Publications by authors named "Josee Dostie"

55Publications

Profiling Chromatin Landscape at High Resolution and Throughput with 2C-ChIP.

Methods Mol Biol 2021 ;2157:127-157

Department of Biochemistry and Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, QC, Canada.

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http://dx.doi.org/10.1007/978-1-0716-0664-3_8DOI Listing
January 2021

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Authors:
Jordan A Ramilowski Chi Wai Yip Saumya Agrawal Jen-Chien Chang Yari Ciani Ivan V Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher JF Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J Makeev Luigi Marchionni Yulia A Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J C Parr Owen J L Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A M Semple Youtaro Shibayama Divya M Sivaraman Takahiro Suzuki Suzannah C Szumowski Michihira Tagami Martin S Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E Vorontsov Chinatsu Yamamoto Robert S Young J Kenneth Baillie Alistair R R Forrest Roderic Guigó Michael M Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki Ken Yagi Michiel J L de Hoon Jay W Shin Piero Carninci

Genome Res 2020 07 27;30(7):1060-1072. Epub 2020 Jul 27.

RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.254219.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397864PMC
July 2020

LAMPS: an analysis pipeline for sequence-specific ligation-mediated amplification reads.

BMC Res Notes 2020 Jun 3;13(1):273. Epub 2020 Jun 3.

School of Computer Science, McGill University, Montréal, Canada.

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http://dx.doi.org/10.1186/s13104-020-05106-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7271454PMC
June 2020

HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution.

Genome Biol 2020 01 14;21(1):11. Epub 2020 Jan 14.

School of Computer Science, McGill University, Montreal, Canada.

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http://dx.doi.org/10.1186/s13059-019-1913-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961295PMC
January 2020

PRC2-Associated Chromatin Contacts in the Developing Limb Reveal a Possible Mechanism for the Atypical Role of PRC2 in HoxA Gene Expression.

Dev Cell 2019 07 13;50(2):184-196.e4. Epub 2019 Jun 13.

Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada; Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.05.021DOI Listing
July 2019

2C-ChIP: measuring chromatin immunoprecipitation signal from defined genomic regions with deep sequencing.

BMC Genomics 2019 Feb 28;20(1):162. Epub 2019 Feb 28.

Department of Biochemistry and Rosalind & Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada.

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http://dx.doi.org/10.1186/s12864-019-5532-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394006PMC
February 2019

Novel long-range regulatory mechanisms controlling PKD2 gene expression.

BMC Genomics 2018 Jul 3;19(1):515. Epub 2018 Jul 3.

Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, Bretagne, France.

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http://dx.doi.org/10.1186/s12864-018-4892-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6038307PMC
July 2018

3D genome mapping and analysis methods.

Methods 2018 06;142:1-2

Department of Biochemistry and Goodman Cancer Research Center McGill University Montréal, Québec, Canada; School of Computer Science McGill University Montréal, Québec, Canada.

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http://dx.doi.org/10.1016/j.ymeth.2018.05.017DOI Listing
June 2018

Complex multi-enhancer contacts captured by genome architecture mapping.

Nature 2017 03 8;543(7646):519-524. Epub 2017 Mar 8.

Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Robert-Rössle Straße, Berlin-Buch 13125, Germany.

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http://dx.doi.org/10.1038/nature21411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5366070PMC
March 2017

Reciprocal regulation of chromatin state and architecture by HOTAIRM1 contributes to temporal collinear HOXA gene activation.

Nucleic Acids Res 2017 02;45(3):1091-1104

Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada.

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http://dx.doi.org/10.1093/nar/gkw966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388432PMC
February 2017

Chromosome folding and its regulation in health and disease.

Curr Opin Genet Dev 2017 Apr 9;43:23-30. Epub 2016 Dec 9.

Department of Biochemistry and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Room 815A, Montréal, Québec, Canada H3G1Y6. Electronic address:

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http://dx.doi.org/10.1016/j.gde.2016.10.006DOI Listing
April 2017

Spatial Organization of Epigenomes.

Curr Mol Biol Rep 2016 Mar 4;2(1):1-9. Epub 2016 Feb 4.

Department of Biochemistry and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Room 815A, Montréal, Québec, Canada, H3G1Y6.

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http://dx.doi.org/10.1007/s40610-016-0028-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4723270PMC
March 2016

PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing.

Nat Commun 2015 Dec 8;6:10124. Epub 2015 Dec 8.

Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.

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http://www.nature.com/articles/ncomms10124
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http://dx.doi.org/10.1038/ncomms10124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4686818PMC
December 2015

Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements.

Nucleic Acids Res 2016 Apr 28;44(6):2564-76. Epub 2015 Nov 28.

Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France

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http://dx.doi.org/10.1093/nar/gkv1300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824072PMC
April 2016

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Authors:
Hou-Feng Zheng Vincenzo Forgetta Yi-Hsiang Hsu Karol Estrada Alberto Rosello-Diez Paul J Leo Chitra L Dahia Kyung Hyun Park-Min Jonathan H Tobias Charles Kooperberg Aaron Kleinman Unnur Styrkarsdottir Ching-Ti Liu Charlotta Uggla Daniel S Evans Carrie M Nielson Klaudia Walter Ulrika Pettersson-Kymmer Shane McCarthy Joel Eriksson Tony Kwan Mila Jhamai Katerina Trajanoska Yasin Memari Josine Min Jie Huang Petr Danecek Beth Wilmot Rui Li Wen-Chi Chou Lauren E Mokry Alireza Moayyeri Melina Claussnitzer Chia-Ho Cheng Warren Cheung Carolina Medina-Gómez Bing Ge Shu-Huang Chen Kwangbom Choi Ling Oei James Fraser Robert Kraaij Matthew A Hibbs Celia L Gregson Denis Paquette Albert Hofman Carl Wibom Gregory J Tranah Mhairi Marshall Brooke B Gardiner Katie Cremin Paul Auer Li Hsu Sue Ring Joyce Y Tung Gudmar Thorleifsson Anke W Enneman Natasja M van Schoor Lisette C P G M de Groot Nathalie van der Velde Beatrice Melin John P Kemp Claus Christiansen Adrian Sayers Yanhua Zhou Sophie Calderari Jeroen van Rooij Chris Carlson Ulrike Peters Soizik Berlivet Josée Dostie Andre G Uitterlinden Stephen R Williams Charles Farber Daniel Grinberg Andrea Z LaCroix Jeff Haessler Daniel I Chasman Franco Giulianini Lynda M Rose Paul M Ridker John A Eisman Tuan V Nguyen Jacqueline R Center Xavier Nogues Natalia Garcia-Giralt Lenore L Launer Vilmunder Gudnason Dan Mellström Liesbeth Vandenput Najaf Amin Cornelia M van Duijn Magnus K Karlsson Östen Ljunggren Olle Svensson Göran Hallmans François Rousseau Sylvie Giroux Johanne Bussière Pascal P Arp Fjorda Koromani Richard L Prince Joshua R Lewis Bente L Langdahl A Pernille Hermann Jens-Erik B Jensen Stephen Kaptoge Kay-Tee Khaw Jonathan Reeve Melissa M Formosa Angela Xuereb-Anastasi Kristina Åkesson Fiona E McGuigan Gaurav Garg Jose M Olmos Maria T Zarrabeitia Jose A Riancho Stuart H Ralston Nerea Alonso Xi Jiang David Goltzman Tomi Pastinen Elin Grundberg Dominique Gauguier Eric S Orwoll David Karasik George Davey-Smith Albert V Smith Kristin Siggeirsdottir Tamara B Harris M Carola Zillikens Joyce B J van Meurs Unnur Thorsteinsdottir Matthew T Maurano Nicholas J Timpson Nicole Soranzo Richard Durbin Scott G Wilson Evangelia E Ntzani Matthew A Brown Kari Stefansson David A Hinds Tim Spector L Adrienne Cupples Claes Ohlsson Celia M T Greenwood Rebecca D Jackson David W Rowe Cynthia A Loomis David M Evans Cheryl L Ackert-Bicknell Alexandra L Joyner Emma L Duncan Douglas P Kiel Fernando Rivadeneira J Brent Richards

Nature 2015 Oct 14;526(7571):112-7. Epub 2015 Sep 14.

Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada.

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http://dx.doi.org/10.1038/nature14878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714PMC
October 2015

Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing.

Genome Med 2015 Aug 27;7:93. Epub 2015 Aug 27.

Department of Biochemistry, McGill University, Montréal, Québec, H3G 1Y6, Canada.

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http://genomemedicine.com/content/7/1/93
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http://dx.doi.org/10.1186/s13073-015-0215-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4550049PMC
August 2015

An Overview of Genome Organization and How We Got There: from FISH to Hi-C.

Microbiol Mol Biol Rev 2015 Sep;79(3):347-72

Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada

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http://dx.doi.org/10.1128/MMBR.00006-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517094PMC
September 2015

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization.

Genes Dev 2014 Dec;28(24):2778-91

MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom;

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http://dx.doi.org/10.1101/gad.251694.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265680PMC
December 2014

Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage.

PLoS One 2014 2;9(10):e109213. Epub 2014 Oct 2.

Department of Biochemistry, McGill University, Montreal, Québec, Canada; The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Québec, Canada; Department of Oncology, McGill University, Montreal, Québec, Canada.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109213PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183563PMC
December 2015

Clustering of tissue-specific sub-TADs accompanies the regulation of HoxA genes in developing limbs.

PLoS Genet 2013 26;9(12):e1004018. Epub 2013 Dec 26.

Unité de génétique et développement, Institut de recherches cliniques de Montréal, Montréal, Québec, Canada ; Department of Medicine, University of Montréal, Montréal, Québec, Canada.

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https://dx.plos.org/10.1371/journal.pgen.1004018
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http://dx.doi.org/10.1371/journal.pgen.1004018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873244PMC
August 2014

Repurposing CRISPR/Cas9 for in situ functional assays.

Genes Dev 2013 Dec;27(23):2602-14

Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6 Canada,;

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http://dx.doi.org/10.1101/gad.227132.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861673PMC
December 2013

Hox in motion: tracking HoxA cluster conformation during differentiation.

Nucleic Acids Res 2014 Feb 29;42(3):1524-40. Epub 2013 Oct 29.

Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada and School of Computer Science and McGill Centre for Bioinformatics, McGill University, Montréal, Québec, H3A 0E9, Canada.

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http://dx.doi.org/10.1093/nar/gkt998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919592PMC
February 2014

A polymer model explains the complexity of large-scale chromatin folding.

Nucleus 2013 Jul-Aug;4(4):267-73. Epub 2013 Jun 19.

Universita' di Napoli "Federico II"; Dipartimento di Fisica; INFN Sezione di Napoli; CNR-SPIN, Complesso Universitario di Monte S. Angelo; Napoli, Italy; Department of Biochemistry and Goodman Cancer Research Center; McGill University; Montréal, Québec Canada; Berlin Institute for Medical Systems Biology; Max Delbrück Center for Molecular Medicine; Berlin-Buch, Germany; Genome Function Group; MRC Clinical Sciences Centre; Imperial College London; Hammersmith Hospital Campus; London, UK.

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http://dx.doi.org/10.4161/nucl.25432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810333PMC
October 2014

A model of the large-scale organization of chromatin.

Biochem Soc Trans 2013 Apr;41(2):508-12

Università di Napoli 'Federico II', Dipartimento di Scienze Fisiche, INFN Sezione di Napoli, CNR-SPIN, Complesso Universitario di Monte S. Angelo, Via Cintia, 80126 Napoli, Italy.

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http://dx.doi.org/10.1042/BST20120238DOI Listing
April 2013

From cells to chromatin: capturing snapshots of genome organization with 5C technology.

Methods 2012 Nov 5;58(3):255-67. Epub 2012 Nov 5.

Department of Biochemistry and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Room 815A, Montréal, Québec, Canada H3G1Y6.

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http://dx.doi.org/10.1016/j.ymeth.2012.10.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874844PMC
November 2012

Complexity of chromatin folding is captured by the strings and binders switch model.

Proc Natl Acad Sci U S A 2012 Oct 17;109(40):16173-8. Epub 2012 Sep 17.

Dipartimento di Scienze Fisiche, Università di Napoli Federico II, 80126 Naples, Italy.

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http://dx.doi.org/10.1073/pnas.1204799109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3479593PMC
October 2012

A Torrent of data: mapping chromatin organization using 5C and high-throughput sequencing.

Methods Enzymol 2012 ;513:113-41

Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada.

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http://dx.doi.org/10.1016/B978-0-12-391938-0.00005-7DOI Listing
December 2012

Chromosome organization in the nucleus - charting new territory across the Hi-Cs.

Curr Opin Genet Dev 2012 Apr 19;22(2):125-31. Epub 2012 Jan 19.

Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec, H3G1Y6, Canada.

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http://linkinghub.elsevier.com/retrieve/pii/S0959437X1100188
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http://dx.doi.org/10.1016/j.gde.2011.12.006DOI Listing
April 2012

p53 inhibits angiogenesis by inducing the production of Arresten.

Cancer Res 2012 Mar 17;72(5):1270-9. Epub 2012 Jan 17.

Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montréal, Québec, Canada.

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http://dx.doi.org/10.1158/0008-5472.CAN-11-2348DOI Listing
March 2012

Discovering genome regulation with 3C and 3C-related technologies.

Biochim Biophys Acta 2012 May 20;1819(5):401-10. Epub 2011 Dec 20.

Department of Biochemistry, McGill University, Quebec, Canada.

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http://dx.doi.org/10.1016/j.bbagrm.2011.12.004DOI Listing
May 2012

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling.

BMC Bioinformatics 2011 Oct 25;12:414. Epub 2011 Oct 25.

McGill Centre for Bioinformatics, Bellini Building, Life Sciences Complex, 3649 Promenade Sir William Osler, Montréal, Québec, H3G 0B1, Canada.

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http://dx.doi.org/10.1186/1471-2105-12-414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245522PMC
October 2011

Shaping the Genome with Non-Coding RNAs.

Curr Genomics 2011 Aug;12(5):307-21

Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William- Osler, Room 815A, Montréal, Québec, H3G1Y6, Canada.

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http://dx.doi.org/10.2174/138920211796429772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145261PMC
August 2011

Computing chromosome conformation.

Methods Mol Biol 2010 ;674:251-68

Department of Biochemistry, Goodman Cancer Research Center, McGill University, Montréal, QC, Canada.

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http://dx.doi.org/10.1007/978-1-60761-854-6_16DOI Listing
December 2010

Chromatin conformation signatures: ideal human disease biomarkers?

Biomark Med 2010 Aug;4(4):611-29

Department of Biochemistry, McGill University, Montréal, Québec, Canada.

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http://dx.doi.org/10.2217/bmm.10.68DOI Listing
August 2010

The three-dimensional architecture of Hox cluster silencing.

Nucleic Acids Res 2010 Nov 25;38(21):7472-84. Epub 2010 Jul 25.

Department of Biochemistry, and Goodman Cancer Research Center, McGill University, 3655 Promenade Sir-William-Osler, Montréal, Québec, Canada.

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http://dx.doi.org/10.1093/nar/gkq644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995065PMC
November 2010

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

Chromatin conformation signatures of cellular differentiation.

Genome Biol 2009 19;10(4):R37. Epub 2009 Apr 19.

Department of Biochemistry and McGill Cancer Center, McGill University, 3655 Promenade Sir-William-Osler, Montréal, H3G1Y6, Canada.

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http://dx.doi.org/10.1186/gb-2009-10-4-r37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688928PMC
September 2009

Chromosome conformation capture carbon copy technology.

Curr Protoc Mol Biol 2007 Oct;Chapter 21:Unit 21.14

University of Massachusetts Medical School, Worcester, Massachusetts, USA.

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http://dx.doi.org/10.1002/0471142727.mb2114s80DOI Listing
October 2007

Mapping chromatin interactions by chromosome conformation capture.

Curr Protoc Mol Biol 2006 May;Chapter 21:Unit 21.11

University of Massachusetts Medical School, Worcester, Massachusetts, USA.

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http://dx.doi.org/10.1002/0471142727.mb2111s74DOI Listing
May 2006

Mapping networks of physical interactions between genomic elements using 5C technology.

Nat Protoc 2007 ;2(4):988-1002

Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Room 519, Worcester, Massachusetts 01605-4321, USA.

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http://www.nature.com/articles/nprot.2007.116
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http://dx.doi.org/10.1038/nprot.2007.116DOI Listing
June 2007

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

Genome Res 2006 Oct 5;16(10):1299-309. Epub 2006 Sep 5.

Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605-0103, USA.

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http://dx.doi.org/10.1101/gr.5571506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581439PMC
October 2006

A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay.

J Cell Biol 2005 Sep;170(6):913-24

Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada.

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http://dx.doi.org/10.1083/jcb.200504039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2171455PMC
September 2005

The Gemin6-Gemin7 heterodimer from the survival of motor neurons complex has an Sm protein-like structure.

Structure 2005 Jun;13(6):883-92

Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1016/j.str.2005.03.014DOI Listing
June 2005

Gemins modulate the expression and activity of the SMN complex.

Hum Mol Genet 2005 Jun 20;14(12):1605-11. Epub 2005 Apr 20.

Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA.

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http://dx.doi.org/10.1093/hmg/ddi168DOI Listing
June 2005

eIF4A3 is a novel component of the exon junction complex.

RNA 2004 Feb;10(2):200-9

Howard Hughes Medical Institute and Department of Biochemistry & Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6148, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370532PMC
http://dx.doi.org/10.1261/rna.5230104DOI Listing
February 2004

Numerous microRNPs in neuronal cells containing novel microRNAs.

RNA 2003 Feb;9(2):180-6

Howard Hughes Medical Institute, and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370383PMC
http://dx.doi.org/10.1261/rna.2141503DOI Listing
February 2003

Translation is required to remove Y14 from mRNAs in the cytoplasm.

Curr Biol 2002 Jul;12(13):1060-7

Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia 19104, USA.

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http://dx.doi.org/10.1016/s0960-9822(02)00902-8DOI Listing
July 2002

miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.

Genes Dev 2002 Mar;16(6):720-8

Howard Hughes Medical Institute, Department of Biochemistry & Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6148, USA.

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http://www.genesdev.org/cgi/doi/10.1101/gad.974702
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http://dx.doi.org/10.1101/gad.974702DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC155365PMC
March 2002