Metabolic Control over mTOR-Dependent Diapause-like State
Developmental Cell 52:2, 2020.,
Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana.
Sci Rep 8:1, 2018.,
Associating transcription factors and conserved RNA structures with gene regulation in the human brain.
Sci Rep 7:1, 2017. Stable URL http://rdcu.be/uknk.,
The identification and functional annotation of RNA structures conserved in vertebrates.
Genome Res, 2017.,
Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments
, 2016. bioRxiv
RNA Sequence, Structure and Function: Computational and Bioinformatic Methods
Methods in Molecular Biology, Humana Press:1097, 2014.,
A Microbial Profiling Method for the Human Microbiota Using High-Throughput Sequencing
Metagenomics 2, 2013.,
Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.
Skeletal Muscle 3:1, 2013.,
Accelerating ncRNA homology search with FPGAs
the ACM/SIGDA international symposiumProceedings of the ACM/SIGDA international symposium on Field programmable gate arrays - FPGA '13, ACM Press, 2013.,
Genetic and epigenetic determinants of neurogenesis and myogenesis.
Developmental Cell 22:4, 2012.,
Hardware Acceleration of Short Read Mapping
FCCM 2012: The 20th Annual IEEE International Symposium on Field-Programmable Custom Computing Machines, 2012. (Best Paper Award),
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Nature Methods 9:5, 2012.,
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Direct maximization of protein identifications from tandem mass spectra.
Molecular & cellular proteomics : MCP 11:2, 2012.,
Faster Mass Spectrometry-based Protein Inference: Junction Trees are More Efficient than Sampling and Marginalization by Enumeration.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 2012.,
DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.
Developmental Cell 22:1, 2012.,
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.
Nucleic acids research 40:2, 2012.,
Epigenetic priors for identifying active transcription factor binding sites.
Bioinformatics (Oxford, England) 28:1, 2012.,
Integrative annotation of chromatin elements from ENCODE data
Nucleic Acids Research In Press, 2012.,
A unified multitask architecture for predicting local protein properties.
PloS one 7:3, 2012.,
Faster SEQUEST searching for peptide identification from tandem mass spectra.
Journal of proteome research 10:9, 2011.,
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.
Developmental cell 18:4, 2010.,
De novo prediction of structured RNAs from genomic sequences.
Trends in biotechnology 28:1, 2010.,
Finding non-coding RNAs through genome-scale clustering.
Journal of bioinformatics and computational biology 7:2, 2009.,
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.
Stem cells (Dayton, Ohio) 26:10, 2008.,
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
RNA (New York, N.Y.) 14:5, 2008.,
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
Molecular microbiology 68:4, 2008.,
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.
Genome research 18:2, 2008.,
Finding non-coding RNAs through genome-scale clustering
Sixth Asia-Pacific Bioinformatics Conference, 2008.,
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.
PLoS computational biology 3:7, 2007.,
How accurately is ncRNA aligned within whole-genome multiple alignments?
BMC bioinformatics 8, 2007.,
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
Nucleic acids research 35:14, 2007.,
A Marfan syndrome gene expression phenotype in cultured skin fibroblasts.
BMC genomics 8, 2007.,
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
PLoS biology 4:9, 2006.,
CMfinder--a covariance model based RNA motif finding algorithm.
Bioinformatics (Oxford, England) 22:4, 2006.,
Sequence-based heuristics for faster annotation of non-coding RNA families.
Bioinformatics (Oxford, England) 22:1, 2006.,
Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.
Journal of vascular surgery : official publication, the Society for Vascular Surgery [and] International Society for Cardiovascular Surgery, North American Chapter 43:1, 2006.,
A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.
BMC bioinformatics 7 Suppl 1, 2006.,
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
RNA (New York, N.Y.) 11:5, 2005.,
A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
Science (New York, N.Y.) 306:5694, 2004.,
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.
Bioinformatics (Oxford, England) 20 Suppl 1, 2004.,
http://www.ncbi.nlm.nih.gov/pubmed/15262817?dopt=Abstract http://bio.cs.washington.edu/supplements/zasha-ISMB-2004/ Supplementary Data
Atherosclerotic plaque smooth muscle cells have a distinct phenotype.
Arteriosclerosis, thrombosis, and vascular biology 24:7, 2004.,
Faster Genome Annotation of Non-coding RNA Families Without Loss of Accuracy
Eighth Annual International Conference on Research in Computational Molecular Biology, 2004.,
Improved gene selection for classification of microarrays.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2003.,
Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae.
Neoplasia (New York, N.Y.) 4:2, 2002.,
Pre-mRNA secondary structure prediction aids splice site prediction.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2002.,
Model-based clustering and data transformations for gene expression data.
Bioinformatics (Oxford, England) 17:10, 2001.,
Principal component analysis for clustering gene expression data.
Bioinformatics (Oxford, England) 17:9, 2001.,
Validating clustering for gene expression data.
Bioinformatics (Oxford, England) 17:4, 2001.,
Algorithms for a Simple Point Placement Problem
Algorithms and Complexity, 4th Italian Conference, 2000.,
A Linear Time Algorithm for Finding All Maximal Scoring Subsequences
Seventh International Conference on Intelligent Systems for Molecular Biology, 1999.,
A linear time algorithm for finding all maximal scoring subsequences.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1999.,