Publications by authors named "Altuna Akalin"

49Publications

Single-cell analyses of aging, inflammation and senescence.

Ageing Res Rev 2020 Sep 16:101156. Epub 2020 Sep 16.

Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.arr.2020.101156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493798PMC
September 2020

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

Deep learning for genomics using Janggu.

Nat Commun 2020 07 13;11(1):3488. Epub 2020 Jul 13.

Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 10115, Berlin, Germany.

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http://dx.doi.org/10.1038/s41467-020-17155-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359359PMC
July 2020

Evaluation of colorectal cancer subtypes and cell lines using deep learning.

Life Sci Alliance 2019 12 2;2(6). Epub 2019 Dec 2.

Max-Delbrück-Centrum für Molekulare Medizin, BIMSB, Berlin, Germany

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http://dx.doi.org/10.26508/lsa.201900517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892438PMC
December 2019

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program.

Nat Commun 2019 10 25;10(1):4878. Epub 2019 Oct 25.

Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.

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http://dx.doi.org/10.1038/s41467-019-12894-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814756PMC
October 2019

HOT or not: examining the basis of high-occupancy target regions.

Nucleic Acids Res 2019 06;47(11):5735-5745

Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gkz460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582337PMC
June 2019

Global identification of functional microRNA-mRNA interactions in Drosophila.

Nat Commun 2019 04 9;10(1):1626. Epub 2019 Apr 9.

Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.

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http://dx.doi.org/10.1038/s41467-019-09586-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456604PMC
April 2019

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.

Nucleic Acids Res 2019 03;47(5):2560-2573

Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gky1270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411841PMC
March 2019

PiGx: reproducible genomics analysis pipelines with GNU Guix.

Gigascience 2018 12 1;7(12). Epub 2018 Dec 1.

Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.

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https://academic.oup.com/gigascience/advance-article/doi/10.
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http://dx.doi.org/10.1093/gigascience/giy123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6275446PMC
December 2018

Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs.

Cell 2018 09 6;175(1):239-253.e17. Epub 2018 Sep 6.

Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.08.019DOI Listing
September 2018

FACT Sets a Barrier for Cell Fate Reprogramming in Caenorhabditis elegans and Human Cells.

Dev Cell 2018 09 2;46(5):611-626.e12. Epub 2018 Aug 2.

Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2018.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6137076PMC
September 2018

netSmooth: Network-smoothing based imputation for single cell RNA-seq.

F1000Res 2018 3;7. Epub 2018 Jan 3.

Scientific Bioinformatics Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, 13125, Germany.

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https://f1000research.com/articles/7-8/v3
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http://dx.doi.org/10.12688/f1000research.13511.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814748PMC
January 2018

Nuclear Organization in the Spinal Cord Depends on Motor Neuron Lamination Orchestrated by Catenin and Afadin Function.

Cell Rep 2018 02;22(7):1681-1694

Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; Cluster of Excellence NeuroCure, Neuroscience Research Center, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183010
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http://dx.doi.org/10.1016/j.celrep.2018.01.059DOI Listing
February 2018

Strategies for analyzing bisulfite sequencing data.

J Biotechnol 2017 Nov 16;261:105-115. Epub 2017 Aug 16.

Bioinformatics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jbiotec.2017.08.007DOI Listing
November 2017

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.

Nature 2015 Apr 21;520(7546):243-7. Epub 2015 Jan 21.

1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland [2] University of Basel, Faculty of Sciences, Petersplatz 1, CH-4001 Basel, Switzerland.

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http://dx.doi.org/10.1038/nature14176DOI Listing
April 2015

Genomation: a toolkit to summarize, annotate and visualize genomic intervals.

Bioinformatics 2015 Apr 21;31(7):1127-9. Epub 2014 Nov 21.

Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland, Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA, Faculty of Science, University of Basel, 4051 Basel, Switzerland and Department of Informatics, University of Oslo, NO-0316 Oslo, Norway.

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http://dx.doi.org/10.1093/bioinformatics/btu775DOI Listing
April 2015

Two independent transcription initiation codes overlap on vertebrate core promoters.

Nature 2014 Mar 16;507(7492):381-385. Epub 2014 Feb 16.

Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom.

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http://dx.doi.org/10.1038/nature12974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820030PMC
March 2014

An optimized algorithm for detecting and annotating regional differential methylation.

BMC Bioinformatics 2013 10;14 Suppl 5:S10. Epub 2013 Apr 10.

Department of Physiology and Biophysics,Weill Cornell Medical College, 1305 York Ave., New York, NY 10065, USA.

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http://dx.doi.org/10.1186/1471-2105-14-S5-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3622633PMC
December 2013

Translog, a web browser for studying the expression divergence of homologous genes.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S59. Epub 2010 Jan 18.

Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-S1-S59DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009532PMC
January 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

Transcriptional features of genomic regulatory blocks.

Genome Biol 2009 19;10(4):R38. Epub 2009 Apr 19.

Computational Biology Unit, Bergen Center for Computational Science, and Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway.

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http://dx.doi.org/10.1186/gb-2009-10-4-r38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688929PMC
September 2009

Differential evolution of the 13 Atlantic salmon Hox clusters.

Mol Biol Evol 2008 Jul 18;25(7):1333-43. Epub 2008 Apr 18.

Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, Bergen, Norway.

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http://dx.doi.org/10.1093/molbev/msn097DOI Listing
July 2008

Predicting the binding affinity of MHC class II peptides.

Comput Syst Bioinformatics Conf 2006 :331-4

Computer Science and Engineering, The Ohio State University, OH, USA.

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June 2007