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: about 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 classification
Cited by: 2
Author(s): Huan Peng
Software Mentions: 9
Published: over 4 years ago

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions
Cited by: 14
Author(s): Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphaël Mourad
Software Mentions: 5
Published: about 3 years ago

10.7554/eLife.51325

Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18
Cited 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: over 4 years ago

10.7554/eLife.59404

Massively multiplex single-molecule oligonucleosome footprinting
Cited 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 data
Cited 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: over 6 years ago

10.1186/s12864-018-4459-6

Prediction of enhancer-promoter interactions via natural language processing
Cited 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 networks
Cited 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 data
Cited 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 Sites
Cited 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 network
Cited 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 photoreceptors
Cited 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 walk
Cited 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 mechanism
Cited by: 29
Author(s): Sungjoon Park, Young Hag Koh, Hwisang Jeon, Hyunjae Kim, Yoonsun Yeo, Jaewoo Kang
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pcbi.1005403

Imputation for transcription factor binding predictions based on deep learning
Cited 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 motifs
Cited by: 2
Author(s): Luis Chumpitaz-Diaz, Md. Abul Hassan Samee, Katherine S. Pollard
Software Mentions: 1
Published: about 3 years ago