Timo Lassmann

Timo Lassmann

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Timo Lassmann

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Expression Levels of Therapeutic Targets as Indicators of Sensitivity to Targeted Therapeutics.

Mol Cancer Ther 2019 12 29;18(12):2480-2489. Epub 2019 Aug 29.

Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Western Australia, Australia.

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http://dx.doi.org/10.1158/1535-7163.MCT-19-0273DOI Listing
December 2019

Personalised analytics for rare disease diagnostics.

Nat Commun 2019 Nov 21;10(1):5274. Epub 2019 Nov 21.

Telethon Kids Institute, The University of Western Australia, PO Box 855, West Perth, WA, 6872, Australia.

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http://dx.doi.org/10.1038/s41467-019-13345-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872807PMC
November 2019

Kalign 3: multiple sequence alignment of large data sets.

Authors:
Timo Lassmann

Bioinformatics 2019 Oct 26. Epub 2019 Oct 26.

Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btz795DOI Listing
October 2019

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis.

BMC Genomics 2019 Sep 18;20(1):718. Epub 2019 Sep 18.

Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/s12864-019-6063-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751898PMC
September 2019

A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers.

Cell 2019 03;177(1):32-37

Faculty of Health and Medical Sciences, University of Western Australia Medical School, Perth, WA, Australia; Western Australian Register of Developmental Anomalies, Genetic Services of Western Australia, Perth, WA, Australia; Office of Population Health Genomics, Western Australian Department of Health, Perth, WA, Australia.

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193022
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http://dx.doi.org/10.1016/j.cell.2019.02.040DOI Listing
March 2019

Elucidating the Interaction of CF Airway Epithelial Cells and Rhinovirus: Using the Host-Pathogen Relationship to Identify Future Therapeutic Strategies.

Front Pharmacol 2018 7;9:1270. Epub 2018 Nov 7.

Paediatrics, Medical School, Faculty of Healthy and Medical Science, University of Western Australia, Nedlands, WA, Australia.

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http://dx.doi.org/10.3389/fphar.2018.01270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234657PMC
November 2018

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.

Cerebellum 2018 Jun;17(3):308-325

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

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http://dx.doi.org/10.1007/s12311-017-0912-3DOI Listing
June 2018

A phenotype centric benchmark of variant prioritisation tools.

NPJ Genom Med 2018 5;3. Epub 2018 Feb 5.

Telethon Kids Institute, The University of Western Australia, Subiaco, WA 6008 Australia.

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http://dx.doi.org/10.1038/s41525-018-0044-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799157PMC
February 2018

Correction to: Relatively frequent switching of transcription start sites during cerebellar development.

BMC Genomics 2018 01 11;19(1):39. Epub 2018 Jan 11.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

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http://dx.doi.org/10.1186/s12864-017-4291-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763542PMC
January 2018

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.

EBioMedicine 2017 Oct 12;24:257-266. Epub 2017 Sep 12.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 3510198, Japan; Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo 1058461, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5652006PMC
October 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Bioinformatics 2016 09 9;32(18):2858-60. Epub 2016 Jun 9.

Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.

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http://dx.doi.org/10.1093/bioinformatics/btw337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018375PMC
September 2016

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Nucleic Acids Res 2016 Apr 21;44(7):3233-52. Epub 2016 Mar 21.

Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA

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http://dx.doi.org/10.1093/nar/gkw162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838384PMC
April 2016

Reference genotype and exome data from an Australian Aboriginal population for health-based research.

Sci Data 2016 Apr 12;3:160023. Epub 2016 Apr 12.

Telethon Kids Institute, The University of Western Australia, Subiaco, Western Australia 6008, Australia.

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http://www.nature.com/articles/sdata201623
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http://dx.doi.org/10.1038/sdata.2016.23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828942PMC
April 2016

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Cancer Res 2016 Jan 9;76(2):216-26. Epub 2015 Nov 9.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-0484DOI Listing
January 2016

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line.

Front Genet 2015 18;6:331. Epub 2015 Nov 18.

RIKEN Center for Life Science Technologies Yokohama, Japan ; Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan ; QEII Medical Centre and Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia Nedlands, WA, Australia.

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http://dx.doi.org/10.3389/fgene.2015.00331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650373PMC
December 2015

The frequent evolutionary birth and death of functional promoters in mouse and human.

Genome Res 2015 Oct 30;25(10):1546-57. Epub 2015 Jul 30.

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

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http://dx.doi.org/10.1101/gr.190546.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579340PMC
October 2015

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Nucleic Acids Res 2015 Aug 27;43(14):6969-82. Epub 2015 Jun 27.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan Riken Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

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http://dx.doi.org/10.1093/nar/gkv646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538831PMC
August 2015

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

J Leukoc Biol 2015 May 25;97(5):985-995. Epub 2015 Feb 25.

*The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan

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http://dx.doi.org/10.1189/jlb.6TA1014-477RRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398258PMC
May 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

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http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

Telomerase reverse transcriptase regulates microRNAs.

Int J Mol Sci 2015 Jan 6;16(1):1192-208. Epub 2015 Jan 6.

Cancer Stem Cell Project, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.

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http://dx.doi.org/10.3390/ijms16011192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307298PMC
January 2015

TagDust2: a generic method to extract reads from sequencing data.

Authors:
Timo Lassmann

BMC Bioinformatics 2015 Jan 28;16:24. Epub 2015 Jan 28.

RIKEN Center for Life Science Technologies (CLST), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Kanagawa, Japan.

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http://dx.doi.org/10.1186/s12859-015-0454-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384298PMC
January 2015

MOIRAI: a compact workflow system for CAGE analysis.

BMC Bioinformatics 2014 May 16;15:144. Epub 2014 May 16.

RIKEN Center for Life Science Technologies (CLST), Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Kanagawa, Japan.

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http://dx.doi.org/10.1186/1471-2105-15-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033680PMC
May 2014

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

Blood 2014 Apr 26;123(17):e46-57. Epub 2014 Mar 26.

Department of Bioscience and Nutrition, Center for Biosciences, NOVUM, Karolinska Institutet, Stockholm, Sweden;

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http://dx.doi.org/10.1182/blood-2013-02-483537DOI Listing
April 2014

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Proc Natl Acad Sci U S A 2014 Apr 27;111(14):5289-94. Epub 2014 Mar 27.

Departments of Experimental Immunology and Systems Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.

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http://dx.doi.org/10.1073/pnas.1312717110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986152PMC
April 2014

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

BMC Genomics 2014 Apr 25;15:269. Epub 2014 Apr 25.

RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045 Yokohama, Japan.

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http://dx.doi.org/10.1186/1471-2164-15-269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029093PMC
April 2014

Effects of cytosine methylation on transcription factor binding sites.

BMC Genomics 2014 Mar 26;15:119. Epub 2014 Mar 26.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/1471-2164-15-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986887PMC
March 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Off-target effect of endogenous siRNA derived from RMRP in human cells.

Int J Mol Sci 2013 Apr 29;14(5):9305-18. Epub 2013 Apr 29.

Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.

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http://dx.doi.org/10.3390/ijms14059305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676784PMC
April 2013

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

5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.

Nat Protoc 2012 Feb 23;7(3):542-61. Epub 2012 Feb 23.

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

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http://dx.doi.org/10.1038/nprot.2012.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4094379PMC
February 2012

SAMStat: monitoring biases in next generation sequencing data.

Bioinformatics 2011 Jan 18;27(1):130-1. Epub 2010 Nov 18.

Omics Science Center, Riken Yokohama Institute, Tsurumi-ku, Yokohama, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq614DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008642PMC
January 2011

TagDust--a program to eliminate artifacts from next generation sequencing data.

Bioinformatics 2009 Nov 7;25(21):2839-40. Epub 2009 Sep 7.

Omics Science Center, Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp527DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781754PMC
November 2009

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA.

Nature 2009 Sep 23;461(7261):230-5. Epub 2009 Aug 23.

Cancer Stem Cell Project, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.

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http://www.nature.com/doifinder/10.1038/nature08283
Publisher Site
http://dx.doi.org/10.1038/nature08283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755635PMC
September 2009

Small RNAs derived from snoRNAs.

RNA 2009 Jul 27;15(7):1233-40. Epub 2009 May 27.

Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.

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http://dx.doi.org/10.1261/rna.1528909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704076PMC
July 2009

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

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features.

Nucleic Acids Res 2009 Feb 22;37(3):858-65. Epub 2008 Dec 22.

Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gkn1006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647288PMC
February 2009

Automatic extraction of reliable regions from multiple sequence alignments.

BMC Bioinformatics 2007 May 24;8 Suppl 5:S9. Epub 2007 May 24.

Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2105-8-S5-S9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892097PMC
May 2007

The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function.

BMC Genomics 2007 Mar 15;8:74. Epub 2007 Mar 15.

Department of Cellular and Molecular Biology, Program for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2164-8-74DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1831481PMC
March 2007

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W596-9

Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gkl191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538774PMC
July 2006

Automatic assessment of alignment quality.

Nucleic Acids Res 2005 16;33(22):7120-8. Epub 2005 Dec 16.

Center for Genomics and Bioinformatics, Karolinska Institutet, S-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gki1020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1316116PMC
January 2006

Pfam: clans, web tools and services.

Nucleic Acids Res 2006 Jan;34(Database issue):D247-51

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkj149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347511PMC
January 2006

Kalign--an accurate and fast multiple sequence alignment algorithm.

BMC Bioinformatics 2005 Dec 12;6:298. Epub 2005 Dec 12.

Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius vag 35, S-17177 Stockholm, Sweden.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-6-298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325270PMC
December 2005

Quality assessment of multiple alignment programs.

FEBS Lett 2002 Oct;529(1):126-30

Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177, Stockholm, Sweden.

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http://dx.doi.org/10.1016/s0014-5793(02)03189-7DOI Listing
October 2002