FIND

researchers

DISCOVER

relevant articles

PROMOTE

your research

now for free

David Gifford

Research Profile

Chemicals & Drugs

Concepts & Ideas

Procedures

Living Beings

Devices

Oligonucleotide Array Sequence Analysis

Physiology

Occupations

Computational Biology

Genes & Molecular Sequences

Activities & Behaviors

Computer Simulation

Co-author Network

Publications

TOP 3
Mandana Arbab; Joel M Chick; Hyunjii Cho; David K Gifford; Steven P Gygi; Richard L Maas; Shaun Mahony; Viveca W S Morris; P Alexander Rolfe; John Peter van Hoff; Richard I Sherwood
A multi-parametric flow cytometric assay to analyze DNA-protein interactions.
P Alexander Rolfe; Paula Grisafi; Douglas A Bernstein; Gerald R Fink; David K Gifford
Ruler arrays reveal haploid genomic structural variation.
Yuchun Guo; Shaun Mahony; David K Gifford
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

Register for free to view:

Visualized networks:

See your personal network in
sophisticated graphical views

GeoTargeted Searches:

Locate experts around the world
and connect with global collaborators

Research Profiles:

See the research activity
of experts around the globe

Geonetwork of David Gifford (preview)

Cities where this author has publications
Cities where co-authors of this author have publications

Flash Player Required

All Publications

2013: Mandana Arbab; Joel M Chick; Hyunjii Cho; David K Gifford; Steven P Gygi; Richard L Maas; Shaun Mahony; Viveca W S Morris; P Alexander Rolfe; John Peter van Hoff; Richard I Sherwood
A multi-parametric flow cytometric assay to analyze DNA-protein interactions.
Nucleic acids research 2013;41(2):e38.
2012: P Alexander Rolfe; Paula Grisafi; Douglas A Bernstein; Gerald R Fink; David K Gifford
Ruler arrays reveal haploid genomic structural variation.
PloS one 2012;7(8):e43210.
2012: Yuchun Guo; Shaun Mahony; David K Gifford
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.
PLoS computational biology 2012;8(8):e1002638.
2012: Matthew D Edwards; David K Gifford
High-resolution genetic mapping with pooled sequencing.
BMC bioinformatics 2012;13 Suppl 6():S8.
2011: Esteban O Mazzoni; Carolyn A Morrison; George Mountoufaris; Warren A Whyte; Michael Closser; David K Gifford; Michelina Iacovino; Michael Kyba; Shaun Mahony; Richard A Young; Hynek Wichterle
Embryonic stem cell-based mapping of developmental transcriptional programs.
Nature methods 2011;8(12):1056-8.
2011: P Alexander Rolfe; David K Gifford
ReadDB provides efficient storage for mapped short reads.
BMC bioinformatics 2011;12():278.
2011: Shaun Mahony; Esteban O Mazzoni; Scott McCuine; Hynek Wichterle; Richard A Young; David K Gifford
Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis.
Genome biology 2011;12(1):R2.
2010: Yuchun Guo; Georgios Papachristoudis; Robert C Altshuler; Georg K Gerber; Tommi S Jaakkola; David K Gifford; Shaun Mahony
Discovering homotypic binding events at high spatial resolution.
Bioinformatics (Oxford, England) 2010;26(24):3028-34.
2010: Joshua J Wolf; Robin D Dowell; Shaun Mahony; Michal Rabani; David K Gifford; Gerald R Fink
Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast.
Genetics 2010;185(2):513-22.
2010: Chia-Yung Wu; P Alexander Rolfe; David K Gifford; Gerald R Fink
Control of transcription by cell size.
PLoS biology 2010;8(11):e1000523.
2010: Amy L Williams; David E Housman; Martin C Rinard; David K Gifford
Rapid haplotype inference for nuclear families.
Genome biology 2010;11(10):R108.
2009: Stacie L Bumgarner; Robin D Dowell; Paula Grisafi; David K Gifford; Gerald R Fink
Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(43):18321-6.
2008: Divya Mathur; Timothy Danford; Laurie A Boyer; Richard A Young; David K Gifford; Rudolf Jaenisch
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET.
Genome biology 2008;9(8):R126.
2007: Georg Gerber; Robin D Dowell; Tommi S Jaakkola; David K Gifford
Automated discovery of functional generality of human gene expression programs.
PLoS computational biology 2007;3(8):e148.
2007: Duncan T Odom; Robin D Dowell; Elizabeth S Jacobsen; William Gordon; Timothy Danford; Kenzie D Macisaac; P Alexander Rolfe; Caitlin M Conboy; David K Gifford; Ernest Fraenkel
Tissue-specific transcriptional regulation has diverged significantly between human and mouse.
Nature genetics 2007;39(6):730-2.
2006: Yuan Qi; Alex Rolfe; Kenzie D Macisaac; Georg Gerber; Dmitry K Pokholok; Julia Zeitlinger; Timothy Danford; Robin D Dowell; Ernest Fraenkel; Tommi S Jaakkola; Richard A Young; David K Gifford
High-resolution computational models of genome binding events.
Nature biotechnology 2006;24(8):963-70.
2006: Yuan Qi; Patrycja E Missiuro; Ashish Kapoor; Craig P Hunter; Tommi S Jaakkola; David K Gifford; Hui Ge
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo.
Bioinformatics (Oxford, England) 2006;22(14):e417-23.
2006: Laurie A Boyer; Kathrin Plath; Julia Zeitlinger; Tobias Brambrink; Lea A Medeiros; Tong Ihn Lee; Stuart S Levine; Marius Wernig; Adriana Tajonar; Mridula K Ray; George W Bell; Arie P Otte; Miguel Vidal; David K Gifford; Richard A Young; Rudolf Jaenisch
Polycomb complexes repress developmental regulators in murine embryonic stem cells.
Nature 2006;441(7091):349-53.
2006: Tong Ihn Lee; Richard G Jenner; Laurie A Boyer; Matthew G Guenther; Stuart S Levine; Roshan M. Kumar; Brett Chevalier; Sarah E Johnstone; Megan F Cole; Kyo-ichi Isono; Haruhiko Koseki; Takuya Fuchikami; Kuniya Abe; Heather L Murray; Jacob P Zucker; Bingbing Yuan; George W Bell; Elizabeth Herbolsheimer; Nancy M Hannett; Kaiming Sun; Duncan T Odom; Arie P Otte; Thomas L Volkert; David P Bartel; Douglas A Melton; David K Gifford; Rudolf Jaenisch; Richard A Young
Control of developmental regulators by Polycomb in human embryonic stem cells.
Cell 2006;125(2):301-13.
2006: Joerg Schreiber; Richard G Jenner; Heather L Murray; Georg Gerber; David K Gifford; Richard A Young
Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(15):5899-904.
2006: Kenzie D Macisaac; D Benjamin Gordon; Lena Nekludova; Duncan T Odom; Joerg Schreiber; David K Gifford; Richard A Young; Ernest Fraenkel
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.
Bioinformatics (Oxford, England) 2006;22(4):423-9.
2006: Duncan T Odom; Robin D Dowell; Elizabeth S Jacobsen; Lena Nekludova; P Alexander Rolfe; Timothy Danford; David K Gifford; Ernest Fraenkel; Graeme I Bell; Richard A Young
Core transcriptional regulatory circuitry in human hepatocytes.
Molecular systems biology 2006;2():2006.0017.
2006: Kenzie D Macisaac; Ting Wang; D Benjamin Gordon; David K Gifford; Gary stormo; Ernest Fraenkel
An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
BMC bioinformatics 2006;7():113.
2005: Laurie A Boyer; Tong Ihn Lee; Megan F Cole; Sarah E Johnstone; Stuart S Levine; Jacob P Zucker; Matthew G Guenther; Roshan M. Kumar; Heather L Murray; Richard G Jenner; David K Gifford; Douglas A Melton; Rudolf Jaenisch; Richard A Young
Core transcriptional regulatory circuitry in human embryonic stem cells.
Cell 2005;122(6):947-56.
2005: Dmitry K Pokholok; Christopher T Harbison; Stuart Levine; Megan Cole; Nancy M Hannett; Tong Ihn Lee; George W Bell; Kimberly Walker; P Alexander Rolfe; Elizabeth Herbolsheimer; Julia Zeitlinger; Fran Lewitter; David K Gifford; Richard A Young
Genome-wide map of nucleosome acetylation and methylation in yeast.
Cell 2005;122(4):517-27.
2004: François Robert; Dmitry K Pokholok; Nancy M Hannett; Nicola J Rinaldi; Mark Chandy; Alex Rolfe; Jerry L Workman; David K Gifford; Richard A Young
Global position and recruitment of HATs and HDACs in the yeast genome.
Molecular cell 2004;16(2):199-209.
2004: Christopher T Harbison; D Benjamin Gordon; Tong Ihn Lee; Nicola J Rinaldi; Kenzie D Macisaac; Timothy Danford; Nancy M Hannett; Jean-Bosco Tagne; David B Reynolds; Jane Yoo; Ezra Jennings; Julia Zeitlinger; Dmitry K Pokholok; Manolis Kellis; P Alexander Rolfe; Ken T Takusagawa; Eric S Lander; David K Gifford; Ernest Fraenkel; Richard A Young
Transcriptional regulatory code of a eukaryotic genome.
Nature 2004;431(7004):99-104.
2004: Ziv Bar-Joseph; Shlomit Farkash; David K Gifford; Itamar Simon; Roni Rosenfeld
Deconvolving cell cycle expression data with complementary information.
Bioinformatics (Oxford, England) 2004;20 Suppl 1():i23-30.
2004: Duncan T Odom; Nora Zizlsperger; D Benjamin Gordon; George W Bell; Nicola J Rinaldi; Heather L Murray; Thomas L Volkert; Joerg Schreiber; P Alexander Rolfe; David K Gifford; Ernest Fraenkel; Graeme I Bell; Richard A Young
Control of pancreas and liver gene expression by HNF transcription factors.
Science (New York, N.Y.) 2004;303(5662):1378-81.
2004: K T Takusagawa; David K Gifford
Negative information for motif discovery.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2004;():360-71.
2003: Ziv Bar-Joseph; Georg Gerber; Tong Ihn Lee; Nicola J Rinaldi; Jane Y Yoo; François Robert; D Benjamin Gordon; Ernest Fraenkel; Tommi S Jaakkola; Richard A Young; David K Gifford
Computational discovery of gene modules and regulatory networks.
Nature biotechnology 2003;21(11):1337-42.
2003: Ziv Bar-Joseph; Georg Gerber; Itamar Simon; David K Gifford; Tommi S Jaakkola
Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(18):10146-51.
2003: Ziv Bar-Joseph; Erik D Demaine; David K Gifford; Nathan Srebro; Angèle M Hamel; Tommi S Jaakkola
K-ary clustering with optimal leaf ordering for gene expression data.
Bioinformatics (Oxford, England) 2003;19(9):1070-8.
2003: Ziv Bar-Joseph; Georg Gerber; David K Gifford; Tommi S Jaakkola; Itamar Simon
Continuous representations of time-series gene expression data.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):341-56.
2002: Tong Ihn Lee; Nicola J Rinaldi; François Robert; Duncan T Odom; Ziv Bar-Joseph; Georg Gerber; Nancy M Hannett; Christopher T Harbison; Craig M Thompson; Itamar Simon; Julia Zeitlinger; Ezra Jennings; Heather L Murray; D Benjamin Gordon; Bing Ren; John J Wyrick; Jean-Bosco Tagne; Thomas L Volkert; Ernest Fraenkel; David K Gifford; Richard A Young
Transcriptional regulatory networks in Saccharomyces cerevisiae.
Science (New York, N.Y.) 2002;298(5594):799-804.
2002: Alexander J Hartemink; David K Gifford; Tommi S Jaakkola; Richard A Young
Combining location and expression data for principled discovery of genetic regulatory network models.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():437-49.
2001: Itamar Simon; J Barnett; Nancy M Hannett; Christopher T Harbison; Nicola J Rinaldi; Thomas L Volkert; John J Wyrick; Julia Zeitlinger; David K Gifford; Tommi S Jaakkola; Richard A Young
Serial regulation of transcriptional regulators in the yeast cell cycle.
Cell 2001;106(6):697-708.
2001: David K Gifford
Blazing pathways through genetic mountains.
Science (New York, N.Y.) 2001;293(5537):2049-51.
2001: Ziv Bar-Joseph; David K Gifford; Tommi S Jaakkola
Fast optimal leaf ordering for hierarchical clustering.
Bioinformatics (Oxford, England) 2001;17 Suppl 1():S22-9.
2001: Alexander J Hartemink; David K Gifford; Tommi S Jaakkola; Richard A Young
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():422-33.
1999: Alexander J Hartemink; David K Gifford; Julia Khodor
Automated constraint-based nucleotide sequence selection for DNA computation.
Bio Systems 1999;52(1-3):227-35.
1999: Julia Khodor; David K Gifford
Design and implementation of computational systems based on programmed mutagenesis.
Bio Systems 1999;52(1-3):93-7.