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: repDNA

https://packages.ecosyste.ms/registries/pypi.org/packages/repDNA

a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects
2 versions
Latest release: over 9 years ago
15 downloads last month

Papers Mentioning repDNA 19

10.1186/s13321-018-0270-2

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
Cited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 6 years ago

10.1186/s13321-016-0146-2

BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions
Cited by: 36
Author(s): Jie Dong, Zhi‐Jiang Yao, Ming Wen, Min Zhu, Ningning Wang, Hongyu Miao, Aiping Lu, Wenbin Zeng, Dong‐Sheng Cao
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-017-14945-1

iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features
Cited by: 66
Author(s): Shahana Yasmin Chowdhury, Swakkhar Shatabda, Abdollah Dehzangi
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0178217

Automated prediction of emphysema visual score using homology-based quantification of low-attenuation lung region
Cited by: 8
Author(s): Motohiro Nishio, Kazuaki Nakane, Takeshi Kubo, Masahiro Yakami, Yutaka Emoto, Masaki Nishio, Kaori Togashi
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0167165

Effective Feature Selection for Classification of Promoter Sequences
Cited by: 5
Author(s): K. Kouser, P. G. Lavanya, Lalitha Rangarajan, K Acharya Kshitish
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-020-07033-8

Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features
Cited by: 18
Author(s): Zhixun Zhao, Xiaocai Zhang, Fang Chen, Liang Fang, Jinyan Li
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-018-2535-1

Sequence-based bacterial small RNAs prediction using ensemble learning strategies
Cited by: 14
Author(s): Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue, Wen Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1093/bib/bby028

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites
Cited by: 151
Author(s): Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo‐Chen Chou
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0187371

Selection and classification of gene expression in autism disorder: Use of a combination of statistical filters and a GBPSO-SVM algorithm
Cited by: 26
Author(s): Shilan S. Hameed, Rohayanti Hassan, Fahmi Fariq Muhammad
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0185570

The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies
Cited by: 4
Author(s): Abdulkadir Elmas, Xiaodong Wang, Jacqueline M. Dresch
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-19491-y

A Novel Modeling in Mathematical Biology for Classification of Signal Peptides
Cited by: 68
Author(s): Asma Ehsan, Khalid Mahmood, Yaser Daanial Khan, Sher Afzal Khan, Kuo‐Chen Chou
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes8110326

Taxonomic Classification for Living Organisms Using Convolutional Neural Networks
Cited by: 14
Author(s): Saed Khawaldeh, Usama Pervaiz, Mohammed Elsharnoby, Alaa Eddin Alchalabi, Nayel Al-Zubi
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0174392

ML2Motif—Reliable extraction of discriminative sequence motifs from learning machines
Cited by: 6
Author(s): Marina M.-C. Vidovic, Marius Kloft, Klaus‐Robert Müller, Nico Görnitz
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1006616

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions
Cited by: 117
Author(s): Wen Zhang, Xiang Yue, Guping Tang, Wenjian Wu, Feng Huang, Xining Zhang
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-017-08523-8

iSS-PC: Identifying Splicing Sites via Physical-Chemical Properties Using Deep Sparse Auto-Encoder
Cited by: 21
Author(s): Zhaochun Xu, Peng Wang, Wang-Ren Qiu, Xuan Xiao
Software Mentions: 1
Published: about 7 years ago

10.1155/2016/3981478

Identifying the Types of Ion Channel-Targeted Conotoxins by Incorporating New Properties of Residues into Pseudo Amino Acid Composition
Cited by: 11
Author(s): Yun Wu, Yufei Zheng, Hua Tang
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.13331

Identification of potential genes for human ischemic cardiomyopathy based on RNA-Seq data
Cited by: 6
Author(s): Li Wan, Liansheng Li, Shiying Zhang, Ce Zhang, Hao Huang, Yiran Li, Erqiang Hu, Gun Deng, Shanshan Guo, Yahui Wang, Weimin Liu, Lina Chen
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms18112400

UltraPse: A Universal and Extensible Software Platform for Representing Biological Sequences
Cited by: 15
Author(s): Pu-Feng Du, Wei Zhao, Yang-Yang Miao, Leyi Wei, Likun Wang
Software Mentions: 1
Published: almost 7 years ago

10.3389/fgene.2019.01148

Projection-Based Neighborhood Non-Negative Matrix Factorization for lncRNA-Protein Interaction Prediction
Cited by: 15
Author(s): Yingjun Ma, Tingting He, Xingpeng Jiang
Software Mentions: 1
Published: almost 5 years ago