, Jong-Yeop Im, So Mee Kwon, Hyung Chul Kim, Hyun Goo Woo, Hee-Jung Wang
Software Mentions: 2
Published: almost 8 years ago
10.1186/1471-2105-6-21
Cited by: 273Author(s): John L. Moreland, Apostol Gramada, Oleksandr Buzko, Qing Zhang, Philip E. Bourne
Software Mentions: 2
Published: almost 20 years ago
10.7717/peerj.10864
Expression analysis of genes related to cold tolerance in<i> Dendroctonus valens</i>Cited by: 7
Author(s): Di Zhao, Chunchun Zheng, Fengming Shi, Yecheng Xu, Shixiang Zong, Jing Tao
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pcbi.1002318
The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional SpecificitiesCited by: 48
Author(s): Ying Zhang, Olga Zagnitko, Irina A. Rodionova, Andrei L. Osterman, Adam Godzik
Software Mentions: 2
Published: almost 13 years ago
10.3390/cancers12071890
Identification of Novel microRNA Prognostic Markers Using Cascaded Wx, a Neural Network-Based Framework, in Lung Adenocarcinoma PatientsCited by: 9
Author(s): Jeong Seon Kim, Sang Hoon Chun, Sung Soo Park, Sieun Lee, Sae Eun Kim, Ji Hyung Hong, Keunsoo Kang, Yoon Ho Ko, Young Ho Ahn
Software Mentions: 2
Published: over 4 years ago
10.1186/s12987-020-00209-0
Differential expression of receptors mediating receptor-mediated transcytosis (RMT) in brain microvessels, brain parenchyma and peripheral tissues of the mouse and the humanCited by: 68
Author(s): Wandong Zhang, Qing Yan Liu, Arsalan S. Haqqani, Sonia Leclerc, Ziying Liu, François Fauteux, Ewa Baumann, Christie E. Delaney, Dao Ly, Alexandra T. Star, Eric Brunette, Caroline Sodja, Melissa Hewitt, Jagdeep K. Sandhu, Danica Stanimirovic
Software Mentions: 2
Published: over 4 years ago
10.1038/srep20850
tRNA-Derived Small Non-Coding RNAs in Response to Ischemia Inhibit AngiogenesisCited by: 83
Author(s): Qing Li, Bin Hu, Guowen Hu, Chun-Yuan Chen, Xiamu Niu, Juan Liu, Shumin Zhou, Changqing Zhang, Yan Wang, Zhifeng Deng
Software Mentions: 2
Published: almost 9 years ago
10.1038/s41598-021-82163-x
Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerizationCited by: 40
Author(s): Parmeshwar Vitthal Gavande, Arijita Basak, Subhajit Sen, Khusboo Lepcha, Nensina Murmu, Vijeta Rai, Deepika Mazumdar, Shyama Prasad Saha, Vaskar Das, Shilpi Ghosh
Software Mentions: 2
Published: almost 4 years ago
10.1007/s11548-020-02132-z
Novel platform for development, training, and validation of computer-assisted detection/diagnosis softwareCited by: 6
Author(s): Yukihiro Nomura, Soichiro Miki, Naoto Hayashi, Shouhei Hanaoka, Issei Sato, Tsuneo Yoshikawa, Yoshitaka Masutani, Osamu Abe
Software Mentions: 2
Published: over 4 years ago
10.1098/rsta.2008.0314
Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examplesCited by: 30
Author(s): Robert S. MacLeod, J.G. Stinstra, Seok Lew, Ross T. Whitaker, Darrell Swenson, M.J. Cole, Jens Krüger, Dana H. Brooks, Chris R. Johnson
Software Mentions: 1
Published: over 15 years ago
10.1186/s13099-018-0267-4
Genome characterization of bile-isolated Shewanella algae ACCCCited by: 9
Author(s): Shu-Ying Tseng, Kwong‐Chung Tung, Jan‐Fang Cheng, Yi‐Hsuan Lee, Zong‐Yen Wu, Yu‐Kai Hong, Shi‐Yu Chen, Yao‐Ting Huang, Po‐Yu Liu
Software Mentions: 1
Published: about 6 years ago
10.1186/s13321-016-0148-0
Comparing structural fingerprints using a literature-based similarity benchmarkCited by: 129
Author(s): Noel M. O’Boyle, Roger A. Sayle
Software Mentions: 1
Published: over 8 years ago
10.1186/s12870-019-1766-2
Genetic and cytological analyses reveal the recombination landscape of a partially differentiated plant sex chromosome in kiwifruitCited by: 14
Author(s): Sarah M. Pilkington, Jibran Tahir, Elena Hilario, Susan E. Gardiner, David Chagné, Andrew Catanach, John McCallum, Linley K. Jesson, Lena G. Fraser, M.A. McNeilage, Cecilia Deng, Ross N. Crowhurst, Paul M. Datson, Q. Zhang
Software Mentions: 1
Published: over 5 years ago
10.1186/s12870-018-1415-1
Small RNA and degradome sequencing used to elucidate the basis of tolerance to salinity and alkalinity in wheatCited by: 23
Author(s): Huanan Han, Qi Wang, Wei Lin, Yu Liang, Jing Dai, Guangmin Xia, Shuwei Liu
Software Mentions: 1
Published: about 6 years ago
10.3390/s21030999
Characterisation of Textile Embedded Electrodes for Use in a Neonatal Smart Mattress Electrocardiography SystemCited by: 7
Author(s): Henry Dore, Rodrigo Avilés-Espinosa, Zhenhua Luo, Oana Anton, Heike Rabe, Elizabeth Rendón-Morales
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41598-017-03927-y
Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomassCited by: 22
Author(s): Nandita Pasari, Nidhi Adlakha, Manish Gupta, Zeenat Bashir, Girish H. Rajacharya, Garima Verma, Manoj Munde, Rakesh Bhatnagar, Syed Shams Yazdani
Software Mentions: 1
Published: over 7 years ago
10.1186/s12864-017-3587-8
Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod developmentCited by: 27
Author(s): Chao Gao, Pengfei Wang, Shuzhen Zhao, Chuanzhi Zhao, Han Xia, Lei Hou, Jie Zheng, Ye Zhang, Changsheng Li, Xingjun Wang
Software Mentions: 1
Published: over 7 years ago
10.1038/s41598-018-20384-3
Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomesCited by: 42
Author(s): Masato Kogawa, Masahito Hosokawa, Yohei Nishikawa, Kazuki Mori, Haruko Takeyama
Software Mentions: 1
Published: almost 7 years ago
10.1371/journal.pone.0116222
Fin Whale Sound Reception Mechanisms: Skull Vibration Enables Low-Frequency HearingCited by: 61
Author(s): Ted W. Cranford, Petr Krysl
Software Mentions: 1
Published: almost 10 years ago
10.1186/s12872-017-0735-7
Association of rs662799 in APOA5 with CAD in Chinese Han populationCited by: 14
Author(s): Hua Chen, Shifang Ding, Mei Zhou, Xin-ai Wu, Xi Liu, Yun Wu, Dechao Liu
Software Mentions: 1
Published: almost 7 years ago
10.1002/chem.201604705
Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM BenchmarksCited by: 34
Author(s): Birger Dittrich, Jens Lübben, Stefan Mebs, Armin Wagner, Peter Luger, Ralf Flaig
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0058740
Genome Wide Transcriptional Profile Analysis of Vitis amurensis and Vitis vinifera in Response to Cold StressCited by: 90
Author(s): H. P. Xin, Wei Zhu, Lina Wang, Yue Xiang, Linchuan Fang, Jitao Li, Xiaoming Sun, Nian Wang, Jason P. Londo, Shaohua Li
Software Mentions: 1
Published: over 11 years ago
10.1128/AEM.00388-20
Adaptive Laboratory Evolution and Reverse Engineering of Single-Vitamin Prototrophies in Saccharomyces cerevisiaeCited by: 16
Author(s): Thomas Perli, Dewi P. I. Moonen, Marcel van den Broek, Jack T. Pronk, Jean‐Marc Daran
Software Mentions: 1
Published: over 4 years ago