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ORCIDJournal of Computational Biology, Volume 27
Volume 27, Number 1, January 2020
- Rupeng Zhang, Leifeng Lv, Wenrui Ban, Xiaoqian Dang, Chen Zhang
:
Identification of Hub Genes in Duchenne Muscular Dystrophy: Evidence from Bioinformatic Analysis. 1-8 - Yangchun Xu, Yan Mu, Ling Wang, Xuan Zhang:
Detailed Analysis of Molecular Mechanisms in Primary and Metastatic Melanoma. 9-19 - Yaron Ilan:
Advanced Tailored Randomness: A Novel Approach for Improving the Efficacy of Biological Systems. 20-29 - Jing Zhao, Linlin Yin, Ling He:
The MicroRNA Landscapes Profiling Reveals Potential Signatures of Necrotizing Enterocolitis in Infants. 30-39 - Bao Yang, Keqin Dong, Peiyuan Guo, Peng Guo, Guo Jie, Guanhua Zhang, Tianke Li:
Identification of Key Biomarkers and Potential Molecular Mechanisms in Oral Squamous Cell Carcinoma by Bioinformatics Analysis. 40-54 - Yang-Fan Zou, Ling-Bing Meng, Qing-qing Wang, Zhao-Kai He, Chen-Hao Hu, Meng-Jie Shan, Deng-Yuan Wang, Xin Yu:
Identification and Functional Enrichment Analysis of Potential Diagnostic and Therapeutic Targets in Adamantinomatous Craniopharyngioma. 55-68 - Mengwei Chen, Chengqi Kong, Zhiyuan Zheng, Yin Li:
Identification of Biomarkers Associated with Septic Cardiomyopathy Based on Bioinformatics Analyses. 69-80 - Guozhang Hu, Rui Wang, Bo Wei, Le Wang, Qi Yang, Daliang Kong, Chao Du:
Prognostic Markers Identification in Glioma by Gene Expression Profile Analysis. 81-90 - Partha Sarathi Mohanty, Sandeep Sharma, Farah Naaz, Dilip Kumar, Archana Raikwar, Shripad A. Patil:
Inhibition ofMycobacterium tuberculosis tRNA-LigasesUsing siRNA-Based Gene Silencing Method: A Computational Approach. 91-99 - Shanshan Liu, Wenjuan Tian, Burong Li:
Integrative Bioinformatics Analysis Identifies NEK2 as a Potential Biomarker in Head and Neck Squamous Cell Carcinoma. 100-108 - Ke Shi, Meng-Na Ge, Xiao-Qiao Chen:
Coordinated DNA Methylation and Gene Expression Data for Identification of the Critical Genes Associated with Childhood Atopic Asthma. 109-120 - Zhenan Zhang, Yuqin Liu, Wei Wang, Yue Xing, Nanyang Jiang, Hongrui Zhang, Hanwen Zhang, Lei He, Wei Yue, Lianju Jiang, Kaili Wang:
Identification of Differentially Expressed Genes Associated with Lymph Node Tuberculosis by the Bioinformatic Analysis Based on a Microarray. 121-130
Volume 27, Number 2, February 2020
- Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Preface Special Issue: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019). 131-132 - Ariel Bruner, Roded Sharan:
A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits. 133-143 - Filipe Gouveia, Inês Lynce, Pedro T. Monteiro:
Revision of Boolean Models of Regulatory Networks Using Stable State Observations. 144-155 - Klairton Lima Brito, Géraldine Jean, Guillaume Fertin, Andre Rodrigues Oliveira, Ulisses Dias, Zanoni Dias:
Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes. 156-174 - Zhi-Zhong Chen, Shohei Ueta, Jingyu Li, Lusheng Wang:
Computing a Consensus Phylogeny via Leaf Removal. 175-188 - Francesco Delfino, Yuri Porozov, Eugene Stepanov, Gaik Tamazian, Valentina Tozzini:
Evolutionary Switches Structural Transitions via Coarse-Grained Models. 189-199 - Lixin Liu, Haitao Jiang, Peiqiang Liu, Binhai Zhu, Daming Zhu:
Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear Linear Programming-Rounding. 200-211 - Zihao Wang, Jingrong Zhang, Weifang Gao, Zhiyong Liu, Xiaohua Wan, Fa Zhang:
A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography. 212-222 - Enrico Petrucci, Laurent Noé, Cinzia Pizzi, Matteo Comin:
Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and k-mer Hashing. 223-233 - Jelena Fiosina, Maksims Fiosins, Stefan Bonn:
Explainable Deep Learning for Augmentation of Small RNA Expression Profiles. 234-247 - Heta P. Desai, Anuja P. Parameshwaran, Rajshekhar Sunderraman, Michael Weeks:
Comparative Study Using Neural Networks for 16S Ribosomal Gene Classification. 248-258 - Charles E. Wimberley, Steffen Heber:
PeakPass: Automating ChIP-Seq Blacklist Creation. 259-268 - Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen:
Combining Graph Transformations and Semigroups for Isotopic Labeling Design. 269-287 - Ana A. Hernandez-Lopez, Claudio Alberti, Marco Mattavelli:
Toward a Dynamic Threshold for Quality Score Distortion in Reference-Based Alignment. 288-300
Volume 27, Number 3, March 2020
- Sorin Istrail:
Preface Special Issue: RECOMB 2018. 301 - Édouard Bonnet, Pawel Rzazewski, Florian Sikora:
Designing RNA Secondary Structures Is Hard. 302-316 - Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz:
Graph Traversal Edit Distance and Extensions. 317-329 - Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz:
Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. 330-341 - Franziska Görtler, Marian Schön, Jakob Simeth, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Rainer Spang, Michael Altenbuchinger:
Loss-Function Learning for Digital Tissue Deconvolution. 342-355 - Jan Hoinka, Yijie Wang, Teresa M. Przytycka:
AptaBlocks Online: A Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges. 356-360 - Gary Larson, Jeffrey L. Thorne, Scott C. Schmidler:
Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models. 361-375 - Yaron Orenstein:
Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. 376-385 - Marian Schön, Jakob Simeth, Paul Heinrich, Franziska Görtler, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Michael Altenbuchinger, Rainer Spang:
DTD: An R Package for Digital Tissue Deconvolution. 386-389 - Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl:
A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces cerevisiae. 390-402 - Yuriy Sverchkov, Yi-Hsuan Ho, Audrey P. Gasch, Mark Craven:
Context-Specific Nested Effects Models. 403-417 - Yue Wu, Eleazar Eskin, Sriram Sankararaman:
A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies. 418-428 - Naomi Yamada, Prashant Kumar Kuntala, B. Franklin Pugh, Shaun Mahony:
ChExMix: A Method for Identifying and Classifying Protein-DNA Interaction Subtypes. 429-435 - Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz:
PyGTED: Python Application for Computing Graph Traversal Edit Distance. 436-439
Volume 27, Number 4, April 2020
- Lenore J. Cowen:
Preface Special Issue: RECOMB 2019. 441 - Philipp Benner, Martin Vingron:
ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. 442-457 - Boying Gong, Elizabeth Purdom:
MethCP: Differentially Methylated Region Detection with Change Point Models. 458-471 - Kristoffer Sahlin, Paul Medvedev:
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm. 472-484 - Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro:
An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search. 485-499 - Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. 500-513 - Taher Mun, Alan Kuhnle, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini:
Matching Reads to Many Genomes with the r-Index. 514-518 - Weihua Pan, Tao Jiang, Stefano Lonardi:
OMGS: Optical Map-Based Genome Scaffolding. 519-533 - Leonardo Pellegrina, Cinzia Pizzi, Fabio Vandin:
Fast Approximation of Frequent k-Mers and Applications to Metagenomics. 534-549 - Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald:
Minimization-Aware Recursive K*: A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. 550-564 - Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz:
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. 565-598 - Joel Mefford, Danny S. Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Päivi Pajukanta, Jian Yang, John S. Witte, Noah Zaitlen:
Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models. 599-612 - Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel, Govind Ramnarayan:
How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories. 613-625 - Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles:
Sparse Binary Relation Representations for Genome Graph Annotation. 626-639 - Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru:
On the Complexity of Sequence-to-Graph Alignment. 640-654 - Lodewijk Brand, Xue Yang, Kai Liu, Saad Elbeleidy, Hua Wang, Hao Zhang, Feiping Nie:
Learning Robust Multilabel Sample Specific Distances for Identifying HIV-1 Drug Resistance. 655-672 - Retraction of: Identification of Prognosis Biomarkers of Prostatic Cancer in a Cohort of 498 Patients from TCGA, by Chen Z, Hu H. (J Comput Biol Dec 2019: epub ahead of print; DOI: 10.1089/cmb.2019.0224). 673
Volume 27, Number 5, May 2020
- Yury Gusev, Svyatoslav Mazilov, Irina Volokhina, Mikhail Chumakov:
Agrobacterial, Single-Stranded DNA-Binding Protein VirE2 and Its Complexes. 675-682 - Brenda Ivette Garcia-Maya, Nikolaos Limnios:
Identification of Words in Biological Sequences Under the Semi-Markov Hypothesis. 683-697 - Lixia Zhang, Leonardo O. Rodrigues, Niven R. Narain, Viatcheslav R. Akmaev:
bAIcis: A Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software. 698-708 - Zhicheng Li, Shijian Li, Xian Wei, Xubiao Peng, Qing Zhao:
Recovering the Missing Regions in Crystal Structures from the Nuclear Magnetic Resonance Measurement Data Using Matrix Completion Method. 709-717 - Jingwei Zhao, Le Wang, Daliang Kong, Guozhang Hu, Bo Wei:
Construction of Novel DNA Methylation-Based Prognostic Model to Predict Survival in Glioblastoma. 718-728 - Lei Li, Linhua Jiang, Sihua Peng:
Protein Network Analysis of the Fifth Chromosome of Zebrafish. 729-737 - Rahul Singh Jasrotia, Sarika Jaiswal, Pramod Kumar Yadav, Mustafa Raza, Mir Asif Iquebal, Anil Rai, Dinesh Kumar:
Genome-Wide Analysis of HSP70 Family Protein in Vigna radiata and Coexpression Analysis Under Abiotic and Biotic Stress. 738-754 - Lopamudra Dey, Anirban Mukhopadhyay:
A Graph-Based Approach for Finding the Dengue Infection Pathways in Humans Using Protein-Protein Interactions. 755-768 - Ying Lu, Qixiu Lu, Houlin Liu, Jixiang Yu, Chunlei Xin, Yingping Liu, Yanfang Liu, Linlin Fan:
Time-Series Expression Analysis of Epidermal Stem Cells from High Fat Diet Mice. 769-778 - Guochang Zhang, Juan Li, Hong Sun, Guanzheng Yang:
Screening for the Biomarkers Associated with Myocardial Infarction by Bioinformatics Analysis. 779-785 - Hanadi M. Baeissa, Frances M. G. Pearl:
Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer. 786-795 - Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou:
Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning. 796-814 - Yangchun Xu, Ling Wang, Lanxiang Jiang, Xuan Zhang:
Novel MicroRNA Biomarkers, miR-142-5p, miR-550a, miR-1826, and miR-1201, Were Identified for Primary Melanoma. 815-824 - Xuedong Wang, Xiaoxi Wang, Xiaoqin Li, Yu Chang:
Identification of Specific Candidate Diagnostic Biomarkers for Lung Squamous Cell Carcinoma Based on Methylation. 825-833 - Xihai Wu, Yunhui Han, Fangmei Liu, Lihong Ruan:
Downregulations of miR-449a and miR-145-5p Act as Prognostic Biomarkers for Endometrial Cancer. 834-844
Volume 27, Number 6, June 2020
- Sayanti Guha Majumdar, Anil Rai, Dwijesh Chandra Mishra:
Integrated Framework for Selection of Additive and Nonadditive Genetic Markers for Genomic Selection. 845-855 - Tongchuan Zhang, Guodong Hu, Yuedong Yang, Jihua Wang, Yaoqi Zhou:
All-Atom Knowledge-Based Potential for RNA Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State. 856-867 - Sultan Alyami, Chun-Hsi Huang:
Nongreedy Unbalanced Huffman Tree Compressor for Single and Multifasta Files. 868-876 - Ye Feng, Chunyu Shi, Dayu Wang, Xuefeng Wang, Zhi Chen:
Integrated Analysis of DNA Copy Number Changes and Gene Expression Identifies Key Genes in Gastric Cancer. 877-887 - Fan Yu, Zhong-Sen Le, Li-Hua Chen, Hong Qian, Bo Yu, Wen-Hua Chen:
Identification of Biomolecular Information in Rotenone-Induced Cellular Model of Parkinson's Disease by Public Microarray Data Analysis. 888-903 - Sha-Sha Ruan, Yi-Chen Xiao, Pei-Cheng He, Yi Wang, Tao Ma:
Identification of Potential Gene Signatures Related to Sleep Deprivation. 904-913 - Lujiao Mo, Guanhua Xu, Channi Wu, Kanda Pan, Ping Pan, Lingfeng Yu, Xiaoyuan Shen:
Key Regulatory Effect of Activated HIF-1α/VEGFA Signaling Pathway in Systemic Capillary Leak Syndrome Confirmed by Bioinformatics Analysis. 914-922 - Xihua Dong, Xiaoou Yu, Hua Li, Hui Kang:
Identification of Marker Genes and Pathways in Patients with Primary Biliary Cholangitis. 923-933 - Chian Chen, Hsiuying Wang:
Logistic Regression Method for Ligand Discovery. 934-940 - Nermin Jukan, David Zagorsek, Julija Lazarevic, Irena Preloznik Zupan, Natasa Debeljak, Miha Moskon:
ViDis: A Platform for Constructing and Sharing of Medical Algorithms. 941-947 - Teng Zhao, Kun Qian, Yi Zhang:
High Expression of FGF5 Is an Independent Prognostic Factor for Poor Overall Survival and Relapse-Free Survival in Lung Adenocarcinoma. 948-957 - Fangping Jiang, Hong Fan, Lian Luo, Yun Li:
An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding RNAs and Their Transcriptional Regulation Relationships in Heart Failure. 958-964 - Lianmei Bai, Yu Ren, Tianqing Cui:
Overexpression of CDCA5, KIF4A, TPX2, and FOXM1 Coregulated Cell Cycle and Promoted Hepatocellular Carcinoma Development. 965-974 - Krishna Kanhaiya, Dwitiya Tyagi-Tiwari:
Identification of Drug Targets in Breast Cancer Metabolic Network. 975-986 - Ying Liu, Sheng-Hua Xiong, Shiying Liu, Jie Chen, Hao Yang, Gang Liu, Gengmi Li:
Analysis of Gene Expression in Bladder Cancer: Possible Involvement of Mitosis and Complement and Coagulation Cascades Signaling Pathway. 987-998
Volume 27, Number 7, July 2020
- Icaro Alves Pinto, Nelson José Freitas da Silveira:
In Silico Identification of Potential Inhibitors of the Wnt Signaling Pathway in Human Breast Cancer. 999-1010 - Aanchal Mongia, Debarka Sengupta, Angshul Majumdar:
deepMc: Deep Matrix Completion for Imputation of Single-Cell RNA-seq Data. 1011-1019 - Sai H. Sankara Subramanian, Karpaga Raja Sundari Balachandran, Vijaya Raghavan Rangamaran, Dharani Gopal:
RemeDB: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets. 1020-1029 - Yifan Gu, Guoqing Chen, Yibao Du:
Screening of Prognosis-Related Genes in Primary Breast Carcinoma Using Genomic Expression Data. 1030-1040 - Weiqing Wang, Shaohua Wang, Xiao Chu, Hui Liu, Ming Xiang:
Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique DNA Methylation and Gene Expression Profiles. 1041-1054 - Xiaochen Jia, Yehui Shi, Yuehong Zhu, Wenjing Meng, Lihong He, Yongsheng Jia, Zhongsheng Tong:
Integrated Analysis of mRNA-miRNA-lncRNA ceRNA Network in Human HR+/Her-2- Breast Cancer and Triple Negative Breast Cancer. 1055-1066 - Yingxuan Tian, Min Yu, Li Sun, Linghua Liu, Jun Wang, Ke Hui, Qiaofeng Nan, Xinyu Nie, Yajuan Ren, Xiaoping Ren:
Distinct Patterns of mRNA and lncRNA Expression Differences Between Lung Squamous Cell Carcinoma and Adenocarcinoma. 1067-1078 - Meng Zhang, Chenyi Di, Peng Guo, Ling-Bing Meng, Meng-Jie Shan, Yong Qiu, Peiyuan Guo, Keqin Dong, Qi Xie, Qiang Wang:
Screening and Identification of Key Biomarkers in Pancreatic Cancer: Evidence from Bioinformatic Analysis. 1079-1091 - Tian Zeng, Can Chen, Pan Yang, Wenwei Zuo, Xiaoqing Liu, Yanling Zhang:
A Protective Role for RHOJ in NonSmall Cell Lung Cancer Based on Integrated Bioinformatics Analysis. 1092-1103 - Ruike Wang, Xia Du, Yaqin Zhi:
Screening of Critical Genes Involved in Metastasis and Prognosis of High-Grade Serous Ovarian Cancer by Gene Expression Profile Data. 1104-1114 - Xiaoguang Niu, Yongtao Xu, Ni Gao, Aiwu Li:
Weighted Gene Coexpression Network Analysis Reveals the Critical lncRNAs and mRNAs in Development of Hirschsprung's Disease. 1115-1129 - Chao Deng, Timothy Daley, Peter Calabrese, Jie Ren, Andrew D. Smith:
Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments. 1130-1143 - Kumar Saurabh, Maxim Solovchuk, Tony Wen-Hann Sheu:
Solution of Ion Channel Flow Using Immersed Boundary-Lattice Boltzmann Methods. 1144-1156 - Amir Asiaee T., Zachary B. Abrams, Samantha Nakayiza, Deepa Sampath, Kevin R. Coombes:
Explaining Gene Expression Using Twenty-One MicroRNAs. 1157-1170 - Vitara Pungpapong, Min Zhang, Dabao Zhang:
Integrating Biological Knowledge Into Case-Control Analysis Through Iterated Conditional Modes/Medians Algorithm. 1171-1179
Volume 27, Number 8, August 2020
- Dan F. DeBlasio, Kwanho Kim, Carl Kingsford:
More Accurate Transcript Assembly via Parameter Advising. 1181-1189 - Trung Ngo Trong, Juha Mehtonen, Gerardo González, Roger Kramer, Ville Hautamäki, Merja Heinäniemi:
Semisupervised Generative Autoencoder for Single-Cell Data. 1190-1203 - Zhenghao Chen, Ilya Soifer, Hugo Hilton, Leeat Keren, Vladimir Jojic:
Modeling Multiplexed Images with Spatial-LDA Reveals Novel Tissue Microenvironments. 1204-1218 - Brandon Carter, Maxwell L. Bileschi, Jamie Smith, Theo Sanderson, Drew Bryant, David Belanger, Lucy J. Colwell:
Critiquing Protein Family Classification Models Using Sufficient Input Subsets. 1219-1231 - Katarzyna Górczak, Jürgen Claesen, Tomasz Burzykowski:
A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads. 1232-1247 - Evaldo Bezerra Costa, Gabriel Pereira Silva, Marcello Goulart Teixeira:
An Approach to Parallel Algorithms for Long DNA Sequences Alignment on Manycore Architecture. 1248-1252 - Elif Pala, Tuba Denkçeken:
Evaluation of miRNA Expression Profiles in Schizophrenia Using Principal-Component Analysis-Based Unsupervised Feature Extraction Method. 1253-1263 - Danni Cui, Yingying Liu, Gang Liu, Lei Liu:
A Multiple-Instance Learning-Based Convolutional Neural Network Model to Detect the IDH1 Mutation in the Histopathology Images of Glioma Tissues. 1264-1272 - Daniele Pepe, Jin Hwan Do:
Analyzing Apomorphine-Mediated Effects in a Cell Model for Parkinson's Disease with Partial Least Squares Structure Equation Modeling. 1273-1282 - Stefano Pirrò, Filomena Spada, Emanuela Gadaleta, Federica Ferrentino, Graeme J. Thorn, Gianni Cesareni, Claude Chelala:
HiPPO and PANDA: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data. 1283-1294