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Sequence analysis

BBMerge – Accurate paired shotgun read merging via overlap

Brian Bushnell, Jonathan Rood, Esther Singer

Compression of FASTQ and SAM Format Sequencing Data

James K. Bonfield, Matthew V. Mahoney

RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

Kevin Liu, C. Randal Linder, Tandy Warnow

Pseudogenes as Weaknesses of ACTB (Actb) and GAPDH (Gapdh) Used as Reference Genes in Reverse Transcription and Polymerase Chain Reactions

Yuan Sun, Yan Li, Dianzhong Luo, D. Joshua Liao

Ago2 Immunoprecipitation Identifies Predicted MicroRNAs in Human Embryonic Stem Cells and Neural Precursors

Loyal A. Goff, Jonathan Davila, [ ... ], Ronald P. Hart

Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks

Krista L. McGuire, Sara G. Payne, [ ... ], Noah Fierer

Noninvasive Prenatal Diagnosis of Fetal Trisomy 18 and Trisomy 13 by Maternal Plasma DNA Sequencing

Eric Z. Chen, Rossa W. K. Chiu, [ ... ], Y. M. Dennis Lo

Proline: The Distribution, Frequency, Positioning, and Common Functional Roles of Proline and Polyproline Sequences in the Human Proteome

Alexander A. Morgan, Edward Rubenstein

Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

Antonio M. Ramos, Richard P. M. A. Crooijmans, [ ... ], Martien A. M. Groenen

miRWalk: An online resource for prediction of microRNA binding sites

Carsten Sticht, Carolina De La Torre, Alisha Parveen, Norbert Gretz

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Wan-Ping Lee, Michael P. Stromberg, [ ... ], Gabor T. Marth

The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life

Gemma C. Atkinson, Tanel Tenson, Vasili Hauryliuk

SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation

Brejnev Muhizi Muhire, Arvind Varsani, Darren Patrick Martin

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