ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
PLoS Comput. Biol., 2021
DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment.
PLoS Comput. Biol., 2021
Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.
Bioinform., 2017
Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response.
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PLoS Comput. Biol., 2015
Optimization of turn-back primers in isothermal amplification.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011
NGSView: an extensible open source editor for next-generation sequencing data.
Bioinform., 2010
GRAT - genome-scale rapid alignment tool.
Comput. Methods Programs Biomed., 2007
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
BMC Bioinform., 2006
ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aid.
Bioinform., 2004
TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences.
Comput. Methods Programs Biomed., 2003
Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs.
Bioinform., 2002