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June 2014 Bioinformatics Papers of Note

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Dasgupta S, Ghosh Z, et al.
PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis.
BMC Bioinformatics. 2014 Jun 4;15:167. doi: 10.1186/1471-2105-15-167.


Eisenhaber B, Eisenhaber F, et al.
On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation.
BMC Bioinformatics. 2014 Jun 2;15:166. doi: 10.1186/1471-2105-15-166.


Chen CC2, Chang YJ et al.
CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce.
PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146.


Bhagwate A, Bockol M, et al.
CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data.
BMC Genomics. 2014 Jun 3;15:423. doi: 10.1186/1471-2164-15-423.


Bresler M, Curtis K, et al.
SMaSH: a benchmarking toolkit for human genome variant calling.
Bioinformatics. 2014 Jun 3. pii: btu345. [Epub ahead of print]


Johnson TD, Lin YH, et al.
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data.
Bioinformatics. 2014 Jun 3. pii: btu372. [Epub ahead of print]


Zytnicki M, Akhunov E, Quesneville H.
Tedna: a transposable element de novo assembler.
Bioinformatics. 2014 Jun 3. pii: btu365. [Epub ahead of print]


Abecasis GR, Feng S, et al.
RAREMETAL: fast and powerful meta-analysis for rare variants.
Bioinformatics. 2014 Jun 3. pii: btu367. [Epub ahead of print]


Curtis RE, Kinnaird P, et al.
GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap.
PLoS One. 2014 Jun 6;9(6):e97524. doi: 10.1371/journal.pone.0097524


Araya CL, Boyle AP, et al.
Sushi.R: Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.
Bioinformatics. 2014 Jun 5. pii: btu379. [Epub ahead of print]


Hayes DN, Parker JS, et al.
ABRA: improved coding indel detection via assembly based re-alignment.
Bioinformatics. 2014 Jun 6. pii: btu376. [Epub ahead of print]


Anderson N, Choiniere J, et al.
MOPED 2.5-An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data.
OMICS. 2014 Jun;18(6):335-43. doi: 10.1089/omi.2014.0061.


Ding SW, Jiang H, et al.
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
BMC Bioinformatics. 2014 Jun 12;15(1):182.


Guillot EG, Cox MP
SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.
BMC Bioinformatics. 2014 Jun 9;15:175. doi: 10.1186/1471-2105-15-175.


Bradbury LM, Frelin O, et al.
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource.
Proc Natl Acad Sci U S A. 2014 Jun 9. pii: 201401329. [Epub ahead of print]


McGeachie MJ, Chang HH, Weiss ST.
CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data.
PLoS Comput Biol. 2014 Jun 12.


Dingerdissen H, Mazumder R, et al.
HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis.
PLoS One. 2014 Jun 11;9(6):e99033. doi: 10.1371/journal.pone.0099033


Feng J, He Y, et al.
dbCerEx: A Web-Based Database for the Analysis of Cervical Cancer Transcriptomes.
PLoS One. 2014 Jun 11;9(6):e99033. doi: 10.1371/journal.pone.0099033


Burgess KE, Breitling R, et al.
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach.
Bioinformatics. 2014 Jun 9. pii: btu370. [Epub ahead of print]


English AC, Salerno WJ, Reid JG.
PBHoney: Identifying Genomic Variants via Long-Read Discordance and Interrupted Mapping.
BMC Bioinformatics. 2014 Jun 10;15(1):180. [Epub ahead of print]


Anand P, Chaudhary K, et al.
ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures.
Database (Oxford). 2014 Jun 12.


Aanensen DM, Baguelin M, et al.
OutbreakTools: A new platform for disease outbreak analysis using the R software.
Epidemics. 2014 Jun;7:28-34. doi: 10.1016/j.epidem.2014.04.003. Epub 2014 Apr 18.


Triapthi S, Dehmer M, Emmert-Streib F.
NetBioV: An R package for visualizing large network data in biology and medicine.
Bioinformatics. 2014 Jun 12. pii: btu384. [Epub ahead of print].


Mrozek D, Małysiak-Mrozek B, Kłapciński A.
Cloud4Psi: Cloud Computing for 3D Protein Structure Similarity Searching.
Bioinformatics. 2014 Jun 14. pii: btu389. [Epub ahead of print]


Cheng L, Ju P, et al.
SemFunSim: A New Method for Measuring Disease Similarity by Integrating Semantic and Gene Functional Association.
PLoS One. 2014 Jun 16;9(6):e99415. doi: 10.1371/journal.pone.0099415.


Hajirasouliha I, Mahmoody A, Raphael BJ.
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data.
Bioinformatics. 2014 Jun 15;30(12):i78-i86.


Bao E, Jiang T, Girke T.
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.
Bioinformatics. 2014 Jun 15;30(12):i319-i328.


Bankevich A, Gurevich A, et al.
ExSPAnder: a universal repeat resolver for DNA fragment assembly.
Bioinformatics. 2014 Jun 15;30(12):i293-i301.


Backofen R, Costa F, et al.
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.
Bioinformatics. 2014 Jun 15;30(12):i274-i282.


Cicek AE, Roeder K, Ozsoyoglu G
MIRA: mutual information-based reporter algorithm for metabolic networks.
Bioinformatics. 2014 Jun 15;30(12):i175-i184.


DeZiel C, Heckerman D, et al.
Literome: PubMed-Scale Genomic Knowledge Base in the Cloud.
Bioinformatics. 2014 Jun 17. pii: btu383. [Epub ahead of print]


Faoro H, Pedrosa FO, et al.
FGAP: an automated gap closing tool.
BMC Res Notes. 2014 Jun 18;7(1):371. [Epub ahead of print]


Chan KC, Chiu RW, et al.
Methy-pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis.
PLoS One. 2014 Jun 19;9(6):e100360. doi: 10.1371/journal.pone.0100360.


Carazzolle MF, de Carvalho LM, et al.
IIs - integrated interactome system: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.
PLoS One. 2014 Jun 20;9(6):e100385. doi: 10.1371/journal.pone.0100385.


Cuevas DA, Dutilh BE, et al.
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
PeerJ. 2014 Jun 5;2:e425. doi: 10.7717/peerj.425. eCollection 2014.


Ahn TH, Bushnell B, et al.
Omega: an Overlap-graph de novo Assembler for Metagenomics.
Bioinformatics. 2014 Jun 19. pii: btu395. [Epub ahead of print]


Speed D, Balding DJ.
MultiBLUP: improved SNP-based prediction for complex traits.
Genome Res. 2014 Jun 24. pii: gr.169375.113. [Epub ahead of print]


Layer RM, Chiang C, Quinlan AR, Hall IM
LUMPY: A probabilistic framework for structural variant discovery.
Genome Biol. 2014 Jun 26;15(6):R84. [Epub ahead of print]

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