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ORCIDJournal of Computational Biology, Volume 31
Volume 31, Number 1, January 2024
- Acknowledgment of Reviewers 2023. 1
- Minh Hoang
, Guillaume Marçais, Carl Kingsford:
Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme. 2-20 - Ivan A. Croydon-veleslavov, Michael P. H. Stumpf:
Repeated Decision Stumping Distils Simple Rules from Single-Cell Data. 21-40 - Hao Jiang, Jingxin Liu, You Song, Jinzhi Lei:
Quantitative Modeling of Stemness in Single-Cell RNA Sequencing Data: A Nonlinear One-Class Support Vector Machine Method. 41-57 - Yuanyuan Qi, Mohammed El-Kebir:
Consensus Tree Under the Ancestor-Descendant Distance is NP-Hard. 58-70 - Hajoung Lee, Jaejik Kim:
A Gene Selection Method Considering Measurement Errors. 71-82
Volume 31, Number 2, February 2024
- Junrong Song, Zhiming Song, Jinpeng Zhang, Yuanli Gong:
Privacy-Preserving Identification of Cancer Subtype-Specific Driver Genes Based on Multigenomics Data with Privatedriver. 99-116 - Guy Karlebach, Peter N. Robinson:
Computing Minimal Boolean Models of Gene Regulatory Networks. 117-127 - Zihan Wang, Mengxia Xu, Zonglin Yang, Yu Jin, Yong Zhang:
Comparing the Performance of Three Computational Methods for Estimating the Effective Reproduction Number. 128-146 - Xiaoyang Xiang, Jiaxuan Gao, Yanrui Ding:
DeepPPThermo: A Deep Learning Framework for Predicting Protein Thermostability Combining Protein-Level and Amino Acid-Level Features. 147-160 - Jianhua Jia, Genqiang Wu, Meifang Li:
iGly-IDN: Identifying Lysine Glycation Sites in Proteins Based on Improved DenseNet. 161-174 - Aleksey Y. Ogurtsov, Gelio Alves, Alex Rubio, Brendan Joyce, Björn Andersson, Roger Karlsson, Edward R. B. Moore, Yi-Kuo Yu:
MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall. 175-178
Volume 31, Number 3, 2024
- Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir:
DERNA Enables Pareto Optimal RNA Design. 179-196 - Magsarjav Bataa, Siwoo Song, Kunsoo Park, Miran Kim, Jung Hee Cheon, Sun Kim:
Finding Highly Similar Regions of Genomic Sequences Through Homomorphic Encryption. 197-212 - Hehuan Ma, Feng Jiang, Yu Rong, Yuzhi Guo, Junzhou Huang:
Toward Robust Self-Training Paradigm for Molecular Prediction Tasks. 213-228 - Tarrion Baird, Rahul Roychoudhuri:
GS-TCGA: Gene Set-Based Analysis of The Cancer Genome Atlas. 229-240 - Hai-bin Yao, Zhen-jie Hou, Wen-guang Zhang, Han Li, Yan Chen:
Prediction of MicroRNA-Disease Potential Association Based on Sparse Learning and Multilayer Random Walks. 241-256 - Heewon Park:
Unveiling Gene Regulatory Networks That Characterize Difference of Molecular Interplays Between Gastric Cancer Drug Sensitive and Resistance Cell Lines. 257-274
Volume 31, Number 4, 2024
- Tomás Vinar:
RECOMB Satellite Conference on Comparative Genomics(RECOMB-CG 2023). 275-276 - Wend Yam Donald Davy Ouedraogo, Aïda Ouangraoua:
Orthology and Paralogy Relationships at Transcript Level. 277-293 - Leonard Bohnenkämper:
The Floor Is Lava: Halving Natural Genomes with Viaducts, Piers, and Pontoons. 294-311 - Sanket Wagle, Alexey Markin, Pawel Górecki, Tavis K. Anderson, Oliver Eulenstein:
Asymmetric Cluster-Based Measures for Comparative Phylogenetics. 312-327 - Elahe Khayatian, Gabriel Valiente, Louxin Zhang:
The k-Robinson-Foulds Dissimilarity Measures for Comparison of Labeled Trees. 328-344 - Yufeng Wu, Louxin Zhang:
Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees. 345-359 - Kaari Landry, Olivier Tremblay Savard, Manuel Lafond:
A Fixed-Parameter Tractable Algorithm for Finding Agreement Cherry-Reduced Subnetworks in Level-1 Orchard Networks. 360-379
Volume 31, Number 5, 2024
- Yun William Yu:
On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis. 381-395 - Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir:
Enforcing Temporal Consistency in Migration History Inference. 396-415 - Claudio Arbib, Andrea D'Ascenzo, Fabrizio Rossi, Daniele Santoni:
An Integer Linear Programming Model to Optimize Coding DNA Sequences By Joint Control of Transcript Indicators. 416-428 - Jannatul Ferdous, George Matthew Fricke, Melanie E. Moses:
More Is Faster: Why Population Size Matters in Biological Search. 429-444 - Juan Xia, Yuxia Li, Haotian Zhu, Feiyang Xue, Feng Shi, Nana Li:
A Bayesian Change Point Model for Dynamic Alternative Transcription Start Site Usage During Cellular Differentiation. 445-457 - Isra Mohammed, Murtada K. Elbashir, Areeg S. Faggad:
Singular Value Decomposition-Based Penalized Multinomial Regression for Classifying Imbalanced Medulloblastoma Subgroups Using Methylation Data. 458-471
Volume 31, Number 6, 2024
- Murray Patterson:
Special Issue, Part I 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023). 473-474 - Michael Souza, Nilton Maia, Rômulo S. Marques, Carlile Lavor:
A Branch-and-Bound Algorithm for the Molecular Ordered Covering Problem. 475-485 - Xiaodi Hou, Guoming Sang, Zhi Liu, Xiaobo Li, Yi-Jia Zhang:
Visual Recalibration and Gating Enhancement Network for Radiology Report Generation. 486-497 - Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle:
Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases. 498-512 - Mathieu Bolteau, Lokmane Chebouba, Laurent David, Jérémie Bourdon, Carito Guziolowski:
Boolean Network Models of Human Preimplantation Development. 513-523 - Enrico Rossignolo, Matteo Comin:
Enhanced Compression of k-Mer Sets with Counters via de Bruijn Graphs. 524-538 - Carissa Bleker, Stephen K. Grady, Michael A. Langston:
A Comparative Study of Gene Co-Expression Thresholding Algorithms. 539-548 - Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler:
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. 549-563 - Zhidong Yang, Hongjia Li, Dawei Zang, Renmin Han, Fa Zhang:
Improved Denoising of Cryo-Electron Microscopy Micrographs with Simulation-Aware Pretraining. 564-575 - Tian-Jing Qiao, Feng Li, Shasha Yuan, Ling-Yun Dai, Juan Wang:
A Fusion Learning Model Based on Deep Learning for Single-Cell RNA Sequencing Data Clustering. 576-588 - Gatis Melkus, Andrejs Sizovs, Peteris Rucevskis, Sandra Silina:
Transcriptional Hubs Within Cliques in Ensemble Hi-C Chromatin Interaction Networks. 589-596
Volume 31, Number 7, 2024
- Guillaume Marçais, Dan F. DeBlasio, Carl Kingsford:
Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets. 597-615 - Neda Tavakoli, Daniel Gibney, Srinivas Aluru:
GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants. 616-637 - Ran Libeskind-Hadas:
Pairwise Distances and the Problem of Multiple Optima. 638-650 - Preeti P, Azeen Riyaz, Alakto Choudhury, Priyanka Ray Choudhury, Nischal Pradhan, Abhishek Singh, Mihir Nakul, Chhavi Dudeja, Abhijeet Yadav, Swarsat Kaushik Nath, Vrinda Khanna, Trapti Sharma, Gayatri Pradhan, Simran Takkar, Kamal Rawal:
DNASCANNER v2: A Web-Based Tool to Analyze the Characteristic Properties of Nucleotide Sequences. 651-669 - Juntao Li, Shan Xiang, Xuekun Song:
Screening Nonlinear miRNA Features of Breast Cancer by Using Ensemble Regularized Polynomial Logistic Regression. 670-690 - V. A. Jisna, Ajay Abhaysing Pawar, P. B. Jayaraj:
Using Attention-UNet Models to Predict Protein Contact Maps. 691-702
Volume 31, Number 8, 2024
- Nguyen Huy Tinh, Cuong Cao Dang, Le Sy Vinh:
QMix: An Efficient Program to Automatically Estimate Multi-Matrix Mixture Models for Amino Acid Substitution Process. 703-707 - Yuexuan Wang, Ritabrata Dutta, Andreas Futschik:
Estimating Haplotype Structure and Frequencies: A Bayesian Approach to Unknown Design in Pooled Genomic Data. 708-726 - Jurate Saltyte Benth, Fred Espen Benth, Espen Rostrup Nakstad:
Nearly Instantaneous Time-Varying Reproduction Number for Contagious Diseases - a Direct Approach Based on Nonlinear Regression. 727-741 - Xin Zhang, Liangwei Zhao, Ziyi Chai, Hao Wu, Wei Yang, Chen Li, Yu Jiang, Quanzhong Liu:
NPI-DCGNN: An Accurate Tool for Identifying ncRNA-Protein Interactions Using a Dual-Channel Graph Neural Network. 742-756 - M. Tamilarasi, S. Kumarganesh, K. Martin Sagayam, J. Andrew:
Detection and Segmentation of Glioma Tumors Utilizing a UNet Convolutional Neural Network Approach with Non-Subsampled Shearlet Transform. 757-768 - Gargi Biswas, Debasish Mukherjee, Sankar Basu:
Combining Complementarity and Binding Energetics in the Assessment of Protein Interactions: EnCPdock - A Practical Manual. 769-781
Volume 31, Number 9, 2024
- Teresa M. Przytycka:
Rosalind Franklin Society Proudly Announces the 2023 Award Recipient for Journal of Computational Biology. 783 - Zhao Ling, Yu Wei Zhang, Shuai Cheng Li:
SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization. 784-796 - Qian Gao, Chi Zhang, Ming Li, Tianfei Yu:
Protein-Protein Interaction Prediction Model Based on ProtBert-BiGRU-Attention. 797-814 - Reza Kalhor, Guillaume Beslon, Manuel Lafond, Céline Scornavacca:
A Rigorous Framework to Classify the Postduplication Fate of Paralogous Genes. 815-833 - Biao Mei, Yu Jiang, Yifan Sun:
Unveiling Commonalities and Differences in Genetic Regulations via Two-Way Fusion. 834-870 - Jiayuan Ding, Lingxiao Li, Qiaolin Lu, Julian Venegas, Yixin Wang, Lidan Wu, Wei Jin, Hongzhi Wen, Renming Liu, Wenzhuo Tang, Xinnan Dai, Zhaoheng Li, Wangyang Zuo, Yi Chang, Yu Leo Lei, Lulu Shang, Patrick Danaher, Yuying Xie, Jiliang Tang:
SpatialCTD: A Large-Scale Tumor Microenvironment Spatial Transcriptomic Dataset to Evaluate Cell Type Deconvolution for Immuno-Oncology. 871-885 - Xiao-Yan Sun, Zhen-jie Hou, Wen-guang Zhang, Yan Chen, Hai-bin Yao:
HTFSMMA: Higher-Order Topological Guided Small Molecule-MicroRNA Associations Prediction. 886-906
Volume 31, Number 10, 2024
- Jian Ma, Mona Singh:
RECOMB 2024 Special Issue. 907 - C. S. Elder, Minh Hoang, Mohsen Ferdosi, Carl Kingsford:
Approximate and Exact Optimization Algorithms for the Beltway and Turnpike Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements. 908-926 - Rudolf Schill, Maren Klever, Andreas Lösch, Y. Linda Hu, Stefan Vocht, Kevin Rupp, Lars Grasedyck, Rainer Spang, Niko Beerenwinkel:
Correcting for Observation Bias in Cancer Progression Modeling. 927-945 - Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová:
Fast Context-Aware Analysis of Genome Annotation Colocalization. 946-964 - Henry Childs, Nathan Guerin, Pei Zhou, Bruce Randall Donald:
Protocol for Designing De Novo Noncanonical Peptide Binders in OSPREY. 965-974 - Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier:
Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes. 975-989 - Kapil Devkota, Anselm Blumer, Xiaozhe Hu, Lenore Cowen:
Approximate IsoRank for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks. 990-1007 - Yuxuan Du, Wenxuan Zuo, Fengzhu Sun:
Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart. 1008-1021 - Alessio Campanelli, Giulio Ermanno Pibiri, Jason Fan, Rob Patro:
Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn Graphs*. 1022-1044 - Spencer Krieger, John D. Kececioglu:
Robust Optimal Metabolic Factories. 1045-1086
Volume 31, Number 11, 2024
- Hao Zhu, Donna Slonim:
From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory Networks. 1087-1103 - Amit K. Chakraborty, Hao Wang, Pouria Ramazi:
From Policy to Prediction: Assessing Forecasting Accuracy in an Integrated Framework with Machine Learning and Disease Models. 1104-1117 - Maryam Jafari Khanghahi, Reza Khoshsiar Ghaziani:
Bifurcations and Homoclinic Orbits of a Model Consisting of Vegetation-Prey-Predator Populations. 1118-1145 - Pedro Quesado, Luis H. M. Torres, Bernardete Ribeiro, Joel P. Arrais:
A Hybrid GNN Approach for Improved Molecular Property Prediction. 1146-1157 - Heewon Park, Satoru Miyano:
Network-Constrained Eigen-Single-Cell Profile Estimation for Uncovering Crucial Immunogene Regulatory Systems in Human Bone Marrow. 1158-1178 - Wimonnat Sukpol, Teeraphan Laomettachit, Anuwat Tangthanawatsakul:
A Cancer Subpopulation Competition Model Reveals Optimal Levels of Immune Response that Minimize Tumor Size. 1179-1194
Volume 31, Number 12, 2024
- John L. Spouge, Pijush Das, Ye Chen, Martin C. Frith:
The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches. 1195-1210 - Boyuan Yu, Hao Zhang, Cong Pian, Yuanyuan Chen:
MMG4: Recognition of G4-Forming Sequences Based on Markov Model. 1211-1223 - Lin Zhang, Jigen Peng, Yongbin Ge, Haiyang Li, Yuchao Tang:
High-Accuracy Positivity-Preserving Finite Difference Approximations of the Chemotaxis Model for Tumor Invasion. 1224-1258 - Han Ma, Yanyan Du, Zong Wang, Qimin Zhang:
Positivity and Boundedness Preserving Numerical Scheme for a Stochastic Multigroup Susceptible-Infected-Recovering Epidemic Model with Age Structure. 1259-1290 - Jing Yang, Shaojuan Ma, Juan Ma, Jinhua Ran, Xinyu Bai:
Stochastic Analysis for the Dual Virus Parallel Transmission Model with Immunity Delay. 1291-1304 - Filippo Ascolani, Stefano Damato, Matteo Ruggiero:
An R Package for Nonparametric Inference on Dynamic Populations with Infinitely Many Types. 1305-1311
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