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Journal of Computational Biology, Volume 24
Volume 24, Number 1, January 2017
- Jing He, Nurit Haspel, Brian Chen:
Preface: Selected Articles from 2015 Computational Structural Bioinformatics Workshop. 1 - Hu Cao, Yonggang Lu
:
Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment. 2-12 - Jin Seob Kim, Bijan Afsari, Gregory S. Chirikjian:
Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy. 13-30 - Wen Cheng, Changhui Yan:
A Graph Approach to Mining Biological Patterns in the Binding Interfaces. 31-39 - Roshanak Farhoodi, Bahar Akbal-Delibas
Machine Learning Approaches for Predicting Protein Complex Similarity. 40-51 - Stephanie Zeil, Julio A. Kovacs, Willy Wriggers
Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix. 52-67 - Bridget E. Nolan, Emily Levenson, Brian Y. Chen:
Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity. 68-78 - Anastasia Novinskaya, Didier Devaurs
Defining Low-Dimensional Projections to Guide Protein Conformational Sampling. 79-89
Volume 24, Number 2, February 2017
- Adrian-Horia Dediu
Preface: Selected Articles of the Second International Conference on Algorithms for Computational Biology (AlCoB 2015). 91-92 - Nikita Alexeev
Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs. 93-105 - Jesper Jansson
A More Practical Algorithm for the Rooted Triplet Distance. 106-126 - Ron Zeira, Ron Shamir:
Sorting by Cuts, Joins, and Whole Chromosome Duplications. 127-137 - Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level. 138-152 - Elizabeth S. Allman
Statistically Consistent k-mer Methods for Phylogenetic Tree Reconstruction. 153-171 - Xin Tian, Ming-Yuan Xin, Jian Luo
Identification of Genes Involved in Breast Cancer Metastasis by Integrating Protein-Protein Interaction Information with Expression Data. 172-182 - Jie Zhou:
Effect of Protein Repetitiveness on Protein-Protein Interaction Prediction Results Using Support Vector Machines. 183-192
Volume 24, Number 3, March 2017
- Bartek Wilczynski
FastBill: An Improved Tool for Prediction of Cis-Regulatory Modules. 193-199 - Celine Prakash
An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile. 200-212 - David M. Budden, Mitchell Jones
Cautionary Tales of Inapproximability. 213-216 - Li Zhang, Han Wang
OMPcontact: An Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method. 217-228 - Marc Cole, Steffen E. Eikenberry, Takahide Kato, Roman A. Sandler
Nonparametric Model of Smooth Muscle Force Production During Electrical Stimulation. 229-237 - James Gigrich, Shahryar Sarkani, Thomas H. Holzer:
A New Approach in Applying Systems Engineering Tools and Analysis to Determine Hepatocyte Toxicogenomics Risk Levels to Human Health. 238-254 - Bruno Borguesan
NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins. 255-265
Volume 24, Number 4, April 2017
- Serge Sverdlov, Elizabeth Thompson:
Combinatorial Methods for Epistasis and Dominance. 267-279 - Anas Al-Okaily
Toward a Better Compression for DNA Sequences Using Huffman Encoding. 280-288 - Doo Yang, Ilya Ioshikhes:
Drosophila H2A and H2A.Z Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns. 289-298 - Lianping Yang
A Multiresolution Graphical Representation for Similarity Relationship and Multiresolution Clustering for Biological Sequences. 299-310 - Viktor Jonsson
Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes. 311-326 - Priya S. Venkat, Krishna R. Narayanan, Aniruddha Datta:
A Bayesian Network-Based Approach to Selection of Intervention Points in the Mitogen-Activated Protein Kinase Plant Defense Response Pathway. 327-339 - Grigoriy Gogoshin, Eric Boerwinkle, Andrei S. Rodin:
New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data. 340-356 - Audrone Jakaitiene
Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments. 357-367 - Ying Wang, Haiyan Hu, Xiaoman Li:
rRNAFilter: A Fast Approach for Ribosomal RNA Read Removal Without a Reference Database. 368-375
Volume 24, Number 5, May 2017
- Amrit Dhar, Vladimir N. Minin
Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time. 377-399 - Gira Lee, Hokeun Sun:
Selection Probability for Rare Variant Association Studies. 400-411 - Nicola Yanev, Metodi Traykov, Peter Milanov
Protein Folding Prediction in a Cubic Lattice in Hydrophobic-Polar Model. 412-421 - Damian Bogdanowicz, Krzysztof Giaro
Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions. 422-435 - Sihai Yang, Xian-Hua Han, Yukako Tohsato, Koji Kyoda, Shuichi Onami, Ikuko Nishikawa, Yen-Wei Chen:
Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of Caenorhabditis elegans. 436-446 - David Barrios
D3GB: An Interactive Genome Browser for R, Python, and WordPress. 447-449 - Ngoc Tam L. Tran, Chun-Hsi Huang:
Cloud-based MOTIFSIM: Detecting Similarity in Large DNA Motif Data Sets. 450-459 - Rajat Anand, Samrat Chatterjee:
Extracting Genes Involved in Disease from a Connected Network of Perturbed Biological Processes. 460-469
Volume 24, Number 6, June 2017
- Preface: Selected Papers from RECOMB 2016. 471
- Chandler Zuo, Kailei Chen, Sündüz Keles:
A MAD-Bayes Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets. 472-485 - Hao Wang, Joel McManus, Carl Kingsford:
Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. 486-500 - Meghana Kshirsagar, Keerthiram Murugesan, Jaime G. Carbonell, Judith Klein-Seetharaman:
Multitask Matrix Completion for Learning Protein Interactions Across Diseases. 501-514 - Nilgun Donmez, Salem Malikic
Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data. 515-523 - Nicoló Fusi, Jennifer Listgarten:
Flexible Modeling of Genetic Effects on Function-Valued Traits. 524-535 - Mark A. Hallen, Jonathan D. Jou, Bruce Randall Donald:
LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency. 536-546 - David Pellow, Darya Filippova, Carl Kingsford:
Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters. 547-557 - Alexander Artyomenko, Nicholas C. Wu
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. 558-570 - Mingfu Shao, Bernard M. E. Moret:
On Computing Breakpoint Distances for Genomes with Duplicate Genes. 571-580 - Kristoffer Sahlin
Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias. 581-589 - Alexandru I. Tomescu
Safe and Complete Contig Assembly Through Omnitigs. 590-602 - Simona Cristea, Jack Kuipers
pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics. 603-615 - Daniel Doerr, Luis Antonio Brasil Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas, Bernard M. E. Moret, Jens Stoye
New Genome Similarity Measures based on Conserved Gene Adjacencies. 616-634
Volume 24, Number 7, July 2017
- Haiyan Huang, Hua Tang, Jing Huang, Bin Chen, Ruixiao Liu, Rui (Sammi) Tang, Ying Lu, Peng Yang:
Special Issue: Selected Papers of the Inaugural DahShu Data Science Symposium: Computational Precision Health (CPH 2017). 635-636 - Yangyang Hao
RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants. 637-646 - Tianzhou Ma, Faming Liang, Steffi Oesterreich, George C. Tseng:
A Joint Bayesian Model for Integrating Microarray and RNA Sequencing Transcriptomic Data. 647-662 - Funan Shi, Haiyan Huang:
Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell RNA-Seq Data Using a Biclustering Approach. 663-674 - Sara M. Clifton
Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain. 675-688 - Hu Yang, Xiaoqin Liu
Studies on the Clustering Algorithm for Analyzing Gene Expression Data with a Bidirectional Penalty. 689-698 - Huaying Fang
gCoda: Conditional Dependence Network Inference for Compositional Data. 699-708 - Minhyeok Lee
A Comparison of Two-Stage Approaches Based on Penalized Regression for Estimating Gene Networks. 709-720 - Yoonha Choi, Marc Coram
A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data. 721-731
Volume 24, Number 8, August 2017
- Abdoulaye Baniré Diallo, Engelbert Mephu Nguifo
Preface: Selected Papers from the Workshop Bioinformatics and Artificial Intelligence Joined with the International Joint Conference on Artificial Intelligence. 733 - Vincent Picard, Anne Siegel
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. 734-745 - Abedalrhman Alkhateeb
Zseq: An Approach for Preprocessing Next-Generation Sequencing Data. 746-755 - Forough Firoozbakht, Iman Rezaeian, Michele D'agnillo, Lisa A. Porter
An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data. 756-766 - Ieva Vasiljeva, Ognjen Arandjelovic
Diagnosis Prediction from Electronic Health Records Using the Binary Diagnosis History Vector Representation. 767-786 - Ham Ching Lam, Xuan Bi, Srinand Sreevatsan, Daniel Boley:
Evolution and Vaccination of Influenza Virus. 787-798 - Ahmed Halioui
T-GOWler: Discovering Generalized Process Models Within Texts. 799-808 - Ricardo de Souza Jacomini, David Correa Martins Jr., Felipe Leno da Silva, Anna Helena Reali Costa
GeNICE: A Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis. 809-830
Volume 24, Number 9, September 2017
- Filippo Disanto, Noah A. Rosenberg
Enumeration of Ancestral Configurations for Matching Gene Trees and Species Trees. 831-850 - Zheng Dai, David Becerra, Jérôme Waldispühl
On Stable States in a Topologically Driven Protein Folding Model. 851-862 - Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S. Heath:
PEAK: Integrating Curated and Noisy Prior Knowledge in Gene Regulatory Network Inference. 863-873 - Daniel J. White
Assessing the Impact of Assemblers on Virus Detection in a De Novo Metagenomic Analysis Pipeline. 874-881 - Radhika Khanna, Sangeeta Mittal
Development of Computer Algorithm for Editing of Next Generation Sequencing Metagenome Data. 882-894 - Ngoc Tam L. Tran, Chun-Hsi Huang:
MOTIFSIM 2.1: An Enhanced Software Platform for Detecting Similarity in Multiple DNA Motif Data Sets. 895-905 - Noa Godin, Jerry Eichler
The Mitochondrial Protein Atlas: A Database of Experimentally Verified Information on the Human Mitochondrial Proteome. 906-916 - Byeonghyeok Park, Min-Jeong Baek, Byoungnam Min, In-Geol Choi
Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package. 917-922 - Xiuli Ma, Guangyu Zhou, Jingbo Shang, Jingjing Wang, Jian Peng, Jiawei Han:
Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining. 923-941 - Yu Zheng, Xiaoyang Li, Lydia C. Manor, Hongbao Cao, Qiusheng Chen:
An Integrative Computational Approach to Evaluate Genetic Markers for Chronic Lymphocytic Leukemia. 942-952
Volume 24, Number 10, October 2017
- Paola Bonizzoni
FSG: Fast String Graph Construction for De Novo Assembly. 953-968 - Irina Balaur
EpiGeNet: A Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer. 969-980 - Cheng-Hong Yang, Yu-Shiun Lin, Li-Yeh Chuang, Hsueh-Wei Chang:
A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding. 981-994 - Pedro Pablo González Pérez, Daniel J. Orta, Irving Peña, Eduardo C. Flores, José U. Ramírez, Hiram Isaac Beltrán, Salomón de Jesús Alas
A Computational Approach to Studying Protein Folding Problems Considering the Crucial Role of the Intracellular Environment. 995-1013 - Marek C. Milewski, Karol Kamel, Anna Kurzynska-Kokorniak
EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments. 1014-1028 - Lebin Thomas
Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya. 1029-1042 - Rajashekar Varma Kadumuri
LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures. 1043-1049 - Haixin Ai, Runlin Wu, Li Zhang, Xuewei Wu, Junchao Ma, Huan Hu, Liangchao Huang, Wen Chen, Jian Zhao, Hongsheng Liu:
pSuc-PseRat: Predicting Lysine Succinylation in Proteins by Exploiting the Ratios of Sequence Coupling and Properties. 1050-1059 - Feilong Deng, Shi-Yi Chen, Zhou-Lin Wu
GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome. 1060-1064 - Aldona Krupska:
Influence of Oscillatory Enzyme Activity on the Reaction Kinetics: Mathematical Model. 1065-1070
Volume 24, Number 11, November 2017
- Christina J. Castro
U50: A New Metric for Measuring Assembly Output Based on Non-Overlapping, Target-Specific Contigs. 1071-1080 - Mahmut Samil Sagiroglu, M. Oguzhan Külekci:
A System Architecture for Efficient Transmission of Massive DNA Sequencing Data. 1081-1088 - Pawel Blazej
Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences. 1089-1098 - Yan Zhou, Baoxue Zhang, Gaorong Li
GD-RDA: A New Regularized Discriminant Analysis for High-Dimensional Data. 1099-1111 - Shengqing Lv, Yimin Chen, Zeyu Li, Jiahui Lu, Ming-ke Gao, Rongrong Lu:
Application of Time-Frequency Domain Transform to Three-Dimensional Interpolation of Medical Images. 1112-1124 - Gesiele Almeida Barros-Carvalho, Marie-Anne Van Sluys
An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy. 1125-1133 - Natacha Cerisier
Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets. 1134-1137 - Andrey Kechin
cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. 1138-1143 - Álvaro Rubio-Largo
Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences. 1144-1154
Volume 24, Number 12, December 2017
- Nikita A. Sakhanenko
The Information Content of Discrete Functions and Their Application in Genetic Data Analysis. 1153-1178 - Ron Zeira, Meirav Zehavi
A Linear-Time Algorithm for the Copy Number Transformation Problem. 1179-1194 - Wenbin Chen, William Hendrix, Nagiza F. Samatova:
The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways. 1195-1211 - Cheng-Hong Yang, Yu-Da Lin
Joint Analysis of SNP-SNP-Environment Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm. 1212-1225 - Haitham Elmarakeby
Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language. 1226-1229 - Wenhe Su, Xiangke Liao, Yutong Lu, Quan Zou
Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: A Linear Method for Multiple Nucleotide Sequence Alignment on Spark Parallel Framework. 1230-1242 - Chao Pei, Shu-Lin Wang, Jianwen Fang, Wei Zhang:
GSMC: Combining Parallel Gibbs Sampling with Maximal Cliques for Hunting DNA Motif. 1243-1253 - Shin-Fu Tsai, Chih-Wei Tung
An Exhaustive Scan Method for SNP Main Effects and SNP × SNP Interactions Over Highly Homozygous Genomes. 1254-1264 - Samana Shrestha, Adam Vanasse, Leon N. Cooper, Michael Antosh:
Gene Expression as a Dosimeter in Irradiated Drosophila melanogaster. 1265-1274 - MD Shahinuzzaman
A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein-Protein Interaction. 1275-1283
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