Journal: Journal of Computational Biology

Volume 29, Issue 9

943 -- 960Harshit Kumar, Manjit Panigrahi, Anuradha Panwar, Divya Rajawat, Sonali Sonejita Nayak, K. A. Saravanan, Kaiho Kaisa, Subhashree Parida, Bharat Bhushan, Triveni Dutt. Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data
961 -- 973Yi Kung Shieh, Dao-Yuan Peng, Yu-Han Chen, Tsung-Wei Wu, Chin Lung Lu. An Integer Linear Programming Approach for Scaffolding Based on Exemplar Breakpoint Distance
974 -- 986Zehavit Leibovich, Ilan Gronau. Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites
987 -- 1000Sunho Lee, Seokchol Hong, Jonathan Woo, Jae-Hak Lee, Kyunghee Kim, Lucia Kim, Kunsoo Park, Jongsun Jung. RDscan: A New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution
1001 -- 1021Ruohan Ren, Changchuan Yin, Stephen S.-T. Yau. kmer2vec: A Novel Method for Comparing DNA Sequences by word2vec Embedding
1022 -- 1030Minglu Zhao, Ning Tang, Annya L. Dahmani, Yixin Zhu, Federico Rossano, Tao Gao. Sharing Rewards Undermines Coordinated Hunting
1031 -- 1044Sandeep Kambhampati, Sean Murphy, Hideki Uosaki, Chulan Kwon. Cross-Organ Transcriptomic Comparison Reveals Universal Factors During Maturation
1045 -- 1058Saravanan Vijayakumar. Leishmania donovani

Volume 29, Issue 8

769 -- 781Ran Hu, Xianghong Jasmine Zhou, Wenyuan Li 0006. Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis
782 -- 801Chengze Shen, Minhyuk Park, Tandy J. Warnow. WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment
802 -- 824Frederick A. Matsen, Peter L. Ralph. Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency
825 -- 838Dan Flomin, David Pellow, Ron Shamir. k-Mer Counting
839 -- 856Shaokun An, Jie Ren 0006, Fengzhu Sun, Lin Wan. A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses
857 -- 866Kjong-Van Lehmann, André Kahles, Magdalena Murr, Gunnar Rätsch. RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection
867 -- 879Aidan Mcloughlin, Haiyan Huang. Shared Differential Expression-Based Distance Reflects Global Cell Type Relationships in Single-Cell RNA Sequencing Data
880 -- 891Wei Jiang, Liang Chen. Tissue Specificity of Gene Expression Evolves Across Mammal Species
892 -- 907Sehwan Moon, Jeongyoung Hwang, Hyunju Lee. SDGCCA: Supervised Deep Generalized Canonical Correlation Analysis for Multi-Omics Integration
908 -- 931Rong Jiao, Xiangning Chen, Eric Boerwinkle, Momiao Xiong. Genome-Wide Causation Studies of Complex Diseases
932 -- 941Xiangrui Zeng, Ziqian Lin, Mostofa Rafid Uddin, Bo Zhou 0009, Chao Cheng, Jing Zhang, Zachary Freyberg, Min Xu 0009. Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series

Volume 29, Issue 7

599 -- 600Sorin Istrail, Pavel A. Pevzner, Fengzhu Sun, Martin Vingron. Special Issue: Professor Michael Waterman's 80th Birthday, Part 1
601 -- 615Pavel A. Pevzner, Martin Vingron, Christian M. Reidys, Fengzhu Sun, Sorin Istrail. Michael Waterman's Contributions to Computational Biology and Bioinformatics
616 -- 618Peter Calabrese. Quantitative Biology Undergraduate Major at the University of Southern California
619 -- 633Siwei Xu, Mario Skarica, Ahyeon Hwang, Yi Dai, Cheyu Lee, Matthew J. Girgenti, Jing Zhang. Reference Dataset
634 -- 649Mengqiu Zhu, Yinglei Lai. Improvements Achieved by Multiple Imputation for Single-Cell RNA-Seq Data in Clustering Analysis and Differential Expression Analysis
650 -- 663Xu Shan, Jinyu Chen, Kangning Dong, Wei Zhou, Shihua Zhang. Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data
664 -- 678Baqiao Liu, Tandy J. Warnow. Scalable Species Tree Inference with External Constraints
679 -- 703Rohan S. Mehta, Mike Steel, Noah A. Rosenberg. The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree
704 -- 723Liang Chen, Hui Wan, Qiuyan He, Shun He, Minghua Deng. Statistical Methods for Microbiome Compositional Data Network Inference: A Survey
724 -- 737Shibu Yooseph, Sahar Tavakoli. Variational Approximation-Based Model Selection for Microbial Network Inference
738 -- 751Wontack Han, Haixu Tang, Yuzhen Ye. Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype
752 -- 768Javier Pardo-Diaz, Mariano Beguerisse-Díaz, Philip S. Poole, Charlotte M. Deane, Gesine Reinert. Rhizobium leguminosarum

Volume 29, Issue 6

495 -- 496Sandeep Kumar. Special Issue: Computational Intelligence
497 -- 514Lina Alkhathlan, Abdul Khader Jilani Saudagar. Predicting and Classifying Breast Cancer Using Machine Learning
515 -- 529Timea Bezdan, Miodrag Zivkovic, Nebojsa Bacanin, Amit Chhabra, Muthusamy Suresh. Feature Selection by Hybrid Brain Storm Optimization Algorithm for COVID-19 Classification
530 -- 544Ayman Altameem, Basetty Mallikarjuna, Abdul Khader Jilani Saudagar, Meenakshi Sharma, Ramesh Chandra Poonia. Improvement of Automatic Glioma Brain Tumor Detection Using Deep Convolutional Neural Networks
545 -- 564Priyanka Harjule, Manva Mohd. Tokir, Tanuj Mehta, Shivam Gurjar, Anupam Kumar, Basant Agarwal. Texture Enhancement of Medical Images for Efficient Disease Diagnosis with Optimized Fractional Derivative Masks
565 -- 584Rabia Aziz Musheer. Cuckoo Search-Based Optimization for Cancer Classification: A New Hybrid Approach
585 -- 596Yujung Kim, Jaejik Kim. Identification of New Clusters from Labeled Data Using Mixture Models
597 -- 0. Retraction of: Screening of Clinical Factors Related to Prognosis of Breast Cancer Based on the Cox Proportional Risk Model (doi: 10.1089/cmb.2019.0110)

Volume 29, Issue 5

409 -- 424Jeremy Bigness, Xavier Loinaz, Shalin Patel, Erica Larschan, Ritambhara Singh. Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks
425 -- 440Qiang-Hui Guo, Yinglie Jin, Mengqin Li, Lisa Hui Sun, Yanyan Xu. On the Number of Saturated and Optimal Extended 2-Regular Simple Stacks in the Nussinov-Jacobson Energy Model
441 -- 452Aanchal Mongia, Stuti Jain, Émilie Chouzenoux, Angshul Majumdar. DeepVir: Graphical Deep Matrix Factorization for In Silico Antiviral Repositioning - Application to COVID-19
453 -- 464Micah Thornton, Monnie McGee. Use of DFT Distance Metrics for Classification of SARS-CoV-2 Genomes
465 -- 482Luqin Gan, Giuseppe Vinci, Genevera I. Allen. Correlation Imputation for Single-Cell RNA-seq
483 -- 493Cristian C. Espitia, Miguel A. Botina, Marco A. Solarte, Ivan Hernandez, Ricardo A. Riascos, João F. Meyer. Mathematical Model of HIV/AIDS Considering Sexual Preferences Under Antiretroviral Therapy, a Case Study in San Juan de Pasto, Colombia

Volume 29, Issue 4

305 -- 0Yuval Emek, Saket Navlakha. Special Issue: Biological Distributed Algorithms 2021
306 -- 316Arjun Chandrasekhar, Magdalena M. Julkowska. A Mathematical Framework for Analyzing Wild Tomato Root Architecture
317 -- 343Michael Feldmann 0001, Andreas Padalkin, Christian Scheideler, Shlomi Dolev. Coordinating Amoebots via Reconfigurable Circuits
344 -- 357Emily Zhang, Jiajia Zhao, Nancy A. Lynch. Temnothorax Ant Colonies
358 -- 369Martin Kunev, Petr Kuznetsov, Denis Sheynikhovich. Agreement in Spiking Neural Networks
370 -- 381Keith T. Murray, Mien Brabeeba Wang, Nancy A. Lynch. Emergence of Direction-Selective Retinal Cell Types in Task-Optimized Deep Learning Models
382 -- 408Jiajia Zhao, Nancy A. Lynch, Stephen C. Pratt. Temnothorax Ant House-Hunting: A Computational Modeling Approach

Volume 29, Issue 3

213 -- 232Veronica Tozzo, Chloé-Agathe Azencott, Samuele Fiorini, Emanuele Fava, Andrea Trucco, Annalisa Barla. Where Do We Stand in Regularization for Life Science Studies?
233 -- 242Haohan Wang, Bryon Aragam, Eric P. Xing. Trade-offs of Linear Mixed Models in Genome-Wide Association Studies
243 -- 256Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias. Labeled Cycle Graph for Transposition and Indel Distance
257 -- 275HeeWon Park, Rui Yamaguchi, Seiya Imoto, Satoru Miyano. Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification
276 -- 291Hossein Hassani 0004, Zakieh Avazzadeh, J. A. Tenreiro Machado, Praveen Agarwal, Maryam Bakhtiar. Optimal Solution of a Fractional HIV/AIDS Epidemic Mathematical Model
292 -- 303Muhsen Hammoud, Charles Morphy D. Santos, João Paulo Gois. Comparing Phylogenetic Trees Side by Side Through iPhyloC, a New Interactive Web-Based Framework

Volume 29, Issue 2

91 -- 0Jian Peng. RECOMB 2021 Special Issue
92 -- 105Lupeng Kong, Fusong Ju, Wei-Mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu. ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs
106 -- 120Yuxuan Du, Sarah M. Laperriere, Jed A. Fuhrman, Fengzhu Sun. Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression
121 -- 139Hongyu Zheng, Cong Ma, Carl Kingsford. Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability
140 -- 154Yoshihiro Shibuya, Djamal Belazzougui, Gregory Kucherov. Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation
155 -- 168Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev. The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches
169 -- 187Massimiliano Rossi 0001, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher. MONI: A Pangenomic Index for Finding Maximal Exact Matches
188 -- 194Massimiliano Rossi 0001, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher. Finding Maximal Exact Matches Using the r-Index
195 -- 211Jim Shaw, Yun William Yu. flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning

Volume 29, Issue 12

1269 -- 0Itsik Pe'er. Special Issue: RECOMB 2022, Part 2
1270 -- 1287Shahbaz Khan 0004, Milla Kortelainen, Manuel Cáceres, Lucia Williams, Alexandru I. Tomescu. Improving RNA Assembly via Safety and Completeness in Flow Decompositions
1288 -- 1304Minh Hoang, Hongyu Zheng 0001, Carl Kingsford. Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer
1305 -- 1323Uthsav Chitra, Tae-Yoon Park, Benjamin J. Raphael. NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks
1324 -- 1345Alireza Ganjdanesh, Jipeng Zhang, Sarah Yan, Wei Chen 0074, Heng Huang. Multimodal Genotype and Phenotype Data Integration to Improve Partial Data-Based Longitudinal Prediction
1346 -- 1352Nathan Guerin, Teresa Kaserer, Bruce R. Donald. RESISTOR: A New OSPREY Module to Predict Resistance Mutations
1353 -- 1356Haohan Wang, Oscar Lopez, Eric P. Xing, Wei Wu 0023. Kernel Mixed Model for Transcriptome Association Study
1357 -- 1376Vijini Mallawaarachchi, Yu Lin. Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs
1377 -- 1396Daniel Gibney, Sharma V. Thankachan, Srinivas Aluru. On the Hardness of Sequence Alignment on De Bruijn Graphs
1397 -- 1411Seyran Saeedi, Myrna G. Serrano, Dennis G. Yang, J. Paul Brooks, Gregory A. Buck, Tomasz Arodz. Group Testing Matrix Design for PCR Screening with Real-Valued Measurements

Volume 29, Issue 11

1155 -- 0Itsik Pe'er. Special Issue: RECOMB 2022, Part 1
1156 -- 1172Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman, Md. Shamsuzzoha Bayzid. Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data
1173 -- 1197Max Hill, Sebastien Roch. Inconsistency of Triplet-Based and Quartet-Based Species Tree Estimation under Intralocus Recombination
1198 -- 1212Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert, William Stafford Noble. Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning
1213 -- 1228Pinar Demetci, Rebecca Santorella, Manav Chakravarthy, Björn Sandstede, Ritambhara Singh. SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation
1229 -- 1232Dongshunyi Li, Jun Ding, Ziv Bar-Joseph. UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation
1233 -- 1236Kun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li. The scINSIGHT Package for Integrating Single-Cell RNA-Seq Data from Different Biological Conditions
1237 -- 1251Chirag Jain, Daniel Gibney, Sharma V. Thankachan. Algorithms for Colinear Chaining with Overlaps and Gap Costs
1252 -- 1267Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu. Efficient Minimum Flow Decomposition via Integer Linear Programming

Volume 29, Issue 10

1059 -- 1060Zhipeng Cai 0001, Pavel Skums, Alexander Zelikovsky. 17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021)
1061 -- 1073Tian Bai 0002, Zhenting Zhang, Shuyu Guo, Chen Zhao, Xiao Luo. Semi-Supervised Cell Detection with Reliable Pseudo-Labels
1074 -- 1084Xiaoshu Zhu, Jian Li, Yongchang Lin, Liquan Zhao, Jian-xin Wang 0001, Xiaoqing Peng. Dimensionality Reduction of Single-Cell RNA Sequencing Data by Combining Entropy and Denoising AutoEncoder
1085 -- 1094Yixiao Xia, Minchao Jiang, Yizhang Luo, Guanwen Feng, Gangyong Jia, Hua Zhang, Pu Wang, Ruiquan Ge. SuccSPred2.0: A Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm
1095 -- 1103Bin Xin, Yaning Yang, Xiaolan Xie, Jiandong Shang, Zhengyu Liu, Shaoliang Peng. Detecting and Classifying Nuclei Using Multi-Scale Fully Convolutional Network
1104 -- 1116Ming Chen, Wei Jiang, Yi Pan 0001, Jianhua Dai, Yunwen Lei, Chunyan Ji. SGFNNs: Signed Graph Filtering-based Neural Networks for Predicting Drug-Drug Interactions
1117 -- 1131Hongjia Li, Ge Chen, Shan Gao, Jintao Li 0001, Xiaohua Wan, Fa Zhang 0001. A Transfer Learning-Based Classification Model for Particle Pruning in Cryo-Electron Microscopy
1132 -- 1154Kaustubh Khandai, Cristian Navarro-Martinez, Brendan Smith, Rebecca Buonopane, S. Ashley Byun, Murray Patterson. Determining Significant Correlation Between Pairs of Extant Characters in a Small Parsimony Framework

Volume 29, Issue 1

1 -- 0. Acknowledgment of Reviewers 2021
2 -- 0Jian Peng. RECOMB 2021 Special Issue
3 -- 18Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh. SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport
19 -- 22Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh. Single-Cell Multiomics Integration by SCOT
23 -- 26Tianyi Sun, Dongyuan Song, Wei Vivian Li, Jingyi Jessica Li. Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2
27 -- 44Harsh Shrivastava 0001, Xiuwei Zhang, Le Song, Srinivas Aluru. GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks
45 -- 55Rami Nasser, Yonina C. Eldar, Roded Sharan. Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis
56 -- 73Nicholas Franzese, Jason Fan, Roded Sharan, Mark D. M. Leiserson. ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures
74 -- 89Paul Zaharias, Martin Grosshauser, Tandy J. Warnow. Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling