Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach (English)

How to get this document?

Download
Commercial Copyright fee: €27.12 Basic fee: €4.00 Total price: €31.12
Academic Copyright fee: €27.12 Basic fee: €2.00 Total price: €29.12

The de-novo genome assembly is a challenging computational problem for which several pipelines have been developed. The advent of long-read sequencing technology has resulted in a new set of algorithmic approaches for the assembly process. In this work, we identify that one of these new and fast long-read assembly techniques (using Minimap2 and Miniasm) can be modified for the short-read assembly process. This possibility motivated us to customize a long-read assembly approach for applications in a short-read assembly scenario. Here, we compare and contrast our proposed de-novo assembly pipeline (MiniSR) with three other recently developed programs for the assembly of bacterial and small eukaryotic genomes. We have documented two trade-offs: one between speed and accuracy and the other between contiguity and base-calling errors. Our proposed assembly pipeline shows a good balance in these trade-offs. The resulting pipeline is 6 and 2.2 times faster than the short-read assemblers Spades and SGA, respectively. MiniSR generates assemblies of superior N50 and NGA50 to SGA, although assemblies are less complete and accurate than those from Spades. A third tool, SOAPdenovo2, is as fast as our proposed pipeline but had poorer assembly quality.

Table of contents – Volume 17, Issue 1

Show all volumes and issues

The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.

1
State of the Journal
Gusfield, Dan | 2007
1
A Memory Efficient Method for Structure-Based RNA Multiple Alignment
DeBlasio, D. / Bruand, J. / Shaojie Zhang, | 2012
1
Editorial from the Editor-in-Chief
Xu, Ying | 2014
1
Fast Computation of Minimal Cut Sets in Metabolic Networks with a Berge Algorithm that Utilizes Binary Bit Pattern Trees
Jungreuthmayer, Christian / Beurton-Aimar, Marie / Zanghellini, Jurgen | 2013
1
Guest Editorial for the 16th Asia Pacific Bioinformatics Conference
Yamanishi, Yoshihiro / Sakakibara, Yasubumi / Chen, Yi-Ping Phoebe | 2019
1
Computing the Joint Distribution of Tree Shape and Tree Distance for Gene Tree Inference and Recombination Detection
Chung, Yujin / Perna, Nicole T. / Ane, Cecile | 2013
1
Naïve Bayesian Classifiers with Multinomial Models for rRNA Taxonomic Assignment
Liu, Kuan-Liang / Wong, Tzu-Tsung | 2013
1
EIC Editorial
Sagot, Marie-France | 2011
1
2019 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 16
| 2020
1
Welcome Message
Williams, M.R. | 2004
1
Guest Editorial for Special Section on the 10th International Conference on Intelligent Computing (ICIC)
Huang, De-Shuang / Bevilacqua, Vitoantonio / Gromiha, M. Michael | 2016
1
An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach
Bates Congdon, C. / Aman, J.C. / Nava, G.M. / Gaskins, H.R. / Mattingly, C.J. | 2008
1
Editor's Note
| 2010
1
A Graphical Model of Smoking-Induced Global Instability in Lung Cancer
Yanbo Wang, / Weikang Qian, / Bo Yuan, | 2018
1
Statistical Detection of Boolean Regulatory Relationships
Chen, Ting / Braga-Neto, Ulisses M. | 2013
1
Algorithms for Computational Biology: Fifth Edition
Martin-Vide, Carlos / Vega-Rodriguez, Miguel A. | 2020
1
Guest Editorial: WABI Special Section Part II
Junhyong Kim, / Jonassen, I. | 2005
1
Editorial from the New Editor-in-Chief
Xu, Ying | 2013
1
2018 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 15
| 2019
1
Combination of geological data and radon survey results for radon mapping
Zhukovsky, M. / Yarmoshenko, I. / Kiselev, S. | 2012
1
Final, Five-Year End, Editorial
Gusfield, Dan | 2009
1
2017 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 14
| 2018
1
Editorial: Special Section on Bio-Inspired Swarm Computing and Engineering
Tan, Ying / Shi, Yuhui | 2017
2
Jointly analyzing gene expression and copy number data in breast cancer using data reduction models
Berger, J.A. / Hautaniemi, S. / Mitra, S.K. / Astola, J. | 2006
2
A Fast Algorithm for Computing Geodesic Distances in Tree Space
Owen, Megan / Provan, J Scott | 2011
2
Automatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular Distribution
Diaz, E. / Ayala, G. / Diaz, M.E. / Liang-Wei Gong, / Toomre, D. | 2010
2
Associate Editor Appreciation and Welcome
Gusfield, Dan | 2007
2
Heuristics for the Reversal and Transposition Distance Problem
Brito, Klairton Lima / Oliveira, Andre Rodrigues / Dias, Ulisses / Dias, Zanoni | 2020
2
Guest Editors’ Introduction: Selected Papers from ACM-BCB 2013
Aluru, Srinivas / Slonim, Donna K. | 2015
2
RNA Secondary Structure Prediction Using Soft Computing
Ray, Shubhra Sankar / Pal, Sankar K. | 2013
2
SURVEY PAPERS - RNA Secondary Structure Prediction Using Soft Computing
Ray, S S / Pal, S K | 2013
2
Introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics
Gusfield, D. | 2004
3
New EIC Editorial
Sagot, Marie-France | 2009
3
Guest Editor's Introduction to the Special Section on Computational Biology and Bioinformatics (WABI) -- Part 2
Casadio, Rita | 2007
3
A new distance for high level RNA secondary structure comparison
Allali, J. / Sagot, M.-F. | 2005
3
Parallel Computation of the Burrows-Wheeler Transform of Short Reads Using Prefix Parallelism
Kimura, Kouichi / Koike, Asako | 2019
4
Quality assurance for measurements of the radioactivity in the area of the ``Horia Hulubei'' National Institute for Physics and Nuclear Engineering, IFIN-HH
Stochioiu, A. / Luca, A. / Sahagia, M. / Margineanu, R.M. / Tudor, I. | 2012
4
Special Section: Phylogenetics
Huson, Daniel H. / Moulton, Vincent / Steel, Mike | 2009
4
MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search
Daniels, Noah M. / Gallant, Andrew / Ramsey, Norman / Cowen, Lenore J. | 2015
4
Symbiosis-Based Alternative Learning Multi-Swarm Particle Swarm Optimization
Ben Niu, / Huali Huang, / Lijing Tan, / Qiqi Duan, | 2017
4
SPECIAL SECTION ON PHYLOGENETICS - Special Section: Phylogenetics
Huson, D.H. / Moulton, V. / Steel, M. | 2009
4
GeneNetFinder2: Improved Inference of Dynamic Gene Regulatory Relations with Multiple Regulators
Kyungsook Han, / Jeonghoon Lee, | 2016
4
Perfect Sorting by Reversals Is Not Always Difficult
Berard, S. / Bergeron, A. / Chauve, C. / Paul, C. | 2007
4
Introduction of new Associate Editors
Williams, M.R. | 2004
4
SPECIAL SECTION ON COMPUATIONAL BIOLOGY AND BIOINFORMATICS (WABI) -- PART 2 - Perfect Sorting by Reversals Is Not Always Difficult
Bérard, S. / Bergeron, A. / Chauve, C. / Paul, C. | 2007
5
SPECIAL SECTION ON THE INTERNATIONAL CONFERENCE ON GENOME INFORMATICS - Guest Editorial for the International Conference on Genome Informatics (GIW 2013)
Eisenhaber, F / Sung, W-K / Wong, L | 2014
5
Guest Editorial for the International Conference on Genome Informatics (GIW 2013)
Eisenhaber, Frank / Sung, Wing-Kin / Wong, Limsoon | 2014
7
Barking Up The Wrong Treelength: The Impact of Gap Penalty on Alignment and Tree Accuracy
Liu, K. / Nelesen, S. / Raghavan, S. / Linder, C.R. / Warnow, T. | 2009
7
Coupling Graphs, Efficient Algorithmsand B-Cell Epitope Prediction
Zhao, Liang / Hoi, Steven C.H. / Li, Zhenhua / Wong, Limsoon / Nguyen, Hung / Li, Jinyan | 2014
8
Iodine-129, Iodine-127 and Caesium-137 in the environment: soils from Germany and Chile
Daraoui, A. / Michel, R. / Gorny, M. / Jakob, D. / Sachse, R. / Synal, H.-A. / Alfimov, V. | 2012
12
Hybrid Framework Using Multiple-Filters and an Embedded Approach for an Efficient Selection and Classification of Microarray Data
Bonilla-Huerta, Edmundo / Hernandez-Montiel, Alberto / Morales-Caporal, Roberto / Arjona-Lopez, Marco | 2016
12
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations
Pirola, Y. / Bonizzoni, P. / Tao Jiang, | 2012
12
BioExtract Serve — An Integrated Workflow-Enabling System to Access and Analyze Heterogeneous, Distributed Biomolecular Data
Zhu, S / Wang, D / Yu, K / Li, T / Gong, Y | 2010
12
BioExtract Server—An Integrated Workflow-Enabling System to Access and Analyze Heterogeneous, Distributed Biomolecular Data
Lushbough, C. / Bergman, M.K. / Lawrence, C.J. / Jennewein, D. / Brendel, V. | 2010
13
Phylogenetic networks: modeling, reconstructibility, and accuracy
Moret, B.M.E. / Nakhleh, L. / Warnow, T. / Linder, C.R. / Tholse, A. / Padolina, A. / Sun, J. / Timme, R. | 2004
14
A General Framework for Analyzing Data from Two Short Time-Series Microarray Experiments
Shah, Mohak / Corbeil, Jacques | 2011
14
Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation
van Iersel, Leo / Janssen, Remie / Jones, Mark / Murakami, Yukihiro / Zeh, Norbert | 2020
14
Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss Model
Haack, Jordan / Zupke, Eli / Ramirez, Andrew / Wu, Yi-Chieh / Libeskind-Hadas, Ran | 2019
15
An Information Theoretic Exploratory Method for Learning Patterns of Conditional Gene Coexpression from Microarray Data
Boscolo, R. / Liao, J.C. / Roychowdhury, V.P. | 2008
15
Topological rearrangements and local search method for tandem duplication trees
Bertrand, D. / Gascuel, O. | 2005
15
Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree
Jansson, Jesper / Rajaby, Ramesh / Chuanqi Shen, / Wing-Kin Sung, | 2018
15
A New Magnetotactic Bacteria Optimization Algorithm Based on Moment Migration
Hongwei Mo, / Lili Liu, / Jiao Zhao, | 2017
17
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information
Torii, Manabu / Arighi, Cecilia N. / Li, Gang / Wang, Qinghua / Wu, Cathy H. / Vijay-Shanker, K. | 2015
17
Ortholog Clustering on a Multipartite Graph
Vashist, A. / Kulikowski, C.A. / Muchnik, I. | 2007
17
Quantifying Significance of MHC II Residues
Fan, Ying / Lu, Ruoshui / Wang, Lusheng / Andreatta, Massimo / Li, Shuai Cheng | 2014
17
Spatio-temporal analysis of constitutive exocytosis in epithelial cells
Sebastian, R. / Diaz, M.-E. / Ayala, G. / Letinic, K. / Moncho-Bogani, J. / Toomre, D. | 2006
17
SPECIAL SECTION ON COMPUATIONAL BIOLOGY AND BIOINFORMATICS (WABI) -- PART 2 - Ortholog Clustering on a Multipartite Graph
Vashist, A. / Kulikowski, C.A. / Muchnik, I. | 2007
18
A Simple Fixed Parameter Tractable Algorithm for Computing the Hybridization Number of Two (Not Necessarily Binary) Trees
Piovesan, Teresa / Kelk, Steven M. | 2013
22
Budgeted Phylogenetic Diversity on Circular Split Systems
Minh, B.Q. / Pardi, F. / Klaere, S. / von Haeseler, A. | 2009
22 pp
2011 Annual Index
| 2012
23
Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics
Rizzi, Romeo / Cairo, Massimo / Makinen, Veli / Tomescu, Alexandru I. / Valenzuela, Daniel | 2019
23
Vertical distribution and inventories of 239+240Pu and mercury in Sagua la Grande estuary, Cuba
Alonso-Hernandez, C.M. / Martin-Perez, J. / Gasco, C. / Diaz-Asencio, M. / Bolanos-Alvarez, Y. / Gomez-Batista, M. | 2012
24
Biclustering algorithms for biological data analysis: a survey
Madeira, S.C. / Oliveira, A.L. | 2004
25
Feature Selection for Gene Expression Using Model-Based Entropy
Shenghuo Zhu, / Dingding Wang, / Kai Yu, / Tao Li, / Yihong Gong, | 2010
25
RnaPredict—An Evolutionary Algorithm for RNA Secondary Structure Prediction
Wiese, K.C. / Deschenes, A.A. / Hendriks, A.G. | 2008
26
An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework
Doyon, J.-P / Hamel, S. / Chauve, C. | 2012
26
DALIX: Optimal DALI Protein Structure Alignment
Wohlers, Inken / Andonov, Rumen / Klau, Gunnar W. | 2013
26
Intelligent Consensus Modeling for ProlineCis-Trans Isomerization Prediction
Yoo, Paul D. / Muhaidat, Sami / Taha, Kamal / Bentahar, Jamal / Shami, Abdallah | 2014
27
Efficient Formulations for Exact Stochastic Simulation of Chemical Systems
Mauch, Sean / Stalzer, Mark | 2011
27
Predicting Hub Genes Associated with Cervical Cancer through Gene Co-Expression Networks
Su-Ping Deng, / Lin Zhu, / De-Shuang Huang, | 2016
27
A Cooperative Framework for Fireworks Algorithm
Shaoqiu Zheng, / Junzhi Li, / Janecek, Andreas / Ying Tan, | 2017
27
A Promising Method for Calculating True Steady-State Metabolite Concentrations in Large-Scale Metabolic Reaction Network Models
Miyawaki-Kuwakado, Atsuko / Komori, Soichiro / Shiraishi, Fumihide | 2020
27
Application of Genetic Programming (GP) Formalism for Building Disease Predictive Models from Protein-Protein Interactions (PPI) Data
Vyas, Renu / Bapat, Sanket / Goel, Purva / Karthikeyan, Muthukumarasamy / Tambe, Sanjeev S. / Kulkarni, Bhaskar D. | 2018
28
EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps
Lasker, K. / Dror, O. / Shatsky, M. / Nussinov, R. / Wolfson, H.J. | 2007
28
SPECIAL SECTION ON COMPUATIONAL BIOLOGY AND BIOINFORMATICS (WABI) -- PART 2 - EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps
Lasker, K. / Dror, O. / Shatsky, M. / Nussinov, R. / Wolfson, H.J. | 2007
29
Optimizing multiple seeds for protein homology search
Brown, D.G. | 2005
29
Elevated CO2 increases Cs uptake and alters microbial communities and biomass in the rhizosphere of Phytolacca americana Linn (pokeweed) and Amaranthus cruentus L. (purple amaranth) grown on soils spiked with various levels of Cs
Song, N. / Zhang, X. / Wang, F. / Zhang, C. / Tang, S. | 2012
30
Hybridization in Nonbinary Trees
Linz, S. / Semple, C. | 2009
30
Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing
Wang, Kun / Das, Avinash / Xiong, Zheng-Mei / Cao, Kan / Hannenhalli, Sridhar | 2015
31
Taming Asynchrony for Attractor Detection in Large Boolean Networks
Mizera, Andrzej / Pang, Jun / Qu, Hongyang / Yuan, Qixia | 2019
33
Statistical analysis of RNA backbone
Hershkovitz, E. / Sapiro, G. / Tannenbaum, A. / Williams, L.D. | 2006
33
Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation
Soltan Ghoraie, Laleh / Burkowski, Forbes / Li, Shuai Cheng / Zhu, Mu | 2014
36
Estimating Haplotype Frequencies by Combining Data from Large DNA Pools with Database Information
Gasbarra, D / Kulathinal, S / Pirinen, M / Sillanpaa, M J | 2011
36
Predicting the Subcellular Localization of Proteins with Multiple Sites Based on Multiple Features Fusion
Xumi Qu, / Dong Wang, / Yuehui Chen, / Shanping Qiao, / Qing Zhao, | 2016
37
Heuristic Bayesian Segmentation for Discovery of Coexpressed Genes within Genomic Regions
Pehkonen, P. / Wong, G. / Toronen, P. | 2010
37
A Supervised Ensemble Approach for Sensitive microRNA Target Prediction
Maji, Ranjan Kumar / Khatua, Sunirmal / Ghosh, Zhumur | 2020
37
Growing Seed Genes from Time Series Data and Thresholded Boolean Networks with Perturbation
Higa, Carlos H.A. / Andrade, Tales P. / Hashimoto, Ronaldo F. | 2013
38
Attention Recognition in EEG-Based Affective Learning Research Using CFS+KNN Algorithm
Bin Hu, / Xiaowei Li, / Shuting Sun, / Ratcliffe, Martyn | 2018
38
Radium isotopes in the Polish Outer Carpathian mineral waters of various chemical composition
Chau, N.D. / Lucyna, R. / Jakub, N. / Pawel, J. | 2012
39
State of the transaction [IEEE/ACM Transactions on Computational Biology and Bioinformatics]
Gusfield, D. | 2005
40
An Efficient Method for Modeling Kinetic Behavior of Channel Proteins in Cardiomyocytes
Chong Wang, / Beyerlein, P. / Pospisil, H. / Krause, A. / Nugent, C. / Dubitzky, W. | 2012
40
Global Network Alignment in the Context of Aging
Faisal, Fazle Elahi / Zhao, Han / Milenkovic, Tijana | 2015
40
Bases of motifs for generating repeated patterns with wild cards
Pisanti, N. / Crochemore, M. / Grossi, R. / Sagot, M.F. | 2005
40
Accurate Cancer Classification Using Expressions of Very Few Genes
Lipo Wang, / Feng Chu, / Wei Xie, | 2007
42
Fireworks Algorithm with Enhanced Fireworks Interaction
Bei Zhang, / Yu-Jun Zheng, / Min-Xia Zhang, / Sheng-Yong Chen, | 2017
42
A New Unsupervised Binning Approachfor Metagenomic Sequences Based onN-grams and Automatic Feature Weighting
Liao, Ruiqi / Zhang, Ruichang / Guan, Jihong / Zhou, Shuigeng | 2014
42
Statistical Characterization of Protein Ensembles
Rother, D. / Sapiro, G. / Pande, V. | 2008
43
A Faster cDNA Microarray Gene Expression Data Classifier for Diagnosing Diseases
Sun-Yuan Hsieh, / Yu-Chun Chou, | 2016
43
Adjacent Y-Ion Ratio Distributions and Its Application in Peptide Sequencing
Wang, Tiancong / Ma, Bin | 2019
45
Relationships of 137Cs inventory with magnetic measures of calcareous soils of hilly region in Iran
Ayoubi, S. / Ahmadi, M. / Abdi, M.R. / Afshar, F.A. | 2012
45
$F^2$Dock: Fast Fourier Protein-Protein Docking
Bajaj, C L / Chowdhury, R / Siddahanavalli, V | 2011
46
Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric
Cardona, G. / Llabres, M. / Rossello, F. / Valiente, G. | 2009
46
Sequencing-by-hybridization revisited: the analog-spectrum proposal
Preparata, F.P. | 2004
46
Bi-level and Bi-objective p-Median Type Problems for Integrative Clustering: Application to Analysis of Cancer Gene-Expression and Drug-Response Data
Ushakov, Anton V. / Klimentova, Xenia / Vasilyev, Igor | 2018
47
Gene mapping and marker clustering using Shannon's mutual information
Dawy, Z. / Goebel, B. / Hagenauer, J. / Andreoli, C. / Meitinger, T. / Mueller, J.C. | 2006
47
An Application of the Bayesian Periodicity Test to Identify Diurnal Rhythm Genes in the Brain
Kocak, Mehmet / Mozhui, Khyobeni | 2020
50
Data-Fusion in Clustering Microarray Data: Balancing Discovery and Interpretability
Kustra, R. / Zagdanski, A. | 2010
50
Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thaliana
Muraro, D. / Voss, U. / Wilson, M. / Bennett, M. / Byrne, H. / De Smet, I. / Hodgman, C. / King, J. | 2013
51
Multiseed lossless filtration
Kucherov, G. / Noe, L. / Roytberg, M. | 2005
52
Modelling the transfer of 14C from the atmosphere to grass: A case study in a grass field near AREVA-NC La Hague
Aulagnier, C. / Le Dizes, S. / Maro, D. / Hebert, D. / Lardy, R. / Martin, R. / Gonze, M.-A. | 2012
52
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
Hartmann, Tom / Bernt, Matthias / Middendorf, Martin | 2019
52
An Information Theoretic Approach to Constructing Robust Boolean Gene Regulatory Networks
Vasic, B. / Ravanmehr, V. / Krishnan, A. R. | 2012
53
Pure multiple RNA secondary structure alignments: a progressive profile approach
Hochsmann, M. / Voss, B. / Giegerich, R. | 2004
53
Reachability Analysis in Probabilistic Biological Networks
Gabr, Haitham / Todor, Andrei / Dobra, Alin / Kahveci, Tamer | 2015
54
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly
Degui Zhi, / Keich, U. / Pevzner, P. / Heber, S. / Haixu Tang, | 2007
55
ChIP-PIT: Enhancing the Analysis of ChIP-Seq Data Using Convex-Relaxed Pair-Wise Interaction Tensor Decomposition
Lin Zhu, / Wei-Li Guo, / Su-Ping Deng, / De-Shuang Huang, | 2016
55
Gene Name Disambiguation UsingMulti-Scope Species Detection
Hsiao, Jui-Chen / Wei, Chih-Hsuan / Kao, Hung-Yu | 2014
56
Assessing the Effectiveness of Causality Inference Methods for Gene Regulatory Networks
Ahmed, Syed Sazzad / Roy, Swarup / Kalita, Jugal | 2020
56
A (1.5 + ε)-Approximation Algorithm for Unsigned Translocation Distance
Yun Cui, / Lusheng Wang, / Darning Zhu, / Xiaowen Liu, | 2008
56
A (1.5 + Euro)-Approximation Algorithm for Unsigned Translocation Distance
Cui, Y. / Wang, L. / Zhu, D. / Liu, X. | 2008
56
An Effective Application of Bacteria Quorum Sensing and Circular Elimination in MOPSO
Shan Cheng, / Long-Long Zhao, / Xiao-Yu Jiang, | 2017
57
A hidden Markov model for transcriptional regulation in single cells
Goutsias, J. | 2006
59
Fast Surface-Based Travel Depth Estimation Algorithm for Macromolecule Surface Shape Description
Giard, J / Rondao Alface, Patrice / Gala, J / Macq, B | 2011
60
Calculating the Expected Time to Eradicate HIV-1 Using a Markov Chain
Viswanath, Narayanan C. | 2018
60
Distribution of natural radionuclide concentrations in sediment samples in Didim and Izmir Bay (Aegean Sea-Turkey)
Akozcan, S. | 2012
61
Mathematical Properties of the Deep Coalescence Cost
Than, Cuong V. / Rosenberg, Noah A. | 2013
62
Robustness of Topological Supertree Methods for Reconciling Dense Incompatible Data
Willson, S.J. | 2009
62
Text Mining Biomedical Literature for Discovering Gene-to-Gene Relationships: A Comparative Study of Algorithms
Ying Liu, / Navathe, S.B. / Civera, J. / Dasigi, V. / Ram, A. / Ciliax, B.J. / Dingledine, R. | 2005
63
Reliable and Fast Estimation of Recombination Rates by Convergence Diagnosis and Parallel Markov Chain Monte Carlo
Guo, Jing / Jain, Ritika / Yang, Peng / Fan, Rui / Kwoh, Chee Keong / Zheng, Jie | 2014
63
[Advertisement]
| 2004
63
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution
Li, Lei / Bansal, Mukul S. | 2019
64
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks
Yu-Ting Hsiao, / Wei-Po Lee, / Wei Yang, / Muller, Stefan / Flamm, Christoph / Hofacker, Ivo / Kugler, Philipp | 2016
64
Multi-Objective Particle Swarm Optimization Approach for Cost-Based Feature Selection in Classification
Yong Zhang, / Dun-wei Gong, / Jian Cheng, | 2017
64
Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data
Rubel, O. / Weber, G.H. / Min-Yu Huang, / Bethel, E.W. / Biggin, M.D. / Fowlkes, C.C. / Luengo Hendriks, C.L. / Keranen, S.V.E. / Eisen, M.B. / Knowles, D.W. et al. | 2010
64
Call for Papers
| 2004
64
Inorganic phosphorus fractionation and its translocation dynamics in a low-P soil
Yang, J.C. / Wang, Z.G. / Zhou, J. / Jiang, H.M. / Zhang, J.F. / Pan, P. / Han, Z. / Lu, C. / Li, L.L. / Ge, C.L. | 2012
65
Multiclass Cancer Classification Using Semisupervised Ellipsoid ARTMAP and Particle Swarm Optimization with Gene Expression Data
Rui Xu, / Anagnostopoulos, G.C. / Wunsch, D.C.I.I. | 2007
65
Introduction of new Associate Editor
| 2004
66
Prediction of consensus RNA secondary structures including pseudoknots
Witwer, C. / Hofacker, I.L. / Stadler, P.F. | 2004
66
Assortative mixing in directed biological networks
Piraveenan, M. / Prokopenko, M. / Zomaya, A. | 2012
67
GLProbs: Aligning Multiple Sequences Adaptively
Ye, Yongtao / Cheung, David Wai-lok / Wang, Yadong / Yiu, Siu-Ming / Zhan, Qing / Lam, Tak-Wah / Ting, Hing-Fung | 2015
67
A Novel Biologically and Psychologically Inspired Fuzzy Decision Support System: Hierarchical Complementary Learning
Tuan Zea Tan, / Geok See Ng, / Chai Quek, | 2008
68
Classification of State Trajectories in Gene Regulatory Networks
Karbalayghareh, Alireza / Braga-Neto, Ulisses / Jianping Hua, / Dougherty, Edward Russell | 2018
69
Finding Significant Matches of Position Weight Matrices in Linear Time
Pizzi, Cinzia / Rastas, Pasi / Ukkonen, Esko | 2011
70
Genetic effects of ionizing radiation - some questions with no answers
Mosse, I.B. | 2012
71
Class Balanced Multifactor Dimensionality Reduction to Detect Gene–Gene Interactions
Yang, Cheng-Hong / Lin, Yu-Da / Chuang, Li-Yeh | 2020
72
A hill-climbing approach for automatic gridding of cDNA microarray images
Rueda, L. / Vidyadharan, V. | 2006
73
Mining Minimal Motif Pair Sets Maximally Covering Interactions in a Protein-Protein Interaction Network
Boyen, Peter / Neven, Frank / van Dyck, Dries / Valentim, Felipe L. / van Dijk, Aalt D.J. | 2013
73
Identifying Cis-Regulatory Elements and Modules Using Conditional Random Fields
Gan, Yanglan / Guan, Jihong / Zhou, Shuigeng / Zhang, Weixiong | 2014
76
The Identifiability of Covarion Models in Phylogenetics
Allman, E.S. / Rhodes, J.A. | 2009
76
The Intrinsic Geometric Structure of Protein-Protein Interaction Networks for Protein Interaction Prediction
Yi Fang, / Mengtian Sun, / Guoxian Dai, / Ramain, Karthik | 2016
76
A Novel Cluster Head Selection Algorithm Based on Fuzzy Clustering and Particle Swarm Optimization
Qingjian Ni, / Qianqian Pan, / Huimin Du, / Cen Cao, / Yuqing Zhai, | 2017
76
Environmental assessment of gamma-radiation levels in stream sediments around Sharm El-Sheikh, South Sinai, Egypt
Al-Sharkawy, A. / Hiekal, M.T. / Sherif, M.I. / Badran, H.M. | 2012
77
Resource Cut, a New Bounding Procedure to Algorithms for Enumerating Tree-Like Chemical Graphs
Nishiyama, Yuhei / Shurbevski, Aleksandar / Nagamochi, Hiroshi / Akutsu, Tatsuya | 2019
77
2004 Reviewers list
| 2005
78
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach
Chengbang Huang, / Morcos, F. / Kanaan, S.P. / Wuchty, S. / Chen, D.Z. / Izaguirre, J.A. | 2007
78
The number of recombination events in a sample history: conflict graph and lower bounds
Bafna, V. / Bansal, V. | 2004
79
Prediction and Informative Risk Factor Selection of Bone Diseases
Li, Hui / Li, Xiaoyi / Ramanathan, Murali / Zhang, Aidong | 2015
79
Composition Vector Method Based on Maximum Entropy Principle for Sequence Comparison
Chan, R. H. / Chan, T. H. / Hau Man Yeung, / Wang, R. W. | 2012
80
An Automatic Translation of SBML into Beta-Binders
Ciocchetta, F. / Priami, C. / Quaglia, P. | 2008
80
Fuzzy ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors Using a Small Molecular Data Set
Andonie, Razvan / Fabry-Asztalos, Levente / Abdul-Wahid, Christopher B / Abdul-Wahid, Sarah / Barker, Grant I / Magill, Lukas C | 2011
80
Multidimensional Profiling of Cell Surface Proteins and Nuclear Markers
Ju Han, / Hang Chang, / Andarawewa, K. / Yaswen, P. / Barcellos-Hoff, M.H. / Parvin, B. | 2010
81
Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 1
Ling, C.X. / Noble, W.S. / Qiang Yang, | 2005
82
Deep Learning for Plant Species Classification Using Leaf Vein Morphometric
Tan, Jing Wei / Chang, Siow-Wee / Abdul-Kareem, Sameem / Yap, Hwa Jen / Yong, Kien-Thai | 2020
83
Evolution and Controllability of CancerNetworks: A Boolean Perspective
Srihari, Sriganesh / Raman, Venkatesh / Wai Leong, Hon / Ragan, Mark A. | 2014
83
Attribute clustering for grouping, selection, and classification of gene expression data
Wai-Ho Au, / Chan, K.C.C. / Wong, A.K.C. / Yang Wang, | 2005
83
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes
Hartmann, Tom / An-Chiang Chu, / Middendorf, Martin / Bernt, Matthias | 2018
83
A prediction model for assessing residential radon concentration in Switzerland
Hauri, D.D. / Huss, A. / Zimmermann, F. / Kuehni, C.E. / Roosli, M. | 2012
84
Unicyclic networks: compatibility and enumeration
Semple, C. / Steel, M. | 2006
85
A Gene Selection Method for Microarray Data Based on Binary PSO Encoding Gene-to-Class Sensitivity Information
Fei Han, / Chun Yang, / Ya-Qi Wu, / Jian-Sheng Zhu, / Qing-Hua Ling, / Yu-Qing Song, / De-Shuang Huang, | 2017
86
A Novel Teaching-Learning-Based Optimization for Improved Mutagenic Primer Design in Mismatch PCR-RFLP SNP Genotyping
Yu-Huei Cheng, | 2016
87
Multiclass Gene Selection Using Pareto-Fronts
Rajapakse, Jagath C. / Mundra, Piyushkumar A. | 2013
88
Accuracy Assessment of Diploid Consensus Sequences
Jong Hyun Kim, / Waterman, M.S. / Li, L.M. | 2007
88
Disease Liability Prediction from Large Scale Genotyping Data Using Classifiers with a Reject Option
Quevedo, J. R. / Bahamonde, A. / Perez-Enciso, M. / Luaces, O. | 2012
89
Fourier Transform Inequalities for Phylogenetic Trees
Matsen, F.A. | 2009
90
Retrospective measurements of airborne 129Iodine in Austria
Jabbar, T. / Wallner, G. / Steier, P. / Katzlberger, C. / Kandler, N. | 2012
91
Deep Manifold Preserving Autoencoder for Classifying Breast Cancer Histopathological Images
Feng, Yangqin / Zhang, Lei / Mo, Juan | 2020
91
Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis
Done, B. / Khatri, P. / Done, A. / Draghici, S. | 2010
91
A uniform projection method for motif discovery in DNA sequences
Raphael, B. / Lung-Tien Liu, / Varghese, G. | 2004
91
Modeling and Simulation Studies of Complex Biological Systems for Precision Medicine and Healthcare
Shen, Bairong / Jiang, Xiaoqian / Zhao, Xingming | 2019
91
Combinatorial Approaches for Mass Spectra Recalibration
Bocker, S. / Makinen, V. | 2008
92
Capturing Uncertainty by Modeling Local Transposon Insertion Frequencies Improves Discrimination of Essential Genes
DeJesus, Michael A. / Ioerger, Thomas R. | 2015
92
A short proof that phylogenetic tree reconstruction by maximum likelihood is hard
Roch, S. | 2006
93
SAFETY: Secure gwAs in Federated Environment through a hYbrid Solution
Sadat, Md Nazmus / Al Aziz, Md Momin / Mohammed, Noman / Chen, Feng / Jiang, Xiaoqian / Wang, Shuang | 2019
94
Genetic Networks and Soft Computing
Mitra, Sushmita / Das, Ranajit / Hayashi, Yoichi | 2011
95
A Survey and Comparative Study of Statistical Tests for Identifying Differential Expressionfrom Microarray Data
Bandyopadhyay, Sanghamitra / Mallik, Saurav / Mukhopadhyay, Anirban | 2014
95
SURVEY PAPERS - A Survey and Comparative Study of Statistical Tests for Identifying Differential Expression from Microarray Data
Bandyopadhyay, S / Mallik, S / Mukhopadhyay, A | 2014
95
2005 Reviewers List
| 2006
96
Estimation of the radiological background and dose assessment in areas with naturally occurring uranium geochemical anomalies-a case study in the Iberian Massif (Central Portugal)
Pereira, A.J.S.C. / Neves, L.J.P.F. | 2012
96
Outgoing EIC Editorial for this Special Section of TCBB with the Theme of Phylogenetics
Gusfield, Dan | 2009
96
Complexity and Algorithms for Finding a Perfect Phylogeny from Mixed Tumor Samples
Hujdurovic, Ademir / Kacar, Ursa / Milanic, Martin / Ries, Bernard / Tomescu, Alexandru I. | 2018
97
Three-Dimensional Path Planning for Uninhabited Combat Aerial Vehicle Based on Predator-Prey Pigeon-Inspired Optimization in Dynamic Environment
Bo Zhang, / Haibin Duan, | 2017
97
Maximum Parsimony for Tree Mixtures
Grunewald, S. / Moulton, V. | 2009
98
Bayesian segmental models with multiple sequence alignment profiles for protein secondary structure and contact map prediction
Wei Chu, / Ghahramani, Z. / Podtelezhnikov, A. / Wild, D.L. | 2006
98
Colored de Bruijn Graphs and the Genome Halving Problem
Alekseyev, M.A. / Pevzner, P.A. | 2007
98
Parametric Estimation of the Local False Discovery Rate for Identifying Genetic Associations
Yang, Ye / Aghababazadeh, Farnoosh Abbas / Bickel, David R. | 2013
98
A stochastic downhill search algorithm for estimating the local false discovery rate
Scheid, S. / Spang, R. | 2004
98
Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning
Ying-Xin Li, / Shuiwang Ji, / Kumar, S. / Jieping Ye, / Zhi-Hua Zhou, | 2012
99
Discovering Motifs in Biological Sequences Using the Micron Automata Processor
Roy, Indranil / Aluru, Srinivas | 2016
100
Sparse Support Vector Machines with L_{p} Penalty for Biomarker Identification
Zhenqiu Liu, / Shili Lin, / Tan, M.T. | 2010
101
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele
Barzuza, T. / Beckmann, J.S. / Shamir, R. | 2008
102
Disruption of Protein Complexes from Weighted Complex Networks
Habibi, Mahnaz / Khosravi, Pegah | 2020
102
Joint classification and pairing of human chromosomes
Biyani, P. / Xiaolin Wu, / Sinha, A. | 2005
103
Drawing Rooted Phylogenetic Networks
Huson, D.H. | 2009
103
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction
Spencer, Matt / Eickholt, Jesse / Cheng, Jianlin | 2015
103
Are My EHRs Private Enough? Event-Level Privacy Protection
Mao, Chengsheng / Zhao, Yuan / Sun, Mengxin / Luo, Yuan | 2019
108
Distorted Metrics on Trees and Phylogenetic Forests
Mossel, E. | 2007
108
A Multiple-Filter-Multiple-Wrapper Approach to Gene Selection and Microarray Data Classification
Yukyee Leung, / Yeungsam Hung, | 2010
108
Solving NP-Hard Problems with Physarum-Based Ant Colony System
Yuxin Liu, / Chao Gao, / Zili Zhang, / Yuxiao Lu, / Shi Chen, / Mingxin Liang, / Li Tao, | 2017
108
Identification and Modeling of Genes with Diurnal Oscillations from Microarray Time Series Data
Wenxue Wang, / Ghosh, Bijoy K / Pakrasi, Himadri | 2011
108
Chemical studies on polyaniline titanotungstate and its uses to reduction cesium from solutions and polluted milk
El-Naggar, I.M. / Zakaria, E.S. / Ali, I.M. / Khalil, M. / El-Shahat, M.F. | 2012
109
Constructing splits graphs
Dress, A.W.M. / Huson, D.H. | 2004
109
Detecting Essential Proteins Based on Network Topology, Gene Expression Data, and Gene Ontology Information
Wei Zhang, / Jia Xu, / Yuanyuan Li, / Xiufen Zou, | 2018
109
Probabilistic Biological Network Alignment
Todor, Andrei / Dobra, Alin / Kahveci, Tamer | 2013
110
Consistency of Topological Moves Based on the Balanced Minimum Evolution Principle of Phylogenetic Inference
Bordewich, M. / Gascuel, O. / Huber, K.T. / Moulton, V. | 2009
110
Drug Selection via Joint Push and Learning to Rank
He, Yicheng / Liu, Junfeng / Ning, Xia | 2020
110
DNA Motif Representation with Nucleotide Dependency
Chin, F. / Leung, H.C. | 2008
110
Semisupervised learning for molecular profiling
Furlanello, C. / Serafini, M. / Merler, S. / Jurman, G. | 2005
112
Fractal Behavior of the Pancreatic β-Cell Near the Percolation Threshold: Effect of the KATP Channel On the Electrical Response
Bahlouli, S. / Mokaddem, A. / Hamdache, F. / Riane, H. / Kameche, M. | 2016
113
Inferring the Number of Contributors to Mixed DNA Profiles
Paoletti, D. R. / Krane, D. E. / Raymer, M. L. / Doom, T. E. | 2012
113
A Hierarchical Clustering Method of Selecting Kernel SNP to Unify Informative SNP and Tag SNP
Liao, Bo / Li, Xiong / Cai, Lijun / Cao, Zhi / Chen, Haowen | 2015
113
SecureLR: Secure Logistic Regression Model via a Hybrid Cryptographic Protocol
Jiang, Yichen / Hamer, Jenny / Wang, Chenghong / Jiang, Xiaoqian / Kim, Miran / Song, Yongsoo / Xia, Yuhou / Mohammed, Noman / Sadat, Md Nazmus / Wang, Shuang | 2019
114
Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants
Danziger, S.A. / Swamidass, S.J. / Jue Zeng, / Dearth, L.R. / Qiang Lu, / Chen, J.H. / Cheng, J. / Hoang, V.P. / Saigo, H. / Luo, R. et al. | 2006
116
A New Path Based Hybrid Measurefor Gene Ontology Similarity
Bandyopadhyay, Sanghamitra / Mallick, Koushik | 2014
116
Improved gapped alignment in BLAST
Cameron, M. / Williams, H.E. / Cannane, A. | 2004
117
Efficient Algorithms for Sequence Analysis with Entropic Profiles
Pizzi, Cinzia / Ornamenti, Mattia / Spangaro, Simone / Rombo, Simona E. / Parida, Laxmi | 2018
117
DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions
Aeling, K.A. / Steffen, N.R. / Johnson, M. / Hatfield, G.W. / Lathrop, R.H. / Senear, D.F. | 2007
118
Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony
Taoyang Wu, / Moulton, V. / Steel, M. | 2009
118
A Trade-Off between Sample Complexity and Computational Complexity in Learning Boolean Networks from Time-Series Data
Perkins, T.J. / Hallett, M.T. | 2010
118
Determination of dose rate from Chernobyl-derived radiocaesium in Estonian soil
Lust, M. / Realo, E. | 2012
119
Essential latent knowledge for protein-protein interactions: analysis by an unsupervised learning approach
Mamitsuka, H. | 2005
120
Novel Algorithm for Coexpression Detection in Time-Varying Microarray Datasets
Zong-Xian Yin, / Jung-Hsien Chiang, | 2008
121
A Graph-Theoretical Approach for Motif Discovery in Protein Sequences
Czeizler, Elena / Hirvola, Tommi / Karhu, Kalle | 2017
122
Rearrangement-Based Phylogeny Using the Single-Cut-or-Join Operation
Biller, Priscila / Feijao, Pedro / Meidanis, Joao | 2013
122
Improving the Computational Efficiency of Recursive Cluster Elimination for Gene Selection
Lin-Kai Luo, / Deng-Feng Huang, / Ling-Jun Ye, / Qi-Feng Zhou, / Gui-Fang Shao, / Hong Peng, | 2011
122
gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal
Ullah, Ehsan / Aeron, Shuchin / Hassoun, Soha | 2016
123
A Maximum A Posteriori Probability and Time-Varying Approach for Inferring Gene Regulatory Networks from Time Course Gene Microarray Data
Chan, Shing-Chow / Zhang, Li / Wu, Ho-Chun / Tsui, Kai-Man | 2015
123
Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior
Xiaoning Qian, / Dougherty, E. R. | 2012
Feedback