Publications by authors named "Alexander Stark"

100Publications

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate.

Chemistry 2020 Aug 22;26(43):9407. Epub 2020 Jun 22.

Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309-4479, USA.

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http://dx.doi.org/10.1002/chem.202002715DOI Listing
August 2020

Impact of tumor regression grade on recurrence after preoperative chemoradiation and gastrectomy for gastric cancer.

J Surg Oncol 2020 Sep 27;122(3):422-432. Epub 2020 May 27.

Departments of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1002/jso.25984DOI Listing
September 2020

ASO Author Reflections: In Gastric Cancer Patients with Primary Tumor Pathologic Complete Response, Treatment-Refractory Nodal Disease is an Ominous Sign.

Ann Surg Oncol 2019 12 30;26(Suppl 3):819-820. Epub 2019 Oct 30.

Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1245/s10434-019-07836-4DOI Listing
December 2019

STARR-seq and UMI-STARR-seq: Assessing Enhancer Activities for Genome-Wide-, High-, and Low-Complexity Candidate Libraries.

Curr Protoc Mol Biol 2019 09;128(1):e105

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1002/cpmb.105DOI Listing
September 2019

Characteristics and Survival of Gastric Cancer Patients with Pathologic Complete Response to Preoperative Therapy.

Ann Surg Oncol 2019 Oct 26;26(11):3602-3610. Epub 2019 Jul 26.

Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

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http://link.springer.com/10.1245/s10434-019-07638-8
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http://dx.doi.org/10.1245/s10434-019-07638-8DOI Listing
October 2019

Transcriptional cofactors display specificity for distinct types of core promoters.

Nature 2019 06 15;570(7759):122-126. Epub 2019 May 15.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1038/s41586-019-1210-7DOI Listing
June 2019

Clock transition by continuous dynamical decoupling of a three-level system.

Sci Rep 2018 Oct 4;8(1):14807. Epub 2018 Oct 4.

Center for Macroscopic Quantum States (bigQ), Department of Physics, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.

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http://dx.doi.org/10.1038/s41598-018-31984-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172288PMC
October 2018

Eukaryotic core promoters and the functional basis of transcription initiation.

Nat Rev Mol Cell Biol 2018 10;19(10):621-637

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1038/s41580-018-0028-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205604PMC
October 2018

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.

Genes Dev 2018 02;32(3-4):202-223

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.

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http://dx.doi.org/10.1101/gad.310367.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859963PMC
February 2018

Resolving systematic errors in widely used enhancer activity assays in human cells.

Nat Methods 2018 02 11;15(2):141-149. Epub 2017 Dec 11.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria.

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http://dx.doi.org/10.1038/nmeth.4534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793997PMC
February 2018

Narrow-bandwidth sensing of high-frequency fields with continuous dynamical decoupling.

Nat Commun 2017 10 19;8(1):1105. Epub 2017 Oct 19.

Institute for Quantum Optics, Ulm University, Albert-Einstein-Allee 11, Ulm, 89081, Germany.

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http://dx.doi.org/10.1038/s41467-017-01159-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648921PMC
October 2017

Promoting transcription over long distances.

Nat Genet 2017 Jun;49(7):972-973

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

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http://dx.doi.org/10.1038/ng.3904DOI Listing
June 2017

Probing the canonicity of the Wnt/Wingless signaling pathway.

PLoS Genet 2017 04 3;13(4):e1006700. Epub 2017 Apr 3.

Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.1371/journal.pgen.1006700DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393890PMC
April 2017

Combinatorial function of transcription factors and cofactors.

Curr Opin Genet Dev 2017 Apr 19;43:73-81. Epub 2017 Jan 19.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.12.007DOI Listing
April 2017

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.

Nat Biotechnol 2017 02 26;35(2):136-144. Epub 2016 Dec 26.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.

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http://www.nature.com/articles/nbt.3739
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http://dx.doi.org/10.1038/nbt.3739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870828PMC
February 2017

Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.

Trends Genet 2016 12 2;32(12):801-814. Epub 2016 Nov 2.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.tig.2016.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6795546PMC
December 2016

RNA-binding profiles of CPEB proteins Orb and Orb2.

Proc Natl Acad Sci U S A 2016 Nov 24;113(45):E7030-E7038. Epub 2016 Oct 24.

The Research Institute of Molecular Pathology, 1030 Vienna, Austria;

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http://dx.doi.org/10.1073/pnas.1603715113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111685PMC
November 2016

Gene Regulation: Activation through Space.

Curr Biol 2016 10 10;26(19):R895-R898. Epub 2016 Oct 10.

Research Institute of Molecular Pathology, Vienna Biocenter, Dr. Bohr-Gasse 7, 1030 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.08.031DOI Listing
October 2016

Pancreatic Cyst Disease: A Review.

JAMA 2016 05;315(17):1882-93

Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California.

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http://dx.doi.org/10.1001/jama.2016.4690DOI Listing
May 2016

Long-term survival in patients with pancreatic ductal adenocarcinoma.

Surgery 2016 06 2;159(6):1520-1527. Epub 2016 Feb 2.

Department of Surgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA. Electronic address:

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http://dx.doi.org/10.1016/j.surg.2015.12.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856542PMC
June 2016

A Cutoff of 2 cm Instead of 3 cm Would Detect More Malignant BD-IPMNs: Is There a Reason to Be Wary of the International Consensus Guidelines?

Pancreas 2016 Jan;45(1):5-7

Department of Surgery, University of California Los Angeles, Los Angeles, CA.

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http://dx.doi.org/10.1097/MPA.0000000000000468DOI Listing
January 2016

Accelerated 2D magnetic resonance spectroscopy of single spins using matrix completion.

Sci Rep 2015 Dec 3;5:17728. Epub 2015 Dec 3.

Institute for Quantum Optics and Center for Integrated Quantum Science and Technology (IQST), Albert-Einstein-Allee 11, Universität Ulm, 89069 Ulm, Germany.

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http://dx.doi.org/10.1038/srep17728DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4668552PMC
December 2015

Transcriptional regulators form diverse groups with context-dependent regulatory functions.

Nature 2015 Dec 9;528(7580):147-51. Epub 2015 Nov 9.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria.

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http://dx.doi.org/10.1038/nature15545DOI Listing
December 2015

Robust Early Inflammation of the Peripancreatic Visceral Adipose Tissue During Diet-Induced Obesity in the KrasG12D Model of Pancreatic Cancer.

Pancreas 2016 Mar;45(3):458-65

From the Departments of *Surgery and †Pathology and Laboratory Medicine,David Geffen School of Medicine at UCLA, Los Angeles, CA; and ‡Department of Biostatistics, Fielding School of Public Health at UCLA, Los Angeles, CA.

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http://dx.doi.org/10.1097/MPA.0000000000000497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4854638PMC
March 2016

An Early Warning Score Predicts Risk of Death after In-hospital Cardiopulmonary Arrest in Surgical Patients.

Am Surg 2015 Oct;81(10):916-21

Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, California, USA.

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October 2015

Coordinating the human looks.

Cell 2015 Sep;163(1):24-6

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr Bohr-Gasse 7, 1030 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.09.010DOI Listing
September 2015

E-cadherin expression in obesity-associated, Kras-initiated pancreatic ductal adenocarcinoma in mice.

Surgery 2015 Dec 18;158(6):1564-72. Epub 2015 Aug 18.

Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA. Electronic address:

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http://dx.doi.org/10.1016/j.surg.2015.07.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4637247PMC
December 2015

Endoscopic and operative palliation strategies for pancreatic ductal adenocarcinoma.

Semin Oncol 2015 Feb 9;42(1):163-76. Epub 2014 Dec 9.

Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00937754140028
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http://dx.doi.org/10.1053/j.seminoncol.2014.12.014DOI Listing
February 2015

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

Nature 2015 Feb 15;518(7540):556-9. Epub 2014 Dec 15.

Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria.

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http://dx.doi.org/10.1038/nature13994DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6795551PMC
February 2015

Genomics: Hiding in plain sight.

Nature 2014 Aug;512(7515):374-5

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.

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http://dx.doi.org/10.1038/512374aDOI Listing
August 2014

Genome-scale functional characterization of Drosophila developmental enhancers in vivo.

Nature 2014 Aug 1;512(7512):91-5. Epub 2014 Jun 1.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria.

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http://dx.doi.org/10.1038/nature13395DOI Listing
August 2014

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.

Genome Res 2014 Jul 8;24(7):1147-56. Epub 2014 Apr 8.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.

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http://dx.doi.org/10.1101/gr.169243.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079970PMC
July 2014

Transcriptional enhancers: from properties to genome-wide predictions.

Nat Rev Genet 2014 Apr 11;15(4):272-86. Epub 2014 Mar 11.

Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria.

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http://search.proquest.com/openview/cc5b16020ff10ca47ea14397
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http://dx.doi.org/10.1038/nrg3682DOI Listing
April 2014

cis-regulatory requirements for tissue-specific programs of the circadian clock.

Curr Biol 2014 Jan 12;24(1):1-10. Epub 2013 Dec 12.

Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2013.11.017DOI Listing
January 2014

Identification of transcription factor binding sites from ChIP-seq data at high resolution.

Bioinformatics 2013 Nov 24;29(21):2705-13. Epub 2013 Aug 24.

Research Institute of Molecular Pathology (IMP), Institute of Molecular Biotechnology (IMBA), Vienna, Austria and Stowers Institute for Medical Research, Kansas City, MO, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://www.epigenesys.eu/images/stories/protocols/pdf/201506
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799470PMC
November 2013

Genome-wide quantitative enhancer activity maps identified by STARR-seq.

Science 2013 Mar 17;339(6123):1074-7. Epub 2013 Jan 17.

Research Institute of Molecular Pathology (IMP), Vienna, Austria.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1232542
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http://dx.doi.org/10.1126/science.1232542DOI Listing
March 2013

A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.

PLoS Genet 2012 6;8(12):e1003118. Epub 2012 Dec 6.

Medical University Vienna, Christian Doppler Laboratory for Infection Biology, Max F. Perutz Laboratories, Vienna, Austria.

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http://dx.doi.org/10.1371/journal.pgen.1003118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516536PMC
May 2013

Deciphering the transcriptional cis-regulatory code.

Trends Genet 2013 Jan 23;29(1):11-22. Epub 2012 Oct 23.

Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria.

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http://dx.doi.org/10.1016/j.tig.2012.09.007DOI Listing
January 2013

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.

Genome Res 2012 Oct 25;22(10):2018-30. Epub 2012 Apr 25.

Research Institute of Molecular Pathology, 1030 Vienna, Austria.

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http://dx.doi.org/10.1101/gr.132811.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460196PMC
October 2012

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

Neural-specific elongation of 3' UTRs during Drosophila development.

Proc Natl Acad Sci U S A 2011 Sep 6;108(38):15864-9. Epub 2011 Sep 6.

Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA.

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http://dx.doi.org/10.1073/pnas.1112672108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179109PMC
September 2011

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway.

Proc Natl Acad Sci U S A 2010 Jun 1;107(26):11841-6. Epub 2010 Jun 1.

Center for Animal Transgenesis and Germ Cell Research and Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.1003953107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2900664PMC
June 2010

Developmental gene regulation in the era of genomics.

Dev Biol 2010 Mar 4;339(2):230-9. Epub 2010 Jan 4.

Stowers Institute for Medical Research, Kansas City, MO 64110, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S001216060901464
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http://dx.doi.org/10.1016/j.ydbio.2009.12.039DOI Listing
March 2010

Learning the transcriptional regulatory code.

Authors:
Alexander Stark

Mol Syst Biol 2009 17;5:329. Epub 2009 Nov 17.

Research Institute of Molecular Pathology (IMP), Vienna, Austria.

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http://dx.doi.org/10.1038/msb.2009.88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795480PMC
May 2010

Comparative genomics of gene regulation-conservation and divergence of cis-regulatory information.

Curr Opin Genet Dev 2009 Dec 11;19(6):565-70. Epub 2009 Nov 11.

Research Institute of Molecular Pathology (IMP), Dr. Bohr-Gasse 7, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1016/j.gde.2009.10.006DOI Listing
December 2009

Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile.

Nat Struct Mol Biol 2009 Jun 24;16(6):639-46. Epub 2009 May 24.

European Molecular Biology Laboratory, Grenoble Outstation, France.

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http://dx.doi.org/10.1038/nsmb.1615DOI Listing
June 2009

Accurate prediction of peptide binding sites on protein surfaces.

PLoS Comput Biol 2009 Mar 27;5(3):e1000335. Epub 2009 Mar 27.

European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pcbi.1000335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2653190PMC
March 2009

Coherent but overlapping expression of microRNAs and their targets during vertebrate development.

Genes Dev 2009 Feb;23(4):466-81

Whitehead Institute of Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 01142, USA.

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http://dx.doi.org/10.1101/gad.1745709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648652PMC
February 2009

An epigenetic role for maternally inherited piRNAs in transposon silencing.

Science 2008 Nov;322(5906):1387-92

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory (CSHL), 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1126/science.1165171DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805124PMC
November 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

An endogenous small interfering RNA pathway in Drosophila.

Nature 2008 Jun 7;453(7196):798-802. Epub 2008 May 7.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1038/nature07007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895258PMC
June 2008

Conservation of small RNA pathways in platypus.

Genome Res 2008 Jun 7;18(6):995-1004. Epub 2008 May 7.

Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1101/gr.073056.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2413167PMC
June 2008

Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila.

Curr Biol 2008 Apr;18(7):501-6

European Molecular Biology Laboratory, Developmental Biology Programme, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S096098220800365
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http://dx.doi.org/10.1016/j.cub.2008.02.081DOI Listing
April 2008

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.

Genes Dev 2008 Jan;22(1):8-13

Broad Institute of Massachussetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02141, USA.

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http://dx.doi.org/10.1101/gad.1613108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151017PMC
January 2008

Evolution of genes and genomes on the Drosophila phylogeny.

Authors:
Andrew G Clark Michael B Eisen Douglas R Smith Casey M Bergman Brian Oliver Therese A Markow Thomas C Kaufman Manolis Kellis William Gelbart Venky N Iyer Daniel A Pollard Timothy B Sackton Amanda M Larracuente Nadia D Singh Jose P Abad Dawn N Abt Boris Adryan Montserrat Aguade Hiroshi Akashi Wyatt W Anderson Charles F Aquadro David H Ardell Roman Arguello Carlo G Artieri Daniel A Barbash Daniel Barker Paolo Barsanti Phil Batterham Serafim Batzoglou Dave Begun Arjun Bhutkar Enrico Blanco Stephanie A Bosak Robert K Bradley Adrianne D Brand Michael R Brent Angela N Brooks Randall H Brown Roger K Butlin Corrado Caggese Brian R Calvi A Bernardo de Carvalho Anat Caspi Sergio Castrezana Susan E Celniker Jean L Chang Charles Chapple Sourav Chatterji Asif Chinwalla Alberto Civetta Sandra W Clifton Josep M Comeron James C Costello Jerry A Coyne Jennifer Daub Robert G David Arthur L Delcher Kim Delehaunty Chuong B Do Heather Ebling Kevin Edwards Thomas Eickbush Jay D Evans Alan Filipski Sven Findeiss Eva Freyhult Lucinda Fulton Robert Fulton Ana C L Garcia Anastasia Gardiner David A Garfield Barry E Garvin Greg Gibson Don Gilbert Sante Gnerre Jennifer Godfrey Robert Good Valer Gotea Brenton Gravely Anthony J Greenberg Sam Griffiths-Jones Samuel Gross Roderic Guigo Erik A Gustafson Wilfried Haerty Matthew W Hahn Daniel L Halligan Aaron L Halpern Gillian M Halter Mira V Han Andreas Heger LaDeana Hillier Angie S Hinrichs Ian Holmes Roger A Hoskins Melissa J Hubisz Dan Hultmark Melanie A Huntley David B Jaffe Santosh Jagadeeshan William R Jeck Justin Johnson Corbin D Jones William C Jordan Gary H Karpen Eiko Kataoka Peter D Keightley Pouya Kheradpour Ewen F Kirkness Leonardo B Koerich Karsten Kristiansen Dave Kudrna Rob J Kulathinal Sudhir Kumar Roberta Kwok Eric Lander Charles H Langley Richard Lapoint Brian P Lazzaro So-Jeong Lee Lisa Levesque Ruiqiang Li Chiao-Feng Lin Michael F Lin Kerstin Lindblad-Toh Ana Llopart Manyuan Long Lloyd Low Elena Lozovsky Jian Lu Meizhong Luo Carlos A Machado Wojciech Makalowski Mar Marzo Muneo Matsuda Luciano Matzkin Bryant McAllister Carolyn S McBride Brendan McKernan Kevin McKernan Maria Mendez-Lago Patrick Minx Michael U Mollenhauer Kristi Montooth Stephen M Mount Xu Mu Eugene Myers Barbara Negre Stuart Newfeld Rasmus Nielsen Mohamed A F Noor Patrick O'Grady Lior Pachter Montserrat Papaceit Matthew J Parisi Michael Parisi Leopold Parts Jakob S Pedersen Graziano Pesole Adam M Phillippy Chris P Ponting Mihai Pop Damiano Porcelli Jeffrey R Powell Sonja Prohaska Kim Pruitt Marta Puig Hadi Quesneville Kristipati Ravi Ram David Rand Matthew D Rasmussen Laura K Reed Robert Reenan Amy Reily Karin A Remington Tania T Rieger Michael G Ritchie Charles Robin Yu-Hui Rogers Claudia Rohde Julio Rozas Marc J Rubenfield Alfredo Ruiz Susan Russo Steven L Salzberg Alejandro Sanchez-Gracia David J Saranga Hajime Sato Stephen W Schaeffer Michael C Schatz Todd Schlenke Russell Schwartz Carmen Segarra Rama S Singh Laura Sirot Marina Sirota Nicholas B Sisneros Chris D Smith Temple F Smith John Spieth Deborah E Stage Alexander Stark Wolfgang Stephan Robert L Strausberg Sebastian Strempel David Sturgill Granger Sutton Granger G Sutton Wei Tao Sarah Teichmann Yoshiko N Tobari Yoshihiko Tomimura Jason M Tsolas Vera L S Valente Eli Venter J Craig Venter Saverio Vicario Filipe G Vieira Albert J Vilella Alfredo Villasante Brian Walenz Jun Wang Marvin Wasserman Thomas Watts Derek Wilson Richard K Wilson Rod A Wing Mariana F Wolfner Alex Wong Gane Ka-Shu Wong Chung-I Wu Gabriel Wu Daisuke Yamamoto Hsiao-Pei Yang Shiaw-Pyng Yang James A Yorke Kiyohito Yoshida Evgeny Zdobnov Peili Zhang Yu Zhang Aleksey V Zimin Jennifer Baldwin Amr Abdouelleil Jamal Abdulkadir Adal Abebe Brikti Abera Justin Abreu St Christophe Acer Lynne Aftuck Allen Alexander Peter An Erica Anderson Scott Anderson Harindra Arachi Marc Azer Pasang Bachantsang Andrew Barry Tashi Bayul Aaron Berlin Daniel Bessette Toby Bloom Jason Blye Leonid Boguslavskiy Claude Bonnet Boris Boukhgalter Imane Bourzgui Adam Brown Patrick Cahill Sheridon Channer Yama Cheshatsang Lisa Chuda Mieke Citroen Alville Collymore Patrick Cooke Maura Costello Katie D'Aco Riza Daza Georgius De Haan Stuart DeGray Christina DeMaso Norbu Dhargay Kimberly Dooley Erin Dooley Missole Doricent Passang Dorje Kunsang Dorjee Alan Dupes Richard Elong Jill Falk Abderrahim Farina Susan Faro Diallo Ferguson Sheila Fisher Chelsea D Foley Alicia Franke Dennis Friedrich Loryn Gadbois Gary Gearin Christina R Gearin Georgia Giannoukos Tina Goode Joseph Graham Edward Grandbois Sharleen Grewal Kunsang Gyaltsen Nabil Hafez Birhane Hagos Jennifer Hall Charlotte Henson Andrew Hollinger Tracey Honan Monika D Huard Leanne Hughes Brian Hurhula M Erii Husby Asha Kamat Ben Kanga Seva Kashin Dmitry Khazanovich Peter Kisner Krista Lance Marcia Lara William Lee Niall Lennon Frances Letendre Rosie LeVine Alex Lipovsky Xiaohong Liu Jinlei Liu Shangtao Liu Tashi Lokyitsang Yeshi Lokyitsang Rakela Lubonja 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Lisa Zembek Danni Zhong Andrew Zimmer Zac Zwirko David B Jaffe Pablo Alvarez Will Brockman Jonathan Butler CheeWhye Chin Sante Gnerre Manfred Grabherr Michael Kleber Evan Mauceli Iain MacCallum

Nature 2007 Nov;450(7167):203-18

Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1038/nature06341DOI Listing
November 2007

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo.

Nat Genet 2007 Dec 11;39(12):1512-6. Epub 2007 Nov 11.

Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/ng.2007.26DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824921PMC
December 2007

Reliable prediction of regulator targets using 12 Drosophila genomes.

Genome Res 2007 Dec 7;17(12):1919-31. Epub 2007 Nov 7.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.7090407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2099599PMC
December 2007

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.

Cell 2007 Mar 8;128(6):1089-103. Epub 2007 Mar 8.

Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1016/j.cell.2007.01.043DOI Listing
March 2007

Denoising feedback loops by thresholding--a new role for microRNAs.

Genes Dev 2006 Oct;20(20):2769-72

European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1101/gad.1484606DOI Listing
October 2006

Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.

Cell 2005 Dec;123(6):1133-46

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.cell.2005.11.023DOI Listing
December 2005

Not miR-ly muscular: microRNAs and muscle development.

Genes Dev 2005 Oct;19(19):2261-4

European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1101/gad.1363905DOI Listing
October 2005

Principles of microRNA-target recognition.

PLoS Biol 2005 Mar;3(3):e85

European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pbio.0030085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1043860PMC
March 2005

Finding functional sites in structural genomics proteins.

Structure 2004 Aug;12(8):1405-12

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.str.2004.05.012DOI Listing
August 2004

Identification of Drosophila MicroRNA targets.

PLoS Biol 2003 Dec 13;1(3):E60. Epub 2003 Oct 13.

European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1371/journal.pbio.0000060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC270017PMC
December 2003

The relationship between sequence and interaction divergence in proteins.

J Mol Biol 2003 Oct;332(5):989-98

Structural and Computational Biology Programme, EMBL Heidelberg, Meyerhofstrasse 1, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.jmb.2003.07.006DOI Listing
October 2003

Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.

J Biol Chem 2003 Nov 26;278(47):47253-60. Epub 2003 Aug 26.

European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany.

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http://dx.doi.org/10.1074/jbc.M305922200DOI Listing
November 2003

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

Nucleic Acids Res 2003 Jul;31(13):3341-4

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168913PMC
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July 2003

A model for statistical significance of local similarities in structure.

J Mol Biol 2003 Mar;326(5):1307-16

EMBL, Structural & Computational Biology Programme, Meyerhofstrasse 1, 69117, Heidelberg, Germany.

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http://dx.doi.org/10.1016/s0022-2836(03)00045-7DOI Listing
March 2003