Raluca Gordan

Center for Genomic and Computational Biology, Duke University

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 3	2019

Other Publications

Article	Year
Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics (Oxford, England)\| PubMed ID: 16873497	2006
A nucleosome-guided map of transcription factor binding sites in yeast. PLoS computational biology\| PubMed ID: 17997593	2007
Using DNA duplex stability information for transcription factor binding site discovery. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing\| PubMed ID: 18229707	2008
Distinguishing direct versus indirect transcription factor-DNA interactions. Genome research\| PubMed ID: 19652015	2009
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome research\| PubMed ID: 19996087	2010
Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic acids research\| PubMed ID: 20047961	2010
Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. RNA (New York, N.Y.)\| PubMed ID: 21282347	2011
Identification of cell cycle-regulated, putative hyphal genes in Candida albicans. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing\| PubMed ID: 22174285	2012
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell reports\| PubMed ID: 23562153	2013
Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics (Oxford, England)\| PubMed ID: 23812975	2013
TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic acids research\| PubMed ID: 24214955	2014
Protein-DNA binding: complexities and multi-protein codes. Nucleic acids research\| PubMed ID: 24243859	2014
COUGER--co-factors associated with uniquely-bound genomic regions. Nucleic acids research\| PubMed ID: 24861628	2014
Absence of a simple code: how transcription factors read the genome. Trends in biochemical sciences\| PubMed ID: 25129887	2014
Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome biology\| PubMed ID: 25287278	2014
Protein-DNA binding in the absence of specific base-pair recognition. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25313048	2014
Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Current biology : CB\| PubMed ID: 25702574	2015
Quantitative modeling of transcription factor binding specificities using DNA shape. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25775564	2015
Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. PLoS computational biology\| PubMed ID: 26285121	2015
HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics & chromatin\| PubMed ID: 27087856	2016
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi. eLife\| PubMed ID: 27162172	2016
Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources. Cold Spring Harbor protocols\| PubMed ID: 27803259	2016
Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Developmental cell\| PubMed ID: 27923776	2016
Expression level is a key determinant of E2F1-mediated cell fate. Cell death and differentiation\| PubMed ID: 28211871	2017
Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma. Cancer discovery\| PubMed ID: 28667006	2017
Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005-)\| PubMed ID: 28691125	2017
Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 28784765	2017
Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies. Nucleic acids research\| PubMed ID: 28977539	2017
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. Cell systems\| PubMed ID: 29605182	2018
Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene. Neurogenetics\| PubMed ID: 29730780	2018
The vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation. PloS one\| PubMed ID: 30107003	2018
Genetic variation determines VEGF-A plasma levels in cancer patients. Scientific reports\| PubMed ID: 30397360	2018
DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase. iScience\| PubMed ID: 30428370	2018
QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. Nucleic acids research\| PubMed ID: 31114870	2019
Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine. Biochimica et biophysica acta. General subjects\| PubMed ID: 31170499	2019