Publications

Pre-prints

Full list of pre-prints at bioRxiv.

  1. netSmooth: Network-smoothing based imputation for single cell RNA-seq. Jonathan Ronen, Altuna Akalin bioRxiv 234021; doi: [https://doi.org/10.1101/234021]

  2. Strategies for analyzing bisulfite sequencing data. Katarzyna Wreczycka, Alexander Gosdschan, Dilmurat Yusuf, Bjoern Gruening, Yassen Assenov, Altuna Akalin. bioRxiv 109512; doi: [https://doi.org/10.1101/109512]

  3. HOT or not: Examining the basis of high-occupancy target regions. Katarzyna Wreczycka, Vedran Franke, Bora Uyar, Ricardo Wurmus, Altuna Akalin. bioRxiv 107680; doi: [https://doi.org/10.1101/107680]

  4. Mutations In Disordered Regions Cause Disease By Creating Endocytosis Motifs. Katrina Meyer, Bora Uyar, Marieluise Kirchner, Jingyuan Cheng, Altuna Akalin, Matthias Selbach. bioRxiv 141622; doi: https://doi.org/10.1101/141622

  5. FACT sets a barrier for cell fate reprogramming in C. elegans and Human. Ena Kolundzic, Andreas Ofenbauer, Bora Uyar, Anne Sommermeier, Stefanie Seelk, Mei He, Guelkiz Baytek, Altuna Akalin, Sebastian Diecke, Scott Allen Lacadie, Baris Tursun. bioRxiv 185116; doi: https://doi.org/10.1101/185116

Peer-reviewed publications

(Up-to-date publications at PubMed.)

  1. Dewitz C, Pimpinella S, Hackel P, Akalin A, Jessell TM, Zampieri N.Nuclear Organization in the Spinal Cord Depends on Motor Neuron Lamination Orchestrated by Catenin and Afadin Function. Cell Reports. 2018 Feb 13;22(7):1681-1694. doi: 10.1016/j.celrep.2018.01.059.

  2. Wyler E, Menegatti J, Franke V, Kocks C, Boltengagen A, Hennig T, Theil K, Rutkowski A, Ferrai C, Baer L, Kermas L, Friedel C, Rajewsky N, Akalin A, Dölken L, Grässer F, Landthaler M. Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection. Genome Biol. 2017 Oct 31;18(1):209. doi: 10.1186/s13059-017-1329-5.

  3. Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A. RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation. Mol Syst Biol. 2017 Oct 16;13(10):946. doi: 10.15252/msb.20177754

  4. Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M.RNA localization is a key determinant of neurite-enriched proteome.. Nature Commun., 2017

  5. Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.. Nucleic Acids Res., 2017

  6. Wreczycka K, Gosdschan A, Yusuf D, Grüning B, Assenov Y, Akalin A. Strategies for analyzing bisulfite sequencing data.. J Biotechnol., 2017

  7. Uyar B, Yusuf D, Wurmus R,Rajewsky N, Ohler U, Akalin A. RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.. Nucleic Acids Res., 2017

  8. Baubec T, Colombo DF, Wirbelauer C, Schmidt J, Burger L, Krebs AR, Akalin A, Schübeler D. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature, 2015

  9. Rampal R *, Akalin A *, Madzo J *, Vasanthakumar A *, Pronier E, Patel J, Li Y, Ahn, et al. DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia. Cell Reports, 2014 ( * Equal contribution)

  10. Akalin A * # , Franke V *, Vlahoviček K, Mason CE, Schübeler D. genomation: a toolkit to summarize, annotate and visualize genomic intervals. Bioinformatics , 2014 (# Co-corresponding author, * Equal contribution)

  11. Blin K, Dieterich C, Wurmus R, Nikolaus Rajewsky, Markus Landthaler, Akalin A. DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation. Nucleic Acid Research , 2014

  12. Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, et al. NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Front. Cell. Neurosci., 18 February 2014

  13. Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM,van IJcken W, Armant A, Ferg M, Strähle U, Carninci P, Müller F, Boris Lenhard B. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature, 2014

  14. Lu C, Venneti S, Akalin A, Fang F, Ward PS, Dematteo RG, Intlekofer AM, Chen C et al. Induction of sarcomas by mutant IDH2. Genes Dev. 2013 Sep 15;27(18):1986-98

  15. Nepal C, Hadzhiev Y, Previty C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid R, Anand S, Gehrig J, Akalin A, Kockx C, et al. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Research. 2013 Sep 3

  16. Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, et al. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics. 2013;14 Suppl 5:S10

  17. Akalin A#, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biology, 2012 Oct 3;13(10):R87 #(Co-corresponding author)

  18. Akalin A*, Garrett-Bakelman FE*, Kormaksson M, Busuttil J, et al. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genetics 2012;8(6):e1002781. * (Equal Contribution)

  19. Plessy C*, Pascarella G*, Bertin N*, Akalin A*, Carrieri C, Vassalli A, Lazarevic D, et al. Promoter architecture of mouse olfactory receptor genes. Genome Research. 2011 Dec 22. * (Equal Contribution)

  20. Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK et al. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. PNAS. 2012 Apr 17;109(16):E944-53

  21. Royo JL, Hidalgo C, Roncero Y, Seda MA, Akalin A, Lenhard B, Casares F, Gómez-Skarmeta JL. Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PLoS One. 2011;6(9):e24824

  22. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S et al. An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell 2010, 140:744-752

  23. Dong X, Akalin A, Sharma Y, Lenhard B. Translog, a web browser for studying the expression divergence of homologous genes. BMC bioinformatics 2010, 11 Suppl 1:S5910.1186

  24. Punnamoottil B, Herrmann C, Anaya JP, D’Aniello S, Garcia-Fernàndez J, Akalin A, Becker TS. Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes. Dev Biol. 2010 Feb 6.

  25. Bessa J, Tena JJ, de la Calle-Mustienes E, Fernández-Miñán A, Naranjo S, Fernández A, Montoliu L, Akalin A, Lenhard B, Casares F, Gómez-Skarmeta JL. Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Dev Dyn. 2009 Sep;238(9):2409-17

  26. FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 2009 May;41(5):553-62

  27. Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B. Transcriptional features of genomic regulatory blocks. Genome Biology. 2009;10(4):R38

  28. Mungpakdee S, Seo HC, Angotzi AR, Dong X, Akalin A, Chourrout D. Differential evolution of the 13 Atlantic salmon Hox clusters. Mol Biol Evol. 2008 Jul;25(7):1333-43

  29. Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Research 2007 May;17(5):545-55

  30. Altiparmak F, Akalin A, Ferhatosmanoglu H. Predicting the binding affinity of MHC class II peptides. Comput Syst Bioinformatics Conf. 2006:331-4

  31. Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L. Complex Loci in human and mouse genomes. PLoS Genetics. 2006 Apr;2(4):e47

Book chapters

  1. Baubec T & Akalin A. “Genome-Wide Analysis of DNA Methylation Patterns by High-Throughput Sequencing”. Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer, 2016.

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