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June 2014 Bioinformatics Papers of Note


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]

Filed under

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.