Harmen J Bussemaker

Harmen J Bussemaker

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Harmen J Bussemaker

Harmen J Bussemaker

Publications by authors named "Harmen J Bussemaker"

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Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.

Annu Rev Cell Dev Biol 2019 Oct 5;35:357-379. Epub 2019 Jul 5.

Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA; email:

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http://dx.doi.org/10.1146/annurev-cellbio-100617-062719DOI Listing
October 2019

In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module.

Nat Commun 2019 Aug 9;10(1):3597. Epub 2019 Aug 9.

Centro Andaluz de Biología del Desarrollo (CSIC/JA/UPO), Universidad Pablo de Olavide, 41013, Seville, Spain.

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http://dx.doi.org/10.1038/s41467-019-11416-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689074PMC
August 2019

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding.

Epigenetics Chromatin 2018 02 6;11(1). Epub 2018 Feb 6.

Computational Biology and Bioinformatics Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.

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http://dx.doi.org/10.1186/s13072-018-0174-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5800008PMC
February 2018

A unified approach for quantifying and interpreting DNA shape readout by transcription factors.

Mol Syst Biol 2018 02 22;14(2):e7902. Epub 2018 Feb 22.

Department of Biological Sciences, Columbia University, New York, NY, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5822049PMC
http://dx.doi.org/10.15252/msb.20177902DOI Listing
February 2018

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

Cell Rep 2017 06;19(11):2383-2395

Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.05.069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533174PMC
June 2017

Genome-wide mapping of autonomous promoter activity in human cells.

Nat Biotechnol 2017 02 26;35(2):145-153. Epub 2016 Dec 26.

Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1038/nbt.3754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5498152PMC
February 2017

Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets.

Proc Natl Acad Sci U S A 2016 Mar 10;113(13):E1835-43. Epub 2016 Mar 10.

Department of Biological Sciences, Columbia University, New York, NY 10027; Department of Systems Biology, Columbia University, New York, NY 10032;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1517140113
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http://dx.doi.org/10.1073/pnas.1517140113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822571PMC
March 2016

DSSR: an integrated software tool for dissecting the spatial structure of RNA.

Nucleic Acids Res 2015 Dec 15;43(21):e142. Epub 2015 Jul 15.

Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1093/nar/gkv716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666379PMC
December 2015

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.

Elife 2015 Dec 23;4. Epub 2015 Dec 23.

Department of Biological Sciences, Columbia University, New York, United States.

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http://dx.doi.org/10.7554/eLife.06397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758951PMC
December 2015

Quantitative modeling of transcription factor binding specificities using DNA shape.

Proc Natl Acad Sci U S A 2015 Apr 9;112(15):4654-9. Epub 2015 Mar 9.

Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089;

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http://dx.doi.org/10.1073/pnas.1422023112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403198PMC
April 2015

Deconvolving the recognition of DNA shape from sequence.

Cell 2015 Apr 2;161(2):307-18. Epub 2015 Apr 2.

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422406PMC
April 2015

Recent progress in understanding transcription factor binding specificity.

Brief Funct Genomics 2015 Jan;14(1):1-2

Department of Biological Sciences, Columbia University, 1212 Amsterdam Ave, MC 2441, New York, NY 10027, USA

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http://dx.doi.org/10.1093/bfgp/elu050DOI Listing
January 2015

In search of the determinants of enhancer-promoter interaction specificity.

Trends Cell Biol 2014 Nov 24;24(11):695-702. Epub 2014 Aug 24.

Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tcb.2014.07.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252644PMC
November 2014

ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2.

J Exp Med 2014 Jul 30;211(8):1623-35. Epub 2014 Jun 30.

Department of Microbiology and Immunology, Center for Computational Biology and Bioinformatics, Institute for Cancer Genetics, Department of Pathology, and Department of Pediatrics, Columbia University Medical Center and Department of Biological Sciences and Department of Electrical Engineering, Columbia University, New York, NY 10032

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http://dx.doi.org/10.1084/jem.20132121DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113936PMC
July 2014

Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast.

G3 (Bethesda) 2014 Jun 17;4(8):1539-53. Epub 2014 Jun 17.

Department of Biological Sciences, Columbia University, New York, New York 10027 Department of Systems Biology, Columbia University, New York, New York 10032

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http://dx.doi.org/10.1534/g3.114.012039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132183PMC
June 2014

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast.

BMC Genomics 2014 Jun 19;15:494. Epub 2014 Jun 19.

Department of Biological Sciences, Columbia University, 1212 Amsterdam Ave, New York, NY 10027, USA.

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http://dx.doi.org/10.1186/1471-2164-15-494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4124144PMC
June 2014

Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.

Proc Natl Acad Sci U S A 2014 Apr 2;111(15):5747-52. Epub 2014 Apr 2.

Department of Biological Sciences, Columbia University, New York, NY 10027.

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http://dx.doi.org/10.1073/pnas.1309293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992641PMC
April 2014

DAF-16 and PQM-1: partners in longevity.

Aging (Albany NY) 2014 Jan;6(1):5-6

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927804PMC
http://dx.doi.org/10.18632/aging.100628DOI Listing
January 2014

Probing DNA shape and methylation state on a genomic scale with DNase I.

Proc Natl Acad Sci U S A 2013 Apr 1;110(16):6376-81. Epub 2013 Apr 1.

Department of Electrical Engineering and Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1073/pnas.1216822110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631675PMC
April 2013

Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.

Mol Biol Cell 2012 Aug 13;23(15):3008-24. Epub 2012 Jun 13.

The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1091/mbc.E12-03-0233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408426PMC
August 2012

Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.

Mol Biol Cell 2012 Aug 13;23(15):2993-3007. Epub 2012 Jun 13.

The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1091/mbc.E12-03-0232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408425PMC
August 2012

TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements.

Proc Natl Acad Sci U S A 2012 Apr 29;109(16):6030-5. Epub 2012 Mar 29.

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1073/pnas.1203028109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3341064PMC
April 2012

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.

Cell 2011 Dec;147(6):1270-82

Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA.

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http://dx.doi.org/10.1016/j.cell.2011.10.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319069PMC
December 2011

Identifying the genetic determinants of transcription factor activity.

Mol Syst Biol 2010 Sep;6:412

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1038/msb.2010.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2964119PMC
September 2010

The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.

Nucleic Acids Res 2010 Aug 11;38(14):4868-76. Epub 2010 Mar 11.

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/nar/gkq155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919703PMC
August 2010

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

PLoS One 2008 Sep 3;3(9):e3112. Epub 2008 Sep 3.

Swammerdam Institute for Life Sciences, University of Amsterdam, BioCentrum Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003112PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518834PMC
September 2008

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Bioinformatics 2008 Jul;24(13):i165-71

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718632PMC
July 2008

Global chromatin domain organization of the Drosophila genome.

PLoS Genet 2008 Mar 28;4(3):e1000045. Epub 2008 Mar 28.

Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1371/journal.pgen.1000045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2274884PMC
March 2008

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.

Nucleic Acids Res 2008 Jan 18;36(Database issue):D125-31. Epub 2007 Oct 18.

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

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http://dx.doi.org/10.1093/nar/gkm828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238954PMC
January 2008

Dissecting complex transcriptional responses using pathway-level scores based on prior information.

BMC Bioinformatics 2007 Sep 27;8 Suppl 6:S6. Epub 2007 Sep 27.

Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, MC 2441, New York, NY 10027, USA.

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http://dx.doi.org/10.1186/1471-2105-8-S6-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1995543PMC
September 2007

Predictive modeling of genome-wide mRNA expression: from modules to molecules.

Annu Rev Biophys Biomol Struct 2007 ;36:329-47

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

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http://dx.doi.org/10.1146/annurev.biophys.36.040306.132725DOI Listing
August 2007

Detecting transcriptionally active regions using genomic tiling arrays.

Genome Biol 2006 ;7(7):R59

Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA.

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http://dx.doi.org/10.1186/gb-2006-7-7-r59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779562PMC
May 2007

HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.

EMBO J 2007 Feb 25;26(3):741-51. Epub 2007 Jan 25.

Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/sj.emboj.7601527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794385PMC
February 2007

Modeling gene expression control using Omes Law.

Mol Syst Biol 2006 18;2:2006.0013. Epub 2006 Apr 18.

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http://dx.doi.org/10.1038/msb4100055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681487PMC
August 2006

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.

Proc Natl Acad Sci U S A 2006 Aug 31;103(32):12027-32. Epub 2006 Jul 31.

Department of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1073/pnas.0605003103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1567692PMC
August 2006

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

Bioinformatics 2006 Jul;22(14):e141-9

Department of Biological Sciences, Columbia University New York, NY 10027, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl223DOI Listing
July 2006

Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.

Proc Natl Acad Sci U S A 2005 Dec 29;102(49):17675-80. Epub 2005 Nov 29.

Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1073/pnas.0503803102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1295595PMC
December 2005

T-profiler: scoring the activity of predefined groups of genes using gene expression data.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W592-5

Swammerdam Institute for Life Sciences-Microbiology, University of Amsterdam, Biocentrum Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gki484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160244PMC
July 2005

A gene expression map for the euchromatic genome of Drosophila melanogaster.

Science 2004 Oct;306(5696):655-60

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1101312DOI Listing
October 2004

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

BMC Bioinformatics 2004 Mar 18;5:31. Epub 2004 Mar 18.

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-5-31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC407845PMC
March 2004

REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.

Nucleic Acids Res 2003 Jul;31(13):3487-90

Department of Biological Sciences, Columbia University, New York, NY, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC169192PMC
http://dx.doi.org/10.1093/nar/gkg630DOI Listing
July 2003

Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network.

Genes Dev 2003 May 14;17(9):1101-14. Epub 2003 Apr 14.

Division of Basic Sciences and Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1101/gad.1066903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC196053PMC
May 2003

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.

Nucleic Acids Res 2003 Apr;31(8):2242-51

Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC153734PMC
http://dx.doi.org/10.1093/nar/gkg306DOI Listing
April 2003

Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state.

Genome Biol 2003 17;4(1):R3. Epub 2002 Dec 17.

Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM Amsterdam, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151284PMC
http://dx.doi.org/10.1186/gb-2002-4-1-r3DOI Listing
March 2003

Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding.

Proc Natl Acad Sci U S A 2003 Mar 24;100(5):2580-5. Epub 2003 Feb 24.

Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0438000100
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http://dx.doi.org/10.1073/pnas.0438000100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151383PMC
March 2003

Identification of genes expressed in C. elegans touch receptor neurons.

Nature 2002 Jul;418(6895):331-5

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

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http://dx.doi.org/10.1038/nature00891DOI Listing
July 2002