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: cran: gkmSVM
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/gkmSVM
Gapped-Kmer Support Vector Machine
9 versions
Latest release: over 1 year ago
305 downloads last month
Papers Mentioning gkmSVM 15
10.7717/peerj.8965
CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classificationCited by: 2
Author(s): Huan Peng
Software Mentions: 9
Published: over 4 years ago
10.1371/journal.pcbi.1009308
DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regionsCited by: 14
Author(s): Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphaël Mourad
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.51325
Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18Cited by: 21
Author(s): Huan Liu, Kaylia Duncan, Annika Helverson, Priyanka Kumari, Camille Mumm, Yuchen Xiao, Jenna C. Carlson, Fabrice Darbellay, Axel Visel, Elizabeth J. Leslie, Patrick Breheny, Albert Erives, Robert A. Cornell
Software Mentions: 5
Published: almost 5 years ago
10.7554/eLife.59404
Massively multiplex single-molecule oligonucleosome footprintingCited by: 41
Author(s): Nour J. Abdulhay, Christopher A. McNally, Laura J Hsieh, Sivakanthan Kasinathan, Aidan M. Keith, Laurel S Estes, Mehran Karimzadeh, Jason G. Underwood, Hani Goodarzi, Geeta J. Narlikar, Vijay Ramani
Software Mentions: 5
Published: almost 4 years ago
10.1093/gigascience/gix136
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics, and epigenetics dataCited by: 24
Author(s): Quan Nguyen, Ross L. Tellam, Marina Naval-Sánchez, Laércio R. Porto-Neto, W. Barendse, Antônio Reverter, Ben J. Hayes, James W. Kijas, Brian P. Dalrymple
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12864-018-4459-6
Prediction of enhancer-promoter interactions via natural language processingCited by: 58
Author(s): Wanwen Zeng, Mengmeng Wu, Rui Jiang
Software Mentions: 3
Published: over 6 years ago
10.1186/s12859-017-1878-3
Predicting enhancers with deep convolutional neural networksCited by: 73
Author(s): Min Xu, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang
Software Mentions: 3
Published: about 7 years ago
10.1038/s41598-017-03554-7
WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq dataCited by: 21
Author(s): Hongbo Zhang, Lin Zhu, De-Shuang Huang
Software Mentions: 3
Published: over 7 years ago
10.1038/s41598-018-33321-1
Recurrent Neural Network for Predicting Transcription Factor Binding SitesCited by: 133
Author(s): Zhen Shen, Wenzheng Bao, De-Shuang Huang
Software Mentions: 3
Published: about 6 years ago
10.1186/s12859-019-3327-y
Antimicrobial peptide identification using multi-scale convolutional networkCited by: 40
Author(s): Xin Su, Jing Xu, Yanbin Yin, Xiongwen Quan, Han Zhang
Software Mentions: 2
Published: almost 5 years ago
10.7554/eLife.67403
Information content differentiates enhancers from silencers in mouse photoreceptorsCited by: 10
Author(s): Ryan Z. Friedman, David M Granas, Connie A. Myers, Joseph C. Corbo, Barak A. Cohen, Michael A. White
Software Mentions: 2
Published: about 3 years ago
10.1038/s41598-018-33413-y
Sequence based prediction of enhancer regions from DNA random walkCited by: 21
Author(s): Anand Pratap Singh, Sarthak Mishra, Suraiya Jabin
Software Mentions: 1
Published: about 6 years ago
10.1038/s41598-020-70218-4
Enhancing the interpretability of transcription factor binding site prediction using attention mechanismCited by: 29
Author(s): Sungjoon Park, Young Hag Koh, Hwisang Jeon, Hyunjae Kim, Yoonsun Yeo, Jaewoo Kang
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pcbi.1005403
Imputation for transcription factor binding predictions based on deep learningCited by: 86
Author(s): Qian Qin, Jianxing Feng
Software Mentions: 1
Published: over 7 years ago
10.1186/s12860-021-00382-6
Systematic identification of non-canonical transcription factor motifsCited by: 2
Author(s): Luis Chumpitaz-Diaz, Md. Abul Hassan Samee, Katherine S. Pollard
Software Mentions: 1
Published: about 3 years ago