Publications by authors named "Michael M Hoffman"

26Publications

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

DNAmod: the DNA modification database.

J Cheminform 2019 Apr 23;11(1):30. Epub 2019 Apr 23.

Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Research Tower 15-701, 101 College Street, Toronto, ON, M5G 1L7, Canada.

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http://dx.doi.org/10.1186/s13321-019-0349-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6478773PMC
April 2019

Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.

Inf Fusion 2019 Oct 21;50:71-91. Epub 2018 Sep 21.

Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1016/j.inffus.2018.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6242341PMC
October 2019

Umap and Bismap: quantifying genome and methylome mappability.

Nucleic Acids Res 2018 11;46(20):e120

Princess Margaret Cancer Centre, M5G 1L7, Toronto, ON, Canada.

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http://dx.doi.org/10.1093/nar/gky677DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237805PMC
November 2018

Classification and interaction in random forests.

Proc Natl Acad Sci U S A 2018 02 12;115(8):1690-1692. Epub 2018 Feb 12.

Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1L7;

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http://dx.doi.org/10.1073/pnas.1800256115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828645PMC
February 2018

Genome Informatics 2016.

Genome Biol 2017 01 16;18(1). Epub 2017 Jan 16.

Princess Margaret Cancer Centre, Toronto, Canada.

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http://dx.doi.org/10.1186/s13059-016-1135-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5240446PMC
January 2017

Top considerations for creating bioinformatics software documentation.

Brief Bioinform 2018 07;19(4):693-699

Department of Medical Biophysics, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1093/bib/bbw134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054259PMC
July 2018

ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data.

Genome Biol 2016 Apr 30;17:82. Epub 2016 Apr 30.

Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1186/s13059-016-0925-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852466PMC
April 2016

Determining the epigenome using DNA alone.

Nat Methods 2015 Mar;12(3):191-2

1] Department of Computer Science, University of Toronto, and Princess Margaret Cancer Centre, Toronto, Ontario, Canada [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nmeth.3291DOI Listing
March 2015

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

Genome Res 2015 Apr 12;25(4):544-57. Epub 2015 Feb 12.

Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.184341.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381526PMC
April 2015

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

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http://dx.doi.org/10.1038/nature13415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227084PMC
August 2014

Unsupervised pattern discovery in human chromatin structure through genomic segmentation.

Nat Methods 2012 Mar 18;9(5):473-6. Epub 2012 Mar 18.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.1937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3340533PMC
March 2012

Exploratory analysis of genomic segmentations with Segtools.

BMC Bioinformatics 2011 Oct 26;12:415. Epub 2011 Oct 26.

Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065, USA.

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http://dx.doi.org/10.1186/1471-2105-12-415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224787PMC
October 2011

The Genomedata format for storing large-scale functional genomics data.

Bioinformatics 2010 Jun 29;26(11):1458-9. Epub 2010 Apr 29.

Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872006PMC
June 2010

An effective model for natural selection in promoters.

Genome Res 2010 May 1;20(5):685-92. Epub 2010 Mar 1.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.096719.109
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http://dx.doi.org/10.1101/gr.096719.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860170PMC
May 2010

Estimating the neutral rate of nucleotide substitution using introns.

Mol Biol Evol 2007 Feb 22;24(2):522-31. Epub 2006 Nov 22.

European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England.

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http://dx.doi.org/10.1093/molbev/msl179DOI Listing
February 2007

AANT: the Amino Acid-Nucleotide Interaction Database.

Nucleic Acids Res 2004 Jan;32(Database issue):D174-81

Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712-0159, USA.

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http://dx.doi.org/10.1093/nar/gkh128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308862PMC
January 2004