Journal of Bioinformatics and Computational Biology, Volume 18

Volume 18, Number 1, February 2020

Regular Paper: Research Paper

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  Joshua W. K. Ho:
  Introduction to the Special Issue on GIW/ABACBS 2019. 2002001:1-2002001:3

Research Paper

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  Rui Yin, Yu Zhang, Xinrui Zhou, Chee Keong Kwoh:
  Time series computational prediction of vaccines for influenza A H3N2 with recurrent neural networks. 2040002:1-2040002:17
• 
  Nazmus Salehin, Patrick P. L. Tam, Pierre Osteil:
  Prenet: Predictive network from ATAC-SEQ data. 2040003:1-2040003:15
• 
  Julie M. Deeke, Johann Gagnon-Bartsch:
  Stably expressed genes in single-cell RNA sequencing. 2040004:1-2040004:21

Regular Paper: Research Paper

• 
  Dimitrios Zisis, Pawel Krajewski, Maike Stam, Blaise Weber, Iris Hövel:
  Analysis of 4C-seq data: A comparison of methods. 2050001:1-2050001:20
• 
  Mingyu Oh, Kipoong Kim, Hokeun Sun:
  Covariance thresholding to detect differentially co-expressed genes from microarray gene expression data. 2050002:1-2050002:19
• 
  Gábor Balogh, Stephan H. Bernhart, Peter F. Stadler, Jana Schor:
  A probabilistic version of Sankoff's maximum parsimony algorithm. 2050004:1-2050004:19
• 
  Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Bahram Goliaei:
  A novel pattern matching algorithm for genomic patterns related to protein motifs. 2050011:1-2050011:19
• 
  Samuel Chorlton:
  Reanalysis of Alzheimer's brain sequencing data reveals absence of purported HHV6A and HHV7. 2050012:1-2050012:5

Volume 18, Number 2, April 2020

Regular Research Paper

• 
  Mikhail A. Orlov, Anatoly A. Sorokin:
  DNA sequence, physics, and promoter function: Analysis of high-throughput data On T7 promoter variants activity. 2040001:1-2040001:15
• 
  Yourim Yoon, Yong-Hyuk Kim:
  Optimizing taxon addition order and branch lengths in the construction of phylogenetic trees using maximum likelihood. 2050003:1-2050003:16
• 
  Sanjay S. Bankapur, Nagamma Patil:
  ProgSIO-MSA: Progressive-based single iterative optimization framework for multiple sequence alignment using an effective scoring system. 2050005:1-2050005:28
• 
  Alexsandro Oliveira Alexandrino, Carla Negri Lintzmayer, Zanoni Dias:
  Sorting permutations by fragmentation-weighted operations. 2050006:1-2050006:31
• 
  Pengyu Li, He Zhang, Xuyang Zhao, Cangzhi Jia, Fuyi Li, Jiangning Song:
  Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins. 2050008:1-2050008:21
• 
  Karuppasamy Muthuvel Prasath, Suresh Venkateswaran, Subbiah Parthasarathy:
  PDB-2-PBv3.0: An updated protein block database. 2050009:1-2050009:11
• 
  Soyoun Hwang, Taekeon Lee, Youngmi Yoon:
  Exploring disease comorbidity in a module-module interaction network. 2050010:1-2050010:18
• 
  Parvaiz Ahmad Naik, Jian Zu:
  Modeling and simulation of spatial-temporal calcium distribution in T lymphocyte cell by using a reaction-diffusion equation. 2050013:1-2050013:22
• 
  S. N. Fedotov:
  An approach to computer analysis of the ligand binding assay data on example of radioligand assay data. 2050014:1-2050014:12

Volume 18, Number 3, June 2020

Special Issue: Selected Papers from the 10th International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2019)

• 
  Elisabetta De Maria, Morgan Magnin:
  Introduction to the JBCB special issue on CSBio 2019. 2002002:1-2002002:2

Special Issue: Selected Papers from the 4th CCF Bioinformatics Conference (CBC 2019)

• 
  Shuigeng Zhou:
  Introduction to the JBCB special issue on CBC 2019. 2002003:1-2002003:2

Special Issue: Selected Papers from the 10th International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2019)

• 
  Sofia Almeida, Madalena Chaves, Franck Delaunay:
  Cell cycle period control through modulation of clock inputs. 2040006:1-2040006:16
• 
  Stephanie Kamgnia Wonkap, Gregory Butler:
  BENIN: Biologically enhanced network inference. 2040007:1-2040007:16
• 
  Gatis Melkus, Peteris Rucevskis, Edgars Celms, Karlis Cerans, Karlis Freivalds, Paulis Kikusts, Lelde Lace, Martins Opmanis, Darta Rituma, Juris Viksna:
  Network motif-based analysis of regulatory patterns in paralogous gene pairs. 2040008:1-2040008:19

Special Issue: Selected Papers from the 4th CCF Bioinformatics Conference (CBC 2019)

• 
  Hong-Dong Li, Yunpei Xu, Xiaoshu Zhu, Quan Liu, Gilbert S. Omenn, Jianxin Wang:
  ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets. 2040009:1-2040009:25
• 
  Heng Yao, Jihong Guan, Tianying Liu:
  Denoising Protein-Protein interaction network via variational graph auto-encoder for protein complex detection. 2040010:1-2040010:28

Regular Paper: Research Paper

• 
  Lei Tian, Shu-Lin Wang:
  Exploring the potential microRNA sponge interactions of breast cancer based on some known interactions. 2050007:1-2050007:15
• 
  Houssemeddine Derbel, Anja Habacha Chaïbi, Henda Hajjami Ben Ghézala:
  Disease named entity recognition using long-short dependencies. 2050015:1-2050015:15
• 
  Jorge Francisco Cutigi, Adriane Feijo Evangelista, Adenilso Simão:
  Approaches for the identification of driver mutations in cancer: A tutorial from a computational perspective. 2050016:1-2050016:32
• 
  Zhongbo Cao, Wei Du, Gaoyang Li, Huansheng Cao:
  DEEPSMP: A deep learning model for predicting the ectodomain shedding events of membrane proteins. 2050017:1-2050017:17

Volume 18, Number 4, August 2020

Review Paper

• 
  Ruiyi Li, Jihong Guan, Shuigeng Zhou:
  Single-cell RNA-seq data clustering: A survey with performance comparison study. 2040005:1-2040005:26

Regular Paper

• 
  Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
  PROSPECT: A web server for predicting protein histidine phosphorylation sites. 2050018:1-2050018:17
• 
  K. G. Kulikov, T. V. Koshlan:
  Modeling the impact of point mutations on the stability of proteins. 2050019:1-2050019:16
• 
  K. Athira, G. Gopakumar:
  An integrated method for identifying essential proteins from multiplex network model of protein-protein interactions. 2050020:1-2050020:21
• 
  Nuh Azginoglu, Zafer Aydin, Mete Celik:
  Structural profile matrices for predicting structural properties of proteins. 2050022:1-2050022:20
• 
  Omid Chatrabgoun, Amin Hosseinian Far, Alireza Daneshkhah:
  Constructing gene regulatory networks from microarray data using non-Gaussian pair-copula Bayesian networks. 2050023:1-2050023:21
• 
  Santhosh Amilpur, Raju Bhukya:
  EDeepSSP: Explainable deep neural networks for exact splice sites prediction. 2050024:1-2050024:18
• 
  Madhusudan Paul, Ashish Anand:
  Impact of low-confidence interactions on computational identification of protein complexes. 2050025:1-2050025:16

Volume 18, Number 5, October 2020

Research Paper

• 
  Gihad N. Sohsah, Ali Reza Ibrahimzada, Huzeyfe Ayaz, Ali Cakmak:
  Scalable classification of organisms into a taxonomy using hierarchical supervised learners. 2050026:1-2050026:22
• 
  Shanchen Pang, Lihua Wang, Shudong Wang, Yuanyuan Zhang, Xinzeng Wang:
  PESM: A novel approach of tumor purity estimation based on sample specific methylation sites. 2050027:1-2050027:14
• 
  Anna Visibelli, Pietro Bongini, Alberto Rossi, Neri Niccolai, Monica Bianchini:
  A deep attention network for predicting amino acid signals in the formation of α-helices. 2050028:1-2050028:17
• 
  Xiao Yu, Tongfeng Weng, Changgui Gu, Huijie Yang:
  Comparison of gene regulatory networks to identify pathogenic genes for lymphoma. 2050029:1-2050029:18
• 
  Dongmei Ai, Gang Liu, Xiaoxin Li, Yuduo Wang, Man Guo:
  Calculation of immune cell proportion from batch tumor gene expression profile based on support vector regression. 2050030:1-2050030:15
• 
  Wensheng Zhang, Yan Dong, Kun Zhang:
  Gene expression analysis reveals a pitfall in the molecular research of prostate tumors relevant to Gleason score. 2050032:1-2050032:10
• 
  Tatiana Lenskaia, Daniel Boley:
  Prokaryote autoimmunity in the context of self-targeting by CRISPR-Cas systems. 2050033:1-2050033:12
• 
  Xiangdong Zhou, Keith C. C. Chan, Zhihua Huang, Jingbin Wang:
  Determining dependency and redundancy for identifying gene-gene interaction associated with complex disease. 2050035:1-2050035:26

Volume 18, Number 6, December 2020

• 
  Dmitry A. Suplatov, Yana A. Sharapova, Vytas K. Svedas:
  EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins. 2040011:1-2040011:18
• 
  Albert No, Mikel Hernaez, Idoia Ochoa:
  CROMqs: An infinitesimal successive refinement lossy compressor for the quality scores. 2050031:1-2050031:22
• 
  Hassan B. Kazemian, Cedric Maxime Grimaldi:
  Cascading classifier application for topology prediction of transmembrane beta-barrel proteins. 2050034:1-2050034:15
• 
  Hongwei Wang, Chunling Jiang, Chenjian Li, Hui Liu:
  Quantificational evaluation of the resolving power of qualitative biomarkers with different cardinal numbers based on a magnitude-standardized index. 2050036:1-2050036:14
• 
  Liang Chen, Shun He, Yuyao Zhai, Minghua Deng:
  Direct interaction network inference for compositional data via codaloss. 2050037:1-2050037:26
• 
  Jorge Parraga-Alava, Mario Inostroza-Ponta:
  Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance. 2050038:1-2050038:21
• 
  Devin Camenares:
  ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences. 2050039:1-2050039:12
• 
  Manuel Villalobos-Cid, Francisco Salinas, Mario Inostroza-Ponta:
  Total evidence or taxonomic congruence? A comparison of methods for combining biological evidence. 2050040:1-2050040:17