Ali Mortazavi

Ali Mortazavi

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Ali Mortazavi

Publications by authors named "Ali Mortazavi"

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Intra-individual changes in methylome profiles: an epigenetic 'scar' of early-life adversity?

Neuropsychopharmacology 2020 Jan;45(1):218

Departments of Pediatrics, Anatomy/Neurobiology, Neurology, University of California-Irvine, Irvine, CA, 92697-4475, USA.

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http://dx.doi.org/10.1038/s41386-019-0496-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879488PMC
January 2020

[Calcitonin as an analgesic agent: review of mechanisms of action and clinical applications].

Rev Bras Anestesiol 2019 Nov - Dec;69(6):594-604. Epub 2019 Dec 3.

Tabriz University of Medical Sciences, Department of Oral and Maxillofacial Surgery, Tabriz, Irã. Electronic address:

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http://dx.doi.org/10.1016/j.bjan.2019.08.004DOI Listing
December 2019

Molecular evolution and expression of opsin genes in Hydra vulgaris.

BMC Genomics 2019 Dec 17;20(1):992. Epub 2019 Dec 17.

Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA.

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http://dx.doi.org/10.1186/s12864-019-6349-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918707PMC
December 2019

Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps.

PLoS Comput Biol 2019 11 4;15(11):e1006555. Epub 2019 Nov 4.

Developmental and Cell Biology, University of California Irvine, Irvine, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855564PMC
November 2019

Comparison of analgesic effects of intravenous and intranasal ketorolac in patients with mandibular fracture-A Randomized Clinical Trial.

J Clin Exp Dent 2019 Sep 1;11(9):e768-e775. Epub 2019 Sep 1.

Postgraduate Student, Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Tabriz University of Medical Sciences, Tabriz, Iran.

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http://dx.doi.org/10.4317/jced.55753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6797447PMC
September 2019

Hybrid Assembly of the Genome of the Entomopathogenic Nematode Identifies the X-Chromosome.

G3 (Bethesda) 2019 08 8;9(8):2687-2697. Epub 2019 Aug 8.

Department of Developmental and Cell Biology, University of California, Irvine, CA 92697,

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http://dx.doi.org/10.1534/g3.119.400180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6686942PMC
August 2019

The genome of , natural host for Lyme disease and other emerging infections.

Sci Adv 2019 07 24;5(7):eaaw6441. Epub 2019 Jul 24.

Departments of Microbiology and Molecular Genetics and Medicine, University of California, Irvine, Irvine, CA, USA.

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http://dx.doi.org/10.1126/sciadv.aaw6441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6656541PMC
July 2019

A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema.

PLoS Pathog 2019 05 1;15(5):e1007626. Epub 2019 May 1.

Department of Nematology, University of California, Riverside, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1007626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513111PMC
May 2019

Intra-individual methylomics detects the impact of early-life adversity.

Life Sci Alliance 2019 04 1;2(2). Epub 2019 Apr 1.

Department of Developmental and Cell Biology, University of California, Irvine, CA, USA

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http://dx.doi.org/10.26508/lsa.201800204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445397PMC
April 2019

miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA.

Int J Mol Sci 2019 Apr 21;20(8). Epub 2019 Apr 21.

Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.3390/ijms20081955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6515209PMC
April 2019

Use of Fish Oil Nanoencapsulated with Gum Arabic Carrier in Low Fat Probiotic Fermented Milk.

Food Sci Anim Resour 2019 Apr 30;39(2):309-323. Epub 2019 Apr 30.

Department of Biotechnology and Plant Breeding, College of Agricultural Sciences and Food Industries, Science and Research Branch, Islamic Azad University, Tehran, Iran.

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http://dx.doi.org/10.5851/kosfa.2019.e25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6533394PMC
April 2019

TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts.

Bioinformatics 2019 01;35(2):340-342

Department of Developmental and Cell Biology, UC Irvine, Irvine, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329999PMC
January 2019

A limited capacity for microglial repopulation in the adult brain.

Glia 2018 11 28;66(11):2385-2396. Epub 2018 Oct 28.

Department of Neurobiology and Behavior Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, California.

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http://doi.wiley.com/10.1002/glia.23477
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http://dx.doi.org/10.1002/glia.23477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269202PMC
November 2018

Wound Regeneration Deficit in Rats Correlates with Low Morphogenetic Potential and Distinct Transcriptome Profile of Epidermis.

J Invest Dermatol 2018 06 6;138(6):1409-1419. Epub 2018 Jan 6.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jid.2017.12.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059613PMC
June 2018

TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency.

Development 2018 02 23;145(4). Epub 2018 Feb 23.

Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA

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http://dx.doi.org/10.1242/dev.161075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5869011PMC
February 2018

Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq.

Bio Protoc 2018 Feb;8(4)

Department of Developmental and Cell Biology, University of California, Irvine, California, USA.

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https://bio-protocol.org/e2729
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http://dx.doi.org/10.21769/BioProtoc.2729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5857950PMC
February 2018

Prostaglandin E2 Leads to the Acquisition of DNMT3A-Dependent Tolerogenic Functions in Human Myeloid-Derived Suppressor Cells.

Cell Rep 2017 Oct;21(1):154-167

Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.09.018DOI Listing
October 2017

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation.

Cell Syst 2017 04 29;4(4):416-429.e3. Epub 2017 Mar 29.

Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA; Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697-2300, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5490374PMC
April 2017

Activated entomopathogenic nematode infective juveniles release lethal venom proteins.

PLoS Pathog 2017 Apr 20;13(4):e1006302. Epub 2017 Apr 20.

Department of Nematology, University of California, Riverside, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398726PMC
April 2017

iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.

Neuron 2017 Apr;94(2):278-293.e9

Department of Neurobiology & Behavior, University of California Irvine, Irvine, CA 92697, USA; Sue and Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA 92697, USA; Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA. Electronic address:

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http://dx.doi.org/10.1016/j.neuron.2017.03.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482419PMC
April 2017

Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity.

Nucleic Acids Res 2016 12 26;44(21):e158. Epub 2016 Aug 26.

Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697-2300, USA

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http://dx.doi.org/10.1093/nar/gkw739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137429PMC
December 2016

Erratum to: A survey of best practices for RNA-seq data analysis.

Genome Biol 2016 Aug 26;17(1):181. Epub 2016 Aug 26.

Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA.

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http://dx.doi.org/10.1186/s13059-016-1047-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5000515PMC
August 2016

Better together: multiplexing samples to improve the preparation and reliability of gene expression studies.

Authors:
Ali Mortazavi

Nat Methods 2015 Apr;12(4):304-5

Department of Developmental and Cell Biology, and at the Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA.

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http://dx.doi.org/10.1038/nmeth.3333DOI Listing
April 2015

The common ground of genomics and systems biology.

BMC Syst Biol 2014 13;8 Suppl 2:S1. Epub 2014 Mar 13.

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http://dx.doi.org/10.1186/1752-0509-8-S2-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4101703PMC
March 2015

Effects of storage time on compositional, micro-structural, rheological and sensory properties of low fat Iranian UF-Feta cheese fortified with fish oil or fish oil powder.

J Food Sci Technol 2015 Mar 12;52(3):1372-82. Epub 2013 Sep 12.

Department of Food Science and Technology Engineering, Faculty of Agriculture, Ferdowsi University, Mashhad, Iran.

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http://dx.doi.org/10.1007/s13197-013-1163-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4348299PMC
March 2015

Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns.

Mol Ecol 2014 12 4;23(24):6123-34. Epub 2014 Dec 4.

Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA, 92697-2525, USA.

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http://dx.doi.org/10.1111/mec.12988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4545284PMC
December 2014

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Endovascular iliac rescue technique for complete arterial avulsion after transcatheter aortic valve replacement.

Catheter Cardiovasc Interv 2014 Aug 7;84(2):306-10. Epub 2014 May 7.

Division of Cardiology and Cardiovascular Surgery, Texas Heart Institute, Houston, Texas.

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http://dx.doi.org/10.1002/ccd.25141DOI Listing
August 2014

Genetic and epigenetic characteristics of FSHD-associated 4q and 10q D4Z4 that are distinct from non-4q/10q D4Z4 homologs.

Hum Mutat 2014 Aug 24;35(8):998-1010. Epub 2014 Jun 24.

Department of Biological Chemistry, School of Medicine, University of California, Irvine, California; Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, California.

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http://dx.doi.org/10.1002/humu.22593DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489691PMC
August 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Genome Res 2013 Dec 29;23(12):2136-48. Epub 2013 Oct 29.

Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA;

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http://dx.doi.org/10.1101/gr.158261.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847782PMC
December 2013

Technical considerations for functional sequencing assays.

Nat Immunol 2012 Sep;13(9):802-7

Department of Developmental and Cell Biology, University of California, Irvine, California, USA.

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http://dx.doi.org/10.1038/ni.2407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4138050PMC
September 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

RNA editing in the human ENCODE RNA-seq data.

Genome Res 2012 Sep;22(9):1626-33

Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.134957.111
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http://dx.doi.org/10.1101/gr.134957.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431480PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Incorporating genomics into the toolkit of nematology.

J Nematol 2012 Jun;44(2):191-205

Howard Hughes Medical Institute and Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3578471PMC
June 2012

Low-permeability Gore Excluder device versus the original in abdominal aortic aneurysm size regression.

Tex Heart Inst J 2011 ;38(4):381-5

Division of Cardiology, Texas Heart Institute at St. Luke's Episcopal Hospital, TXx 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3147216PMC
January 2012

Determinants and outcomes of asystole during carotid artery stenting.

J Endovasc Ther 2011 Aug;18(4):513-7

Department of Cardiology, Texas Heart Institute at St. Luke's Episcopal Hospital, Houston, Texas, USA.

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http://dx.doi.org/10.1583/11-3516R.1DOI Listing
August 2011

Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Genome Res 2010 Dec 27;20(12):1740-7. Epub 2010 Oct 27.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.111021.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990000PMC
December 2010

Computation for ChIP-seq and RNA-seq studies.

Nat Methods 2009 Nov;6(11 Suppl):S22-32

Center for Advanced Computing Research, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1038/nmeth.1371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121056PMC
November 2009

Endovascular exclusion of popliteal artery aneurysms with stent-grafts: a prospective single-center experience.

J Endovasc Ther 2009 Apr;16(2):215-23

Division of Cardiology, the Texas Heart Institute at St. Luke's Episcopal Hospital, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1583/08-2412.1DOI Listing
April 2009

A modified technique for carotid cannulation via the transfemoral approach, during angioplasty and stent placement.

Tex Heart Inst J 2008 ;35(3):286-8

Division of Cardiology, Kansas City Veterans Affairs Medical Center, Kansas City, Missouri 64128, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2565529PMC
January 2009

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Nat Methods 2008 Jul 30;5(7):621-8. Epub 2008 May 30.

Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1038/nmeth.1226DOI Listing
July 2008

Endovascular repair of paraanastomotic aneurysms after aortic reconstruction.

Tex Heart Inst J 2007 ;34(2):148-53

Department of Cardiovascular Medicine, Texas Heart Institute at St. Luke's Episcopal Hospital, Houston, Texas 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1894696PMC
August 2007

Genome-wide mapping of in vivo protein-DNA interactions.

Science 2007 Jun 31;316(5830):1497-502. Epub 2007 May 31.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.

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http://dx.doi.org/10.1126/science.1141319DOI Listing
June 2007

Pharmacist-managed vaccination program increased influenza vaccination rates in cardiovascular patients enrolled in a secondary prevention lipid clinic.

Pharmacotherapy 2007 May;27(5):729-33

Department of Clinical Sciences and Administration, University of Houston College of Pharmacy, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1592/phco.27.5.729DOI Listing
May 2007

Predictors of carotid stent restenosis.

Catheter Cardiovasc Interv 2007 Apr;69(5):673-82

Department of Cardiology, St. Luke's Episcopal Hospital, Texas Heart Institute, Houston, Texas, USA.

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http://dx.doi.org/10.1002/ccd.20809DOI Listing
April 2007

Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.

Genome Res 2006 Oct 8;16(10):1208-21. Epub 2006 Sep 8.

Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1101/gr.4997306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581430PMC
October 2006

Mining gene expression data by interpreting principal components.

BMC Bioinformatics 2006 Apr 7;7:194. Epub 2006 Apr 7.

Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.

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http://dx.doi.org/10.1186/1471-2105-7-194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501050PMC
April 2006

Percutaneous intervention for the treatment of hypoplastic aortoiliac syndrome.

Catheter Cardiovasc Interv 2003 Nov;60(3):329-34

Department of Cardiology, St. Luke's Episcopal Hospital and Texas Heart Institute, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1002/ccd.10651DOI Listing
November 2003

Rare chronic gastric volvulus associated with left atrial and mediastinal compression.

Tex Heart Inst J 2002 ;29(4):324-8

Department of Cardiology, Texas Heart Institute, Houston, Texas 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC140297PMC
March 2003

Successful treatment of aortic endograft thrombosis with rheolytic thrombectomy.

J Endovasc Ther 2002 Dec;9(6):756-64

Department of Cardiology, Texas Heart Institute, St Luke's Episcopal Hospital, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1177/152660280200900607DOI Listing
December 2002