Journal: J. Bioinformatics and Computational Biology

Volume 17, Issue 6

0 -- 0Ahmed Bin Zaman, Amarda Shehu. Building maps of protein structure spaces in template-free protein structure prediction
0 -- 0Chun Fang, Yoshitaka Moriwaki, Caihong Li, Kentaro Shimizu. MoRFPred_en: Sequence-based prediction of MoRFs using an ensemble learning strategy
0 -- 0Lei Gao, Cong Wu, Lin Liu. AUSPP: A universal short-read pre-processing package
0 -- 0Kazi Lutful Kabir, Nasrin Akhter, Amarda Shehu. From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state models
0 -- 0Tatsuya Sekiguchi, Hiroyuki Hamada, Masahiro Okamoto. WinBEST-KIT: Biochemical reaction simulator that can define and customize algebraic equations and events as GUI components
0 -- 0Bifang He, Jian Huang 0004, Heng Chen. PVsiRNAPred: Prediction of plant exclusive virus-derived small interfering RNAs by deep convolutional neural network
0 -- 0Qin Ding 0001, Oliver Eulenstein, Hisham Al-Mubaid. Foreword: Special Issue for the 2019 International Conference on Bioinformatics and Computational Biology (BICOB-2019)
0 -- 0Peng Li, Maozu Guo 0001, Bo Sun 0006. Integration of multi-omics data to mine cancer-related gene modules
0 -- 0Huiqing Wang, Yuanyuan Lian, Chun Li, Yue Ma, Zhiliang Yan, Chunlin Dong. SIN-KNO: A method of gene regulatory network inference using single-cell transcription and gene knockout data
0 -- 0Yuan Liu, Yongchao Ma, Evan Salsman, Frank A. Manthey, Elias M. Elias, Xuehui Li, Changhui Yan. An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis
0 -- 0Abolfazl Bahrami, Ali Najafi, Mohammadreza Hashemi, Seyed Reza Miraie-Ashtiani. PSSP: Protein splice site prediction algorithm using Bayesian approach

Volume 17, Issue 5

0 -- 0Yoshihiro Shibuya, Matteo Comin. Indexing k-mers in linear space for quality value compression
0 -- 0Farhad Maleki, Katie L. Ovens, Daniel J. Hogan, Elham Rezaei, Alan M. Rosenberg, Anthony J. Kusalik. Measuring consistency among gene set analysis methods: A systematic study
0 -- 0Qiangrong Jiang, Guang Qiu. Graph kernels combined with the neural network on protein classification
0 -- 0Vishan Kumar Gupta, Prashant Singh Rana. Toxicity prediction of small drug molecules of androgen receptor using multilevel ensemble model
0 -- 0Pietro Bongini, Neri Niccolai, Monica Bianchini. Glycine-induced formation and druggability score prediction of protein surface pockets
0 -- 0Abdelhakim El Fatmi, Ali Bekri, Said Benhlima. RNAknot: A new algorithm for RNA secondary structure prediction based on genetic algorithm and GRASP method
0 -- 0Ting-Hua Huang, Xiali Huang, Min Yao. Min3: Predict microRNA target gene using an improved binding-site representation method and support vector machine
0 -- 0Elisabetta De Maria. Introduction to JBCB Special Issue on BIOINFORMATICS 2019
0 -- 0Rick Gelhausen, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Martin Raden. IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction

Volume 17, Issue 4

1950015 -- 0Shuhei Kimura, Masato Tokuhisa, Mariko Okada. Inference of genetic networks using random forests: Assigning different weights for gene expression data
1950020 -- 0P. V. Sunil Kumar, G. Gopakumar 0001. Inferring disease and pathway associations of long non-coding RNAs using heterogeneous information network model
1950021 -- 0Qiang Yu 0003, Xiang Zhao, Hongwei Huo. A new algorithm for DNA motif discovery using multiple sample sequence sets
1950022 -- 0Huiqing Wang, Chun Li, Jianhui Zhang, Jingjing Wang, Yue Ma, Yuanyuan Lian. A new LSTM-based gene expression prediction model: L-GEPM
1950023 -- 0Luowen Liu, Jing Liu 0006. A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps
1950024 -- 0Ting-Hua Huang, Xiali Huang, Bomei Shi, Min Yao. GEREDB: Gene expression regulation database curated by mining abstracts from literature
1950025 -- 0Sovan Saha, Abhimanyu Prasad, Piyali Chatterjee, Subhadip Basu, Mita Nasipuri. Protein function prediction from dynamic protein interaction network using gene expression data
1950027 -- 0Natalia Rubanova, Nadya Morozova. Centrality and the shortest path approach in the human interactome
1950028 -- 0Md. Ashad Alam, Osamu Komori, Hong-Wen Deng, Vince D. Calhoun, Yu-Ping Wang. Robust kernel canonical correlation analysis to detect gene-gene co-associations: A case study in genetics
1950029 -- 0Fang Yuan, Gan Liu, Xiwen Yang, Shunfang Wang, Xueren Wang. Prediction of oxidoreductase subfamily classes based on RFE-SND-CC-PSSM and machine learning methods

Volume 17, Issue 3

1902002 -- 0Yen-Wei Chu, Yu-Hong Lee. Selected Papers from the International Workshop on Cancer Bioinformatics and Intelligent Medicine (CBIM2018)
1940005 -- 0Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu. Deep learning with evolutionary and genomic profiles for identifying cancer subtypes
1940006 -- 0Jung-Yu Lee, Si-yu Lin, Chun-Yu Lin, Yi-Hsuan Chuang, Sing-Han Huang, Yu-Yao Tseng, Hung-Jung Wang, Jinn-Moon Yang. Identification of the PCA29 gene signature as a predictor in prostate cancer
1940007 -- 0Teppei Matsubara, Tomoshiro Ochiai, Morihiro Hayashida, Tatsuya Akutsu, Jose C. Nacher. Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles
1940008 -- 0Yoshiaki Sota, Shigeto Seno, Hironori Shigeta, Naoki Osato, Masafumi Shimoda, Shinzaburo Noguchi, Hideo Matsuda. Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads
1950011 -- 0Daniel Inostroza, Cecilia Hernández, Diego Seco, Gonzalo Navarro, Alvaro Olivera-Nappa. Cell cycle and protein complex dynamics in discovering signaling pathways
1950014 -- 0Rumen Andonov, Hristo Djidjev, Sebastien François, Dominique Lavenier. Complete assembly of circular and chloroplast genomes based on global optimization
1950017 -- 0Matthew Stephenson, Gerarda A. Darlington, Flavio S. Schenkel, E. James Squires, R. Ayesha Ali. DSRIG: Incorporating graphical structure in the regularized modeling of SNP data
1950018 -- 0Jamshid Pirgazi, Ali Reza Khanteymoori, Maryam Jalilkhani. TIGRNCRN: Trustful inference of gene regulatory network using clustering and refining the network
1950019 -- 0Rishika Sen, Losiana Nayak, Rajat K. De. PyPredT6: A python-based prediction tool for identification of Type VI effector proteins

Volume 17, Issue 2

1950006 -- 0Ashish Runthala, Shibasish Chowdhury. Refined template selection and combination algorithm significantly improves template-based modeling accuracy
1950007 -- 0Farzad Peyravi, Alimohammad Latif, Seyed Mohammad Moshtaghioun. Protein tertiary structure prediction using hidden Markov model based on lattice
1950008 -- 0Sanjeev Kumar, Suneeta Agarwal, Ranvijay. Fast and memory efficient approach for mapping NGS reads to a reference genome
1950009 -- 0Polina Zhornikova, Nina Golyandina, Alexander V. Spirov. Noise model estimation with application to gene expression
1950012 -- 0Ali Cuvitoglu, Joseph Xu Zhou, Sui Huang, Zerrin Isik. Predicting drug synergy for precision medicine using network biology and machine learning
1950013 -- 0Yaxing Zhao, Andrew Chi-Hau Sue, Wilson Wen Bin Goh. Deeper investigation into the utility of functional class scoring in missing protein prediction from proteomics data

Volume 17, Issue 1

1902001 -- 0Yuriy L. Orlov, Ralf Hofestädt, Tatiana V. Tatarinova. Bioinformatics research at BGRS\SB-2018
1940001 -- 0Anastasiya Rudik, Vladislav M. Bezhentsev, Alexander V. Dmitriev, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov. Metatox - Web application for generation of metabolic pathways and toxicity estimation
1940002 -- 0Alexey Penenko, Ulyana S. Zubairova, Zhadyra Mukatova, Sergey Nikolaev. Numerical algorithm for morphogen synthesis region identification with indirect image-type measurement data
1940003 -- 0Anna Sergeevna Batova, Aleksandr Nikolaevich Bugay, Ermuhammad Berdimurodovich Dushanov. Effect of mutant NMDA receptors on the oscillations in a model of hippocampus
1940004 -- 0Natalia G. Novoselova. Numerical constructions of optimal feedback in models of chemotherapy of a malignant tumor
1950001 -- 0Wei Zhang 0079, Jia Xu 0002, Yuanyuan Li, Xiufen Zou. Integrating network topology, gene expression data and GO annotation information for protein complex prediction
1950002 -- 0Youming Lu, Lei Yuan, Xin Chen, Aijun Zhang, Pengqi Zhang, Dongdong Zou. Systematic analysis and identification of unexpected interactions from the neuroprotein drug interactome in hydrocephalus pharmacological intervention
1950003 -- 0Anna V. Kudryavtseva, Elena N. Lukyanova, Sergey L. Kharitonov, Kirill M. Nyushko, Alexey A. Krasheninnikov, Elena A. Pudova, Zulfiya G. Guvatova, Boris Y. Alekseev, Marina V. Kiseleva, Andrey D. Kaprin, Alexey A. Dmitriev, Anastasiya V. Snezhkina, George S. Krasnov. Bioinformatic identification of differentially expressed genes associated with prognosis of locally advanced lymph node-positive prostate cancer
1950004 -- 0Chun Fang, Yoshitaka Moriwaki, Aikui Tian, Caihong Li, Kentaro Shimizu. Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method
1950005 -- 0Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Yu-Yen Ou. Using two-dimensional convolutional neural networks for identifying GTP binding sites in Rab proteins
1950010 -- 0Oxana V. Galzitskaya, Georgii S. Novikov, Nikita V. Dovidchenko, Michail Yu. Lobanov. Is there codon usage bias for poly-Q stretches in the human proteome?