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Journal of Computational Biology, Volume 29
Volume 29, Number 1, January 2022
- Acknowledgment of Reviewers 2021. 1
- Jian Peng:
RECOMB 2021 Special Issue. 2 - Pinar Demetci
, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh
SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport. 3-18 - Pinar Demetci
Single-Cell Multiomics Integration by SCOT. 19-22 - Tianyi Sun, Dongyuan Song, Wei Vivian Li
Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. 23-26 - Harsh Shrivastava
GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks. 27-44 - Rami Nasser
Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis. 45-55 - Nicholas Franzese
ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures. 56-73 - Paul Zaharias
Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling. 74-89
Volume 29, Number 2, February 2022
- Jian Peng:
RECOMB 2021 Special Issue. 91 - Lupeng Kong
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. 92-105 - Yuxuan Du
Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. 106-120 - Hongyu Zheng
Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability. 121-139 - Yoshihiro Shibuya
Set-Min Sketch: A Probabilistic Map for Power-Law Distributions with Application to k-Mer Annotation. 140-154 - Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. 155-168 - Massimiliano Rossi
MONI: A Pangenomic Index for Finding Maximal Exact Matches. 169-187 - Massimiliano Rossi
Finding Maximal Exact Matches Using the r-Index. 188-194 - Jim Shaw
flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning. 195-211
Volume 29, Number 3, March 2022
- Veronica Tozzo, Chloé-Agathe Azencott
Where Do We Stand in Regularization for Life Science Studies? 213-232 - Haohan Wang
Trade-offs of Linear Mixed Models in Genome-Wide Association Studies. 233-242 - Alexsandro Oliveira Alexandrino
Labeled Cycle Graph for Transposition and Indel Distance. 243-256 - Heewon Park
Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification. 257-275 - Hossein Hassani
Optimal Solution of a Fractional HIV/AIDS Epidemic Mathematical Model. 276-291 - Muhsen Hammoud
Comparing Phylogenetic Trees Side by Side Through iPhyloC, a New Interactive Web-Based Framework. 292-303
Volume 29, Number 4, April 2022
- Yuval Emek, Saket Navlakha:
Special Issue: Biological Distributed Algorithms 2021. 305 - Arjun Chandrasekhar
A Mathematical Framework for Analyzing Wild Tomato Root Architecture. 306-316 - Michael Feldmann, Andreas Padalkin
Coordinating Amoebots via Reconfigurable Circuits. 317-343 - Emily Zhang
An Upper and Lower Bound for the Convergence Time of House-Hunting in Temnothorax Ant Colonies. 344-357 - Martin Kunev
Agreement in Spiking Neural Networks. 358-369 - Keith T. Murray
Emergence of Direction-Selective Retinal Cell Types in Task-Optimized Deep Learning Models. 370-381 - Jiajia Zhao
The Power of Population Effect in Temnothorax Ant House-Hunting: A Computational Modeling Approach. 382-408
Volume 29, Number 5, May 2022
- Jeremy Bigness, Xavier Loinaz, Shalin Patel, Erica Larschan, Ritambhara Singh
Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks. 409-424 - Qiang-Hui Guo
On the Number of Saturated and Optimal Extended 2-Regular Simple Stacks in the Nussinov-Jacobson Energy Model. 425-440 - Aanchal Mongia
DeepVir: Graphical Deep Matrix Factorization for In Silico Antiviral Repositioning - Application to COVID-19. 441-452 - Micah Thornton
Use of DFT Distance Metrics for Classification of SARS-CoV-2 Genomes. 453-464 - Luqin Gan, Giuseppe Vinci
Correlation Imputation for Single-Cell RNA-seq. 465-482 - Cristian C. Espitia
Mathematical Model of HIV/AIDS Considering Sexual Preferences Under Antiretroviral Therapy, a Case Study in San Juan de Pasto, Colombia. 483-493
Volume 29, Number 6, June 2022
- Sandeep Kumar
Special Issue: Computational Intelligence. 495-496 - Lina Alkhathlan, Abdul Khader Jilani Saudagar
Predicting and Classifying Breast Cancer Using Machine Learning. 497-514 - Timea Bezdan
Feature Selection by Hybrid Brain Storm Optimization Algorithm for COVID-19 Classification. 515-529 - Ayman Altameem, Basetty Mallikarjuna
Improvement of Automatic Glioma Brain Tumor Detection Using Deep Convolutional Neural Networks. 530-544 - Priyanka Harjule
Texture Enhancement of Medical Images for Efficient Disease Diagnosis with Optimized Fractional Derivative Masks. 545-564 - Rabia Musheer Aziz
Cuckoo Search-Based Optimization for Cancer Classification: A New Hybrid Approach. 565-584 - Yujung Kim, Jaejik Kim
Identification of New Clusters from Labeled Data Using Mixture Models. 585-596 - 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). 597
Volume 29, Number 7, July 2022
- Sorin Istrail, Pavel A. Pevzner, Fengzhu Sun, Martin Vingron:
Special Issue: Professor Michael Waterman's 80th Birthday, Part 1. 599-600 - Pavel A. Pevzner, Martin Vingron, Christian M. Reidys, Fengzhu Sun, Sorin Istrail:
Michael Waterman's Contributions to Computational Biology and Bioinformatics. 601-615 - Peter Calabrese
Quantitative Biology Undergraduate Major at the University of Southern California. 616-618 - Siwei Xu
Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset. 619-633 - Mengqiu Zhu, Yinglei Lai
Improvements Achieved by Multiple Imputation for Single-Cell RNA-Seq Data in Clustering Analysis and Differential Expression Analysis. 634-649 - Xu Shan, Jinyu Chen, Kangning Dong, Wei Zhou, Shihua Zhang
Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data. 650-663 - Baqiao Liu, Tandy J. Warnow
Scalable Species Tree Inference with External Constraints. 664-678 - Rohan S. Mehta
The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree. 679-703 - Liang Chen, Hui Wan
Statistical Methods for Microbiome Compositional Data Network Inference: A Survey. 704-723 - Shibu Yooseph
Variational Approximation-Based Model Selection for Microbial Network Inference. 724-737 - Wontack Han, Haixu Tang
Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype. 738-751 - Javier Pardo-Diaz
Extracting Information from Gene Coexpression Networks of Rhizobium leguminosarum. 752-768
Volume 29, Number 8, August 2022
- Ran Hu
Computational Analysis of High-Dimensional DNA Methylation Data for Cancer Prognosis. 769-781 - Chengze Shen
WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. 782-801 - Frederick A. Matsen IV, Peter L. Ralph
Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency. 802-824 - Dan Flomin
Data Set-Adaptive Minimizer Order Reduces Memory Usage in k-Mer Counting. 825-838 - Shaokun An
A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses. 839-856 - Kjong-Van Lehmann
RNA Instant Quality Check: Alignment-Free RNA-Degradation Detection. 857-866 - Aidan Mcloughlin
Shared Differential Expression-Based Distance Reflects Global Cell Type Relationships in Single-Cell RNA Sequencing Data. 867-879 - Wei Jiang, Liang Chen
Tissue Specificity of Gene Expression Evolves Across Mammal Species. 880-891 - Sehwan Moon, Jeongyoung Hwang, Hyunju Lee
SDGCCA: Supervised Deep Generalized Canonical Correlation Analysis for Multi-Omics Integration. 892-907 - Rong Jiao, Xiangning Chen, Eric Boerwinkle, Momiao Xiong
Genome-Wide Causation Studies of Complex Diseases. 908-931 - Xiangrui Zeng, Ziqian Lin, Mostofa Rafid Uddin, Bo Zhou, Chao Cheng, Jing Zhang
Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series. 932-941
Volume 29, Number 9, September 2022
- Harshit Kumar
Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data. 943-960 - Yi-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. 961-973 - Zehavit Leibovich, Ilan Gronau
Optimal Design of Synthetic DNA Sequences Without Unwanted Binding Sites. 974-986 - Sunho Lee
RDscan: A New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution. 987-1000 - Ruohan Ren, Changchuan Yin
kmer2vec: A Novel Method for Comparing DNA Sequences by word2vec Embedding. 1001-1021 - Minglu Zhao
Sharing Rewards Undermines Coordinated Hunting. 1022-1030 - Sandeep Kambhampati, Sean Murphy, Hideki Uosaki
Cross-Organ Transcriptomic Comparison Reveals Universal Factors During Maturation. 1031-1044 - Saravanan Vijayakumar
Harnessing Fuzzy Rule Based System for Screening Major Histocompatibility Complex Class I Peptide Epitopes from the Whole Proteome: An Implementation on the Proteome of Leishmania donovani. 1045-1058
Volume 29, Number 10, October 2022
- Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021). 1059-1060 - Tian Bai
Semi-Supervised Cell Detection with Reliable Pseudo-Labels. 1061-1073 - Xiaoshu Zhu
Dimensionality Reduction of Single-Cell RNA Sequencing Data by Combining Entropy and Denoising AutoEncoder. 1074-1084 - Yixiao Xia, Minchao Jiang, Yizhang Luo, Guanwen Feng
SuccSPred2.0: A Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm. 1085-1094 - Bin Xin
Detecting and Classifying Nuclei Using Multi-Scale Fully Convolutional Network. 1095-1103 - Ming Chen
SGFNNs: Signed Graph Filtering-based Neural Networks for Predicting Drug-Drug Interactions. 1104-1116 - Hongjia Li
A Transfer Learning-Based Classification Model for Particle Pruning in Cryo-Electron Microscopy. 1117-1131 - Kaustubh 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. 1132-1154
Volume 29, Number 11, November 2022
- Itsik Pe'er:
Special Issue: RECOMB 2022, Part 1. 1155 - Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman
Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data. 1156-1172 - Max Hill
Inconsistency of Triplet-Based and Quartet-Based Species Tree Estimation under Intralocus Recombination. 1173-1197 - Ran Zhang
Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning. 1198-1212 - Pinar Demetci
SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation. 1213-1228 - Dongshunyi Li
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. 1229-1232 - Kun Qian, Shiwei Fu, Hongwei Li, Wei Vivian Li
The scINSIGHT Package for Integrating Single-Cell RNA-Seq Data from Different Biological Conditions. 1233-1236 - Chirag Jain, Daniel Gibney
Algorithms for Colinear Chaining with Overlaps and Gap Costs. 1237-1251 - Fernando H. C. Dias, Lucia Williams, Brendan Mumey
Efficient Minimum Flow Decomposition via Integer Linear Programming. 1252-1267
Volume 29, Number 12, December 2022
- Itsik Pe'er:
Special Issue: RECOMB 2022, Part 2. 1269 - Shahbaz Khan
Improving RNA Assembly via Safety and Completeness in Flow Decompositions. 1270-1287 - Minh Hoang
Differentiable Learning of Sequence-Specific Minimizer Schemes with DeepMinimizer. 1288-1304 - Uthsav Chitra
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. 1305-1323 - Alireza Ganjdanesh, Jipeng Zhang, Sarah Yan, Wei Chen
Multimodal Genotype and Phenotype Data Integration to Improve Partial Data-Based Longitudinal Prediction. 1324-1345 - Nathan Guerin
RESISTOR: A New OSPREY Module to Predict Resistance Mutations. 1346-1352 - Haohan Wang
Kernel Mixed Model for Transcriptome Association Study. 1353-1356 - Vijini Mallawaarachchi
Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs. 1357-1376 - Daniel Gibney
On the Hardness of Sequence Alignment on De Bruijn Graphs. 1377-1396 - Seyran 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. 1397-1411
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