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Altuna Akalin
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methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles
A Akalin, M Kormaksson, S Li, FE Garrett-Bakelman, ME Figueroa, ...
Genome biology 13, 1-9, 2012
17612012
An atlas of combinatorial transcriptional regulation in mouse and man
T Ravasi, H Suzuki, CV Cannistraci, S Katayama, VB Bajic, K Tan, ...
Cell 140 (5), 744-752, 2010
8342010
Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation
T Baubec, DF Colombo, C Wirbelauer, J Schmidt, L Burger, AR Krebs, ...
Nature 520 (7546), 243-247, 2015
6972015
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Nature genetics 41 (5), 553-562, 2009
4182009
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
H Kikuta, M Laplante, P Navratilova, AZ Komisarczuk, PG Engström, ...
Genome research 17 (5), 545-555, 2007
3872007
Complex loci in human and mouse genomes
PG Engström, H Suzuki, N Ninomiya, A Akalin, L Sessa, G Lavorgna, ...
PLoS genetics 2 (4), e47, 2006
3512006
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages
K Schroder, KM Irvine, MS Taylor, NJ Bokil, KA Le Cao, KA Masterman, ...
Proceedings of the National Academy of Sciences 109 (16), E944-E953, 2012
3352012
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia
A Akalin, FE Garrett-Bakelman, M Kormaksson, J Busuttil, L Zhang, ...
PLoS genetics 8 (6), e1002781, 2012
3342012
DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia
R Rampal, A Akalin, J Madzo, A Vasanthakumar, E Pronier, J Patel, Y Li, ...
Cell Reports, 2014
3082014
Genomation: a toolkit to summarize, annotate and visualize genomic intervals
A Akalin, V Franke, K Vlahoviček, CE Mason, D Schübeler
Bioinformatics 31 (7), 1127-1129, 2015
2632015
RNA localization is a key determinant of neurite-enriched proteome
A Zappulo, D Van Den Bruck, C Ciolli Mattioli, V Franke, K Imami, ...
Nature communications 8 (1), 583, 2017
2002017
Two independent transcription initiation codes overlap on vertebrate core promoters
V Haberle, N Li, Y Hadzhiev, C Plessy, C Previti, C Nepal, J Gehrig, ...
Nature 507 (7492), 381-385, 2014
1982014
Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis‐regulatory regions in zebrafish
J Bessa, JJ Tena, E de la Calle‐Mustienes, A Fernández‐Miñán, ...
Developmental dynamics: an official publication of the American Association …, 2009
1882009
Induction of sarcomas by mutant IDH2
C Lu, S Venneti, A Akalin, F Fang, PS Ward, RG DeMatteo, AM Intlekofer, ...
Genes & development 27 (18), 1986-1998, 2013
1842013
Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy
E Wyler, K Mösbauer, V Franke, A Diag, LT Gottula, R Arsiè, F Klironomos, ...
IScience 24 (3), 102151, 2021
1732021
Strategies for analyzing bisulfite sequencing data
K Wreczycka, A Gosdschan, D Yusuf, B Grüning, Y Assenov, A Akalin
Journal of biotechnology 261, 105-115, 2017
1522017
Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells
M Kim, V Franke, B Brandt, ED Lowenstein, V Schöwel, S Spuler, A Akalin, ...
Nature communications 11 (1), 6375, 2020
1432020
Functional annotation of human long noncoding RNAs via molecular phenotyping
JA Ramilowski, CW Yip, S Agrawal, JC Chang, Y Ciani, IV Kulakovskiy, ...
Genome research 30 (7), 1060-1072, 2020
1382020
DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
K Blin, C Dieterich, R Wurmus, N Rajewsky, M Landthaler, A Akalin
Nucleic acids research 43 (D1), D160-D167, 2015
1322015
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
C Nepal, Y Hadzhiev, C Previti, V Haberle, N Li, H Takahashi, ...
Genome research 23 (11), 1938-1950, 2013
1312013
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