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Journal of Computational Biology, Volume 26
Volume 26, Number 1, January 2019
- Yanshen Yang, Jeffrey A. Robertson, Zhen Guo
, Jake Martinez, Christy A. Coghlan, Lenwood S. Heath:
MCAT: Motif Combining and Association Tool. 1-15 - Defne Surujon
Small-World Networks and RNA Secondary Structures. 16-26 - Eliran Avni, Sagi Snir:
A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality. 27-37 - Dat Duong, Wasi Uddin Ahmad, Eleazar Eskin, Kai-Wei Chang, Jingyi Jessica Li
Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. 38-52 - Vaddadi Naga Sai Kavya
Sequence Alignment on Directed Graphs. 53-67 - Eduard Fomin
A Simple Approach to the Reconstruction of a Set of Points from the Multiset of Pairwise Distances in n2 Steps for the Sequencing Problem: III. Noise Inputs for the Beltway Case. 68-75 - Daniel Mellem, Frank Fischer
Mitochondrial Morphologies Driven by Energy-Consuming Cell Sites in a Spatially and Time-Resolved Quality Model. 76-85 - Shih-Chiang Lo, Feng-You Liu, Wun-Sin Jhang, Che-Chi Shu
The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression. 86-95 - Michael Ta, Changchuan Yin
A Workflow to Improve Variant Calling Accuracy in Molecular Barcoded Sequencing Reads. 96-103
Volume 26, Number 2, February 2019
- Gopinath Samykannu, Princy Vijayababu, Christian Bharathi Antonyraj, Perumal Perumal, Sundarabaalaji Narayanan, Syed Ibrahim Basheer Ahamed, Jeyakumar Natarajan:
In Silico Characterization of B Cell and T Cell Epitopes for Subunit Vaccine Design of Salmonella typhi PgtE: A Molecular Dynamics Simulation Approach. 105-116 - Filip Zavadil Kokás, Véronique Bergougnoux
SATrans: New Free Available Software for Annotation of Transcriptome and Functional Analysis of Differentially Expressed Genes. 117-123 - Vasily Ershov
IonHammer: Homopolymer-Space Hamming Clustering for IonTorrent Read Error Correction. 124-127 - Sihai Yang, Xianhua Han, Yen-Wei Chen:
Three-Dimensional Embryonic Image Segmentation and Registration Based on Shape Index and Ellipsoid-Fitting Method. 128-142 - Changchuan Yin
Encoding and Decoding DNA Sequences by Integer Chaos Game Representation. 143-151 - Lisa Uechi, David J. Galas, Nikita A. Sakhanenko
Multivariate Analysis of Data Sets with Missing Values: An Information Theory-Based Reliability Function. 152-171
Volume 26, Number 3, March 2019
- Christopher L. Barrett, Qijun He
A Boltzmann Sampler for 1-Pairs with Double Filtration. 173-192 - Xiaodong Wang, Lei Wang:
Computing Nonoverlapping Inversion Distance Between Two Strings in Linear Average Time. 193-201 - Heewon Park, Makoto Yamada
Robust Sample-Specific Stability Selection with Effective Error Control. 202-217 - Xiaodan Mao, Yichen Xu, Zhenran Jiang:
HColonDB: A Database for Human Colon Cancer Research. 218-224 - Husayn Ahmed P.
INDEX-db: The Indian Exome Reference Database (Phase I). 225-234 - Monika Piwowar
Directional Association Measurement in Contingency Tables: Genomic Case. 235-240 - Yuandi Wang, Qingmei Wen, Zhigang Zhou, Nanjun Yan:
Cell Modeling Based on Bubbles with Weighted Membranes. 241-265 - Roberto Solar, Victor Sepulveda, Alonso Inostrosa-Psijas
A Service-Oriented Platform for Approximate Bayesian Computation in Population Genetics. 266-279 - Baekdoo Kim, Thahmina Ali, Changsu Dong, Carlos Lijeron, Raja Mazumder
miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines. 280-284 - Andreas D. M. Gunawan, Hongwei Yan, Louxin Zhang:
Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. 285-294
Volume 26, Number 4, April 2019
- Soonweng Cho, Hyun-Seok Kim, Martha A. Zeiger, Christopher Umbricht, Leslie M. Cope:
Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays. 295-304 - Rafal Zaborowski, Bartek Wilczynski:
BPscore: An Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations. 305-314 - Yi Wang
Protein Sequence Classification Using Natural Vector and Convex Hull Method. 315-321 - Paulina Urban
Dendritic Spines Taxonomy: The Functional and Structural Classification • Time-Dependent Probabilistic Model of Neuronal Activation. 322-335 - Kyu Min Lee, Minhyeok Lee
Regression-Based Network Estimation for High-Dimensional Genetic Data. 336-349 - Yusong Ye
Stochastic Telomere Shortening and the Route to Limitless Replicative Potential. 350-363 - Yuewen Qi, Haowen Qi, Zeyuan Liu, Peiyuan He, Bingqing Li:
Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer. 364-375 - Bruno César Feltes
CuMiDa: An Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research. 376-386 - Huan Liu, Li Liu, Hong Zhu:
The Role of Significantly Deregulated MicroRNAs in Recurrent Cervical Cancer Based on Bioinformatic Analysis of the Cancer Genome Atlas Data. 387-395 - Luigi Marongiu
Mingle: A Command Line Utility for Merging Multi-fasta Files. 396-404
Volume 26, Number 5, May 2019
- Prachi Kothiyal
Mendelian Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error. 405-419 - Andre Rodrigues Oliveira
Sorting by Weighted Reversals and Transpositions. 420-431 - Jaegyoon Ahn, Junhyeok Choi, Harrim Kim, Jibum Kim
RN+: A Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein-Protein Interaction Network. 432-441 - Guilherme Torres Castro, Luis Enrique Zárate
A Fast Parallel K-Modes Algorithm for Clustering Nucleotide Sequences to Predict Translation Initiation Sites. 442-456 - Guru Raj Rao Ravi
Exploration of N5-CAIR Mutase Novel Inhibitors from Pyrococcus horikoshii OT3: A Computational Study. 457-472 - Xi Hu, Wenling Yi, Ling Jiang, Sijia Wu, Yan Zhang, Jianqiang Du
Classification of Metaphase Chromosomes Using Deep Convolutional Neural Network. 473-484 - Zide Chen, Jiehua Chen, Xuan Huang, Yi Wu, Kuiyuan Huang, Weikang Xu, Linqing Xie, Xiaoyong Zhang, Hongyan Liu:
Identification of Potential Key Genes for Hepatitis B Virus-Associated Hepatocellular Carcinoma by Bioinformatics Analysis. 485-494 - Wei Liang, Yuxiao Yang, Yusi Fang, Zhongying Zhao, Jie Hu
Bayesian Detection of Abnormal Asynchrony of Division Between Sister Cells in Mutant Caenorhabditis elegans Embryos. 495-505
Volume 26, Number 6, June 2019
- Abdoulaye Baniré Diallo, Engelbert Mephu Nguifo, Wajdi Dhifli
Selected Papers from the Workshop on Computational Biology: Joint with the International Joint Conference on Artificial Intelligence and the International Conference on Machine Learning, 2018. 507-508
- Romain Menegaux, Jean-Philippe Vert:
Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics. 509-518 - Dylan Lebatteux, Amine M. Remita
Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences. 519-535 - Andreea Deac, Petar Velickovic, Pietro Sormanni
Attentive Cross-Modal Paratope Prediction. 536-545 - Antonio Khalil Moretti, Andrew Stirn, Gabriel Marks, Itsik Pe'er:
Autoencoding Topographic Factors. 546-560 - Rabie Saidi
Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs. 561-571 - Hamid Eghbal-Zadeh, Lukas Fischer
DeepSNP: An End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data. 572-596 - Brenden K. Petersen
Deep Reinforcement Learning and Simulation as a Path Toward Precision Medicine. 597-604 - Qingyu Chen, Xiuzhen Zhang, Yu Wan
Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. 605-617 - Alexandre Bazin, Didier Debroas, Engelbert Mephu Nguifo
A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data. 618-624
Volume 26, Number 7, July 2019
- Sorin Istrail, Isabelle S. Peter
How Does the Regulatory Genome Work?
- Ute Deichmann:
Special Issue: Genomic Regulation: Experiments, Computational Modeling, and Philosophy. 625-628
- Michel Morange:
A Time to Model and a Time to Experiment. 629-636 - Ute Deichmann:
From Gregor Mendel to Eric Davidson: Mathematical Models and Basic Principles in Biology. 637-652 - Sorin Istrail:
Eric Davidson's Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic cis-Regulatory Code. 653-684 - James Briscoe:
Understanding Pattern Formation in Embryos: Experiment, Theory, and Simulation. 696-702 - Ellen Rothenberg
Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges. 703-718 - Aldo Ciau-Uitz
Gene Regulatory Networks Governing the Generation and Regeneration of Blood. 719-725 - Anthony S. Travis:
Chemical Modeling: From Paul Ehrlich's Dyes to β-Blockers - A Brief History. 726-734 - Douglas H. Erwin
Prospects for a General Theory of Evolutionary Novelty. 735-744 - Jonathan Engel, Isana Veksler-Lublinsky
Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes. 745-766
Volume 26, Number 8, August 2019
- Zhipeng Cai
Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018). 767-768
- Huiyu Li, Shengjun Li, Junliang Shang, Jin-Xing Liu, Chun-Hou Zheng:
A Dynamic Scale-Free Network Particle Swarm Optimization for Extracting Features on Multi-Omics Data. 769-781 - Krzysztof Gogolewski
Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell RNA Sequencing Data. 782-793 - Ben Yohay, Sagi Snir:
Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data. 794-805 - Sagi Snir:
Bounds on Identification of Genome Evolution Pacemakers. 806-821 - Marmar Moussa
Locality Sensitive Imputation for Single Cell RNA-Seq Data. 822-835 - Qingfeng Chen, Canshang Deng, Wei Lan
Identifying Interactions Between Kinases and Substrates Based on Protein-Protein Interaction Network. 836-845
- Wolfgang Kopp
DNA Motif Match Statistics Without Poisson Approximation. 846-865 - Juan Pablo Acosta, Silvia Restrepo
Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments. 866-874 - Dahye Chung, Kaiyuan Zhang, Jihoon Yang:
Method for Identifying Cancer-Related Genes Using Gene Similarity-Based Collaborative Filtering. 875-881 - Shahid Hussain, Javed Ferzund, Raza Ul-Haq:
Prediction of Drug Target Sensitivity in Cancer Cell Lines Using Apache Spark. 882-889
Volume 26, Number 9, September 2019
Preface
- Carlos Martín-Vide, Miguel A. Vega-Rodríguez
Preface. 891-892
- Jesper Jansson
An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. 893-907 - Gabriel H. G. Silva, Edans F. de O. Sandes, George Teodoro, Alba C. M. A. Melo
Using Multiple Fickett Bands to Accelerate Biological Sequence Comparisons. 908-922
- Shuto Hayashi
ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data. 923-937 - Xiaodong Wang, Lei Wang, Daxin Zhu
Efficient Computation of Longest Common Subsequences with Multiple Substring Inclusive Constraints. 938-947 - Paola Bonizzoni, Gianluca Della Vedova
Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array. 948-961 - Muslum Yildiz, Abdulkadir Kocak
Molecular Dynamics Studies of Histo-Blood Group Antigen Blocking Human Immunoglobulin A Antibody and Escape Mechanism in Noroviruses Upon Mutation. 962-974 - Yushuang Yang, Wei Yang, Ling Jin:
The Role of Long Non-coding RNA Prostate Cancer-Associated Transcript 1 in Prostate Cancer. 975-984 - Mohammad S. Rahman
Analyzing Tumor Heterogeneity by Incorporating Long-Range Mutational Influences and Multiple Sample Data into Heterogeneity Factorial Hidden Markov Model. 985-1002 - Jacques Demongeot
Bias for 3′-Dominant Codon Directional Asymmetry in Theoretical Minimal RNA Rings. 1003-1012 - Fangfang Ge, Yi Wang, Huayang Li, Rui Zhang, Xiaotong Wang, Qingyun Li, Zhenchang Liang, Long Yang:
Plant-GQ: An Integrative Database of G-Quadruplex in Plant. 1013-1019 - Zhicheng Li, Shijian Li
Scaled Alternating Steepest Descent Algorithm Applied for Protein Structure Determination from Nuclear Magnetic Resonance Data. 1020-1029 - Guo Mao, Shu-Lin Wang, Wei Zhang:
Prediction of Potential Associations Between MicroRNA and Disease Based on Bayesian Probabilistic Matrix Factorization Model. 1030-1039
Volume 26, Number 10, October 2019
- Sergey A. Solodskikh
Predictive Estimates of Risks Associated with Type 2 Diabetes Mellitus on the Basis of Biochemical Biomarkers and Derived Time-Dependent Parameters. 1041-1049 - Louis Z. Yang, Ming Yang:
Modeling Biological Oscillations: Integration of Short Reaction Pauses into a Stationary Model of a Negative Feedback Loop Generates Sustained Long Oscillations. 1050-1066 - Yan Ye, Chunde Bao, Wei Fan:
Overexpression of miR-101 May Target DUSP1 to Promote the Cartilage Degradation in Rheumatoid Arthritis. 1067-1079 - Qi Li, Zhengqiang Luo:
Identification of Candidate Genes for Skeletal Muscle Injury Prevention in Two Different Types. 1080-1089 - Qi Li, Zhengqiang Luo:
Transcriptional Regulatory Network Analysis to Reveal the Key Genes Involved in Skeletal Muscle Injury. 1090-1099 - Neeraj Budhlakoti, Dwijesh Chandra Mishra, Anil Rai
A Comparative Study of Single-Trait and Multi-Trait Genomic Selection. 1100-1112 - Xiao Liang, William Chad Young, Ling-Hong Hung, Adrian E. Raftery, Ka Yee Yeung:
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. 1113-1129 - Chao Sun, Yifan Gu, Guoqing Chen, Yibao Du:
Bioinformatics Analysis of Stromal Molecular Signatures Associated with Breast and Prostate Cancer. 1130-1139 - Liang Wang, Yuquan Pei, Shaolei Li, Shanyuan Zhang, Yue Yang:
Distinct Molecular Mechanisms Analysis of Three Lung Cancer Subtypes Based on Gene Expression Profiles. 1140-1155 - Fatima Ghrifi, Loubna Allam, Lakhlili Wiame, Azeddine Ibrahimi
Curcumin-Synthetic Analogs Library Screening by Docking and Quantitative Structure-Activity Relationship Studies for AXL Tyrosine Kinase Inhibition in Cancers. 1156-1167 - Yudong Zhang, Wenxiang Wu, Hao Qu:
Integrated Analysis of the Gene Expression Changes During Colorectal Cancer Progression by Bioinformatic Methods. 1168-1176 - Victor Hugo Urrutia-Baca
Immunoinformatics Approach to Design a Novel Epitope-Based Oral Vaccine Against Helicobacter pylori. 1177-1190
Volume 26, Number 11, November 2019
- Michael Rosenthal, Darshan W. Bryner, Fred W. Huffer, Shane Evans, Anuj Srivastava
Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data. 1191-1202 - Yue Wu, Farhad Hormozdiari, Jong Wha J. Joo, Eleazar Eskin:
Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies. 1203-1213 - Luís Felipe I. Cunha, Fábio Protti:
Genome Rearrangements on Multigenomic Models: Applications of Graph Convexity Problems. 1214-1222 - Andre Rodrigues Oliveira
On the Complexity of Sorting by Reversals and Transpositions Problems. 1223-1229 - Chaokun Yan, Wen-Xiu Wang, Ge Zhang, Jian-Lin Wang, Ashutosh Patel:
BiRWDDA: A Novel Drug Repositioning Method Based on Multisimilarity Fusion. 1230-1242 - Chaoxuan Dong, Xiao-Yan Chen, Chao-Yi Dong:
Discerning Functional Connections in the Pulsed Neural Networks with the Dynamic Bayesian Network Structure Search Method Based on a Genetic Algorithm. 1243-1252 - Yulia M. Suvorova, Eugene V. Korotkov
New Method for Potential Fusions Detection in Protein-Coding Sequences. 1253-1261 - Bao-Xinzi Liu, Guan-Jiang Huang
Comprehensive Analysis of Core Genes and Potential Mechanisms in Rectal Cancer. 1262-1277 - Feng Li, Peiyuan Guo, Keqin Dong, Peng Guo, Haoyuan Wang, Xianqiang Lv:
Identification of Key Biomarkers and Potential Molecular Mechanisms in Renal Cell Carcinoma by Bioinformatics Analysis. 1278-1295 - Shangjie Ai, Guanfei Lin, Yong Bai, Xiande Liu
QSAR Classification-Based Virtual Screening Followed by Molecular Docking Identification of Potential COX-2 Inhibitors in a Natural Product Library. 1296-1315 - Shunxin Zheng, Liuhong Yang, Yisong Dai, Lifang Jiang, Yi Wei, Hongwei Wen, Yingfang Xu:
Screening and Survival Analysis of Hub Genes in Gastric Cancer Based on Bioinformatics. 1316-1325 - Yufang Li, Aoshen Wu, Gang Liu, Lei Liu:
A Review of Methods to Quantify the Genomic Similarity of Topological Associating Domains. 1326-1338
Volume 26, Number 12, December 2019
- Denis Kazakiewicz, Jürgen Claesen
A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data. 1339-1348 - David Toubiana
A Genetic Algorithm to Optimize Weighted Gene Co-Expression Network Analysis. 1349-1366 - Kexin Shen, Shujuan Zhang, Shurong Ma, Haishan Zhang:
Molecular Markers and Diagnostic Model Specific for Barrett's Esophagus. 1367-1378 - Yong Qiu, Ling-Bing Meng, Chenyi Di, Yuhu Huo, Bochen Yao, Tengjiao Zhang, Zhen Hua:
Exploration of the Differentially Expressed Long Noncoding RNAs and Genes of Morphine Tolerance via Bioinformatic Analysis. 1379-1393 - Jie Wu, Yijian Zhang, Maolan Li:
Identification of Methylation Markers and Differentially Expressed Genes with Prognostic Value in Breast Cancer. 1394-1408 - Xi Jia, Qian Zhao, Yuanyuan Zhang, Yiping Dong, Li Lei, Ramone A. Williamson, Yutiantian Lei, Xinyue Tan, Dan Zhang, Jinsong Hu
Identification of a Five-CpG Signature with Diagnostic Value in Thyroid Cancer. 1409-1417 - Hengxi Chen, Shuting Cheng, Chang Liu, Jing Fu, Wei Huang:
Bioinformatics Analysis of Differentially Expressed Genes, Methylated Genes, and miRNAs in Unexplained Recurrent Spontaneous Abortion. 1418-1426 - B. Sharan Sharma
A Systematic Bioinformatics Approach to Motif-Based Analysis of Human Locus Control Regions. 1427-1437 - Xinxin Liu, Xinqiang Li:
Key Genes Involved in Diabetic Nephropathy Investigated by Microarray Analysis. 1438-1447 - Mingxiang Wen, Xiang Qu, Yanyan Zhu, Lingfang Tian, Zhongqin Shen, Xiulin Yang, Xianqing Shi:
Exploration of Novel Biomarkers in Vasculitis by Integrated Bioinfomatic Approaches. 1448-1457 - Wilson Alberto Tárraga, Horacio Alberto Garda, Juan Domingo Toledo, Marina Cecilia Gonzalez:
Potential Inhibitors of the Activity of the Cholesterol-Ester Transfer Protein. 1458-1469 - Avinash Mishra
Identification of a Novel Scaffold for Inhibition of Dipeptidyl Peptidase-4. 1470-1486
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