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PiGx: Reproducible genomics analysis pipelines with GNU Guix.
Wurmus, R. and Uyar, B. and Osberg, B. and Franke, V. and Gosdschan, A. and Wreczycka, K. and Ronen, J. and Akalin, A.
GigaScience : giy123. 2 October 2018 (In Press)

Mutations in disordered regions can cause disease by creating dileucine motifs.
Meyer, K. and Kirchner, M. and Uyar, B. and Cheng, J.Y. and Russo, G. and Hernandez-Miranda, L.R. and Szymborska, A. and Zauber, H. and Rudolph, I.M. and Willnow, T.E. and Akalin, A. and Haucke, V. and Gerhardt, H. and Birchmeier, C. and Kühn, R. and Krauss, M. and Diecke, S. and Pascual, J.M. and Selbach, M.
Cell 175 (1): 239-253. 20 September 2018

FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells.
Kolundzic, E. and Ofenbauer, A. and Bulut, S.I. and Uyar, B. and Baytek, G. and Sommermeier, A. and Seelk, S. and He, M. and Hirsekorn, A. and Vucicevic, D. and Akalin, A. and Diecke, S. and Lacadie, S.A. and Tursun, B.
Developmental Cell 46 (5): 611-626. 10 September 2018

netSmooth: Network-smoothing based imputation for single cell RNA-seq.
Ronen, J. and Akalin, A.
F1000Research 7 : 8. 10 July 2018

Long non-coding RNAs defining major subtypes of B cell precursor acute lymphoblastic leukemia.
Rani James, A. and Schroeder, M.P. and Neumann, M. and Bastian, L. and Eckert, C. and Gökbuget, N. and Tanchez, J.O. and Schlee, C. and Isaakidis, K. and Schwartz, S. and Burmeister, T. and von Stackelberg, A. and Rieger, M.A. and Göllner, S. and Horstman, M. and Schrappe, M. and Kirschner-Schwabe, R. and Brüggemann, M. and Müller-Tidow, C. and Serve, H. and Akalin, A. and Baldus, C.D.
bioRxiv : 365429. 9 July 2018

Reproducible genomics analysis pipelines with GNU Guix.
Wurmus, R. and Uyar, B. and Osberg, B. and Franke, V. and Gosdschan, A. and Wreczycka, K. and Ronen, J. and Akalin, A.
bioRxiv : 298653. 21 April 2018

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling.
Karabacak Calviello, A. and Hirsekorn, A. and Wurmus, R. and Yusuf, D. and Ohler, U.
bioRxiv : 284364. 19 March 2018

Nuclear organization in the spinal cord depends on motor neuron lamination orchestrated by catenin and afadin function.
Dewitz, C. and Pimpinella, S. and Hackel, P. and Akalin, A. and Jessell, T.M. and Zampieri, N.
Cell Reports 22 (7): 1681-1694. 13 February 2018


netSmooth: Network-smoothing based imputation for single cell RNA-seq.
Ronen, J. and Akalin, A.
bioRxiv : 234021. 13 December 2017

Strategies for analyzing bisulfite sequencing data.
Wreczycka, K. and Gosdschan, A. and Yusuf, D. and Grüning, B. and Assenov, Y. and Akalin, A.
Journal of Biotechnology 261 : 105-115. 10 November 2017

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E. and Menegatti, J. and Franke, V. and Kocks, C. and Boltengagen, A. and Hennig, T. and Theil, K. and Rutkowski, A. and Ferrai, C. and Baer, L. and Kermas, L. and Friedel, C. and Rajewsky, N. and Akalin, A. and Dölken, L. and Grässer, F. and Landthaler, M.
Genome Biology 18 (1): 209. 31 October 2017

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.
Ferrai, C. and Torlai Triglia, E. and Risner-Janiczek, J.R. and Rito, T. and Rackham, O.J.L. and De Santiago, I. and Kukalev, A. and Nicodemi, M. and Akalin, A. and Li, M. and Ungless, M.A. and Pombo, A.
Molecular Systems Biology 13 (10): 946. 16 October 2017

RNA localization is a key determinant of neurite-enriched proteome.
Zappulo, A. and van den Bruck, D. and Ciolli Mattioli, C. and Franke, V. and Imami, K. and McShane, E. and Moreno-Estelles, M. and Calviello, L. and Filipchyk, A. and Peguero-Sanchez, E. and Müller, T. and Woehler, A. and Birchmeier, C. and Merino, E. and Rajewsky, N. and Ohler, U. and Mazzoni, E.O. and Selbach, M. and Akalin, A. and Chekulaeva, M.
Nature Communications 8 (1): 583. 19 September 2017

FACT sets a barrier for cell fate reprogramming in C. elegans and human.
Kolundzic, E. and Ofenbauer, A. and Uyar, B. and Sommermeier, A. and Seelk, S. and He, M. and Baytek, G. and Akalin, A. and Diecke, S. and Lacadie, S.A. and Tursun, B.
bioRxiv : 185116. 6 September 2017

Strategies for analyzing bisulfite sequencing data.
Wreczycka, K. and Gosdschan, A. and Yusuf, D. and Gruening, B. and Assenov, Y. and Akalin, A.
bioRxiv : 109512. 9 August 2017

HOT or not: Examining the basis of high-occupancy target regions.
Wreczycka, K. and Franke, V. and Uyar, B. and Wurmus, R. and Akalin, A.
bioRxiv : 107680. 31 July 2017

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
Grüning, B.A. and Fallmann, J. and Yusuf, D. and Will, S. and Erxleben, A. and Eggenhofer, F. and Houwaart, T. and Batut, B. and Videm, P. and Bagnacani, A. and Wolfien, M. and Lott, S.C. and Hoogstrate, Y. and Hess, W.R. and Wolkenhauer, O. and Hoffmann, S. and Akalin, A. and Ohler, U. and Stadler, P.F. and Backofen, R.
Nucleic Acids Research 45 (W1): W560-W566. 3 July 2017

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B. and Yusuf, D. and Wurmus, R. and Rajewsky, N. and Ohler, U. and Akalin, A.
Nucleic Acids Research 45 (10): e91. 2 June 2017

Mutations in disordered regions cause disease by creating endocytosis motifs.
Meyer, K. and Uyar, B. and Kirchner, M. and Cheng, J. and Akalin, A. and Selbach, M.
bioRxiv : 141622. 24 May 2017

Degrons in cancer.
Meszaros, B. and Kumar, M. and Gibson, T.J. and Uyar, B. and Dosztanyi, Z.
Science Signaling 10 (470): eaak9982. 14 March 2017


The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Nucleic Acids Research 44 (D1): D27-D37. 4 January 2016


Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation.
Baubec, T. and Colombo, D.F. and Wirbelauer, C. and Schmidt, J. and Burger, L. and Krebs, A.R. and Akalin, A. and Schübeler, D.
Nature 520 (7546): 243-247. 9 April 2015

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin, A. and Franke, V. and Vlahoviček, K. and Mason, C.E. and Schübeler, D.
Bioinformatics 31 (7): 1127-1129. 1 April 2015

DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation.
Blin, K. and Dieterich, C. and Wurmus, R. and Rajewsky, N. and Landthaler, M. and Akalin, A.
Nucleic Acids Research 43 (Database issue): D160-D167. 28 January 2015

Reproducible and user-controlled software environments in HPC with Guix.
Courtes, L. and Wurmus, R.
In: Euro-Par 2015: Parallel Processing Workshops. Lecture Notes in Computer Science, 9523 . Springer (Switzerland), 579-591. ISBN 978-3-319-27307-5 2015


DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia.
Rampal, R. and Akalin, A. and Madzo, J. and Vasanthakumar, A. and Pronier, E. and Patel, J. and Li, Y. and Ahn, J. and Abdel-Wahab, O. and Shih, A. and Lu, C. and Ward, P.S. and Tsai, J.J. and Hricik, T. and Tosello, V. and Tallman, J.E. and Zhao, X. and Daniels, D. and Dai, Q. and Ciminio, L. and Aifantis, I. and He, C. and Fuks, F. and Tallman, M.S. and Ferrando, A. and Nimer, S. and Paietta, E. and Thompson, C.B. and Licht, J.D. and Mason, C.E. and Godley, L.A. and Melnick, A. and Figueroa, M.E. and Levine, R.L.
Cell Reports 9 (5): 1841-1855. 11 December 2014

Two independent transcription initiation codes overlap on vertebrate core promoters.
Haberle, V. and Li, N. and Hadzhiev, Y. and Plessy, C. and Previti, C. and Nepal, C. and Gehrig, J. and Dong, X. and Akalin, A. and Suzuki, A.M. and van IJcken, W.F.J. and Armant, O. and Ferg, M. and Strähle, U. and Carninci, P. and Müller, F. and Lenhard, B.
Nature 507 (7492): 381-385. 20 March 2014

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements.
Pascarella, G. and Lazarevic, D. and Plessy, C. and Bertin, N. and Akalin, A. and Vlachouli, C. and Simone, R. and Faulkner, G.J. and Zucchelli, S. and Kawai, J. and Daub, C.O. and Hayashizaki, Y. and Lenhard, B. and Carninci, P. and Gustincich, S.
Frontiers in Cellular Neuroscience 8 : 41. 18 February 2014


Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
Nepal, C. and Hadzhiev, Y. and Previti, C. and Haberle, V. and Li, N. and Takahashi, H. and Suzuki, A.M.M. and Sheng, Y. and Abdelhamid, R.F. and Anand, S. and Gehrig, J. and Akalin, A. and Kockx, C.E.M. and van der Sloot, A.A.J. and van Ijcken, W.F.J. and Armant, O. and Rastegar, S. and Watson, C. and Strähle, U. and Stupka, E. and Carninci, P. and Lenhard, B. and Müller, F.
Genome Research 23 (11): 1938-1950. November 2013

Induction of sarcomas by mutant IDH2.
Lu, C. and Venneti, S. and Akalin, A. and Fang, F. and Ward, P.S. and Dematteo, R.G. and Intlekofer, A.M. and Chen, C. and Ye, J. and Hameed, M. and Nafa, K. and Agaram, N.P. and Cross, J.R. and Khanin, R. and Mason, C.E. and Healey, J.H. and Lowe, S.W. and Schwartz, G.K. and Melnick, A. and Thompson, C.B.
Genes & Development 27 (18): 1986-1998. 15 September 2013

An optimized algorithm for detecting and annotating regional differential methylation.
Li, S. and Garrett-Bakelman, F.E. and Akalin, A. and Zumbo, P. and Levine, R. and To, B.L. and Lewis, I.D. and Brown, A.L. and D'Andrea, R.J. and Melnick, A. and Mason, C.E.
BMC Bioinformatics 14 (Suppl 5): S10. 2013


methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin, A. and Kormaksson, M. and Li, S. and Garrett-Bakelman, F.E. and Figueroa, M.E. and Melnick, A. and Mason, C.E.
Genome Biology 13 (10): R87. 3 October 2012

Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia.
Akalin, A. and Garrett-Bakelman, F.E. and Kormaksson, M. and Busuttil, J. and Zhang, L. and Khrebtukova, I. and Milne, T.A. and Huang, Y. and Biswas, D. and Hess, J.L. and Allis, C.D. and Roeder, R.G. and Valk, P.J.M. and Loewenberg, B. and Delwel, R. and Fernandez, H.F. and Paietta, E. and Tallman, M.S. and Schroth, G.P. and Mason, C.E. and Melnick, A. and Figueroa, M.E.
PLoS Genetics 8 (6): e1002781. 21 June 2012

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages.
Schroder, K. and Irvine, K.M. and Taylor, M.S. and Bokil, N.J. and Le Cao, K.A. and Masterman, K.A. and Labzin, L.I. and Semple, C.A. and Kapetanovic, R. and Fairbairn, L. and Akalin, A. and Faulkner, G.J. and Baillie, J.K. and Gongora, M. and Daub, C.O. and Kawaji, H. and McLachlan, G.J. and Goldman, N. and Grimmond, S.M. and Carninci, P. and Suzuki, H. and Hayashizaki, Y. and Lenhard, B. and Hume, D.A. and Sweet, M.J.
Proceedings of the National Academy of Sciences of the United States of America 109 (16): E944-E953. 17 April 2012

Promoter architecture of mouse olfactory receptor genes.
Plessy, C. and Pascarella, G. and Bertin, N. and Akalin, A. and Carrieri, C. and Vassalli, A. and Lazarevic, D. and Severin, J. and Vlachouli, C. and Simone, R. and Faulkner, G.J. and Kawai, J. and Daub, C.O. and Zucchelli, S. and Hayashizaki, Y. and Mombaerts, P. and Lenhard, B. and Gustincich, S. and Carninci, P.
Genome Research 22 (3): 486-497. March 2012


Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
Royo, J.L. and Hidalgo, C. and Roncero, Y. and Seda, M.A. and Akalin, A. and Lenhard, B. and Casares, F. and Gomez-Skarmeta, J.L.
PLoS ONE 6 (9): e24824. 13 September 2011


Cis-regulatory characterization of sequence conservation surrounding the Hox4 genes.
Punnamoottil, B. and Herrmann, C. and Pascual-Anaya, J. and D'Aniello, S. and Garcia-Fernandez, J. and Akalin, A. and Becker, T.S. and Rinkwitz, S.
Developmental Biology 340 (2): 269-282. 15 April 2010

An atlas of combinatorial transcriptional regulation in mouse and man.
Ravasi, T. and Suzuki, H. and Cannistraci, C.V. and Katayama, S. and Bajic, V.B. and Tan, K. and Akalin, A. and Schmeier, S. and Kanamori-Katayama, M. and Bertin, N. and Carninci, P. and Daub, C.O. and Forrest, A.R.R. and Gough, J. and Grimmond, S. and Han, J.H. and Hashimoto, T. and Hide, W. and Hofmann, O. and Kamburov, A. and Kaur, M. and Kawaji, H. and Kubosaki, A. and Lassmann, T. and van Nimwegen, E. and MacPherson, C.R. and Ogawa, C. and Radovanovic, A. and Schwartz, A. and Teasdale, R.D. and Tegner, J. and Lenhard, B. and Teichmann, S.A. and Arakawa, T. and Ninomiya, N. and Murakami, K. and Tagami, M. and Fukuda, S. and Imamura, K. and Kai, C. and Ishihara, R. and Kitazume, Y. and Kawai, J. and Hume, D.A. and Ideker, T. and Hayashizaki, Y.
Cell 140 (5): 744-752. 5 March 2010

Translog, a web browser for studying the expression divergence of homologous genes.
Dong, X. and Akalin, A. and Sharma, Y. and Lenhard, B.
BMC Bioinformatics 11 (Suppl 1): S59. 18 January 2010


Zebrafish enhancer detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish.
Bessa, J. and Tena, J.J. and de la Calle-Mustienes, E. and Fernandez-Minan, A. and Naranjo, S. and Fernandez, A. and Montoliu, L. and Akalin, A. and Lenhard, B. and Casares, F. and Gomez-Skarmeta, J.L.
Developmental Dynamics 238 (9): 2409-2417. September 2009

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Suzuki, H and Forrest, ARR and van Nimwegen, E and Daub, CO and Balwierz, PJ and Irvine, KM and Lassmann, T and Ravasi, T and Hasegawa, Y and de Hoon, MJL and Katayama, S and Schroder, K and Carninci, P and Tomaru, Y and Kanamori-Katayama, M and Kubosaki, A and Akalin, A. and Ando, Y and Arner, E and Asada, M and Asahara, H and Bailey, T and Bajic, VB and Bauer, D and Beckhouse, AG and Bertin, N and Björkegren, J and Brombacher, F and Bulger, E and Chalk, AM and Chiba, J and Cloonan, N and Dawe, A and Dostie, J and Engstroem, PG and Essack, M and Faulkner, GJ and Fink, JL and Fredman, D and Fujimori, K and Furuno, M and Gojobori, T and Gough, J and Grimmond, SM and Gustafsson, M and Hashimoto, M and Hashimoto, T and Hatakeyama, M and Heinzel, S and Hide, W and Hofmann, O and Hörnquist, M and Huminiecki, L and Ikeo, K and Imamoto, N and Inoue, S and Inoue, Y and Ishihara, R and Iwayanagi, T and Jacobsen, A and Kaur, M and Kawaji, H and Kerr, MC and Kimura, R and Kimura, S and Kimura, Y and Kitano, H and Koga, H and Kojima, T and Kondo, S and Konno, T and Krogh, A and Kruger, A and Kumar, A and Lenhard, B and Lennartsson, A and Lindow, M and Lizio, M and Macpherson, C and Maeda, N and Maher, CA and Maqungo, M and Mar, J and Matigian, NA and Matsuda, H and Mattick, JS and Meier, S and Miyamoto, S and Miyamoto-Sato, E and Nakabayashi, K and Nakachi, Y and Nakano, M and Nygaard, S and Okayama, T and Okazaki, Y and Okuda-Yabukami, H and Orlando, V and Otomo, J and Pachkov, M and Petrovsky, N and Plessy, C and Quackenbush, J and Radovanovic, A and Rehli, M and Saito, R and Sandelin, A and Schmeier, S and Schönbach, C and Schwartz, AS and Semple, CA and Sera, M and Severin, J and Shirahige, K and Simons, C and St Laurent, G and Suzuki, M and Suzuki, T and Sweet, MJ and Taft, RJ and Takeda, S and Takenaka, Y and Tan, K and Taylor, MS and Teasdale, RD and Tegnér, J and Teichmann, S and Valen, E and Wahlestedt, C and Waki, K and Waterhouse, A and Wells, CA and Winther, O and Wu, L and Yamaguchi, K and Yanagawa, H and Yasuda, J and Zavolan, M and Hume, DA and Arakawa, T and Fukuda, S and Imamura, K and Kai, C and Kaiho, A and Kawashima, T and Kawazu, C and Kitazume, Y and Kojima, M and Miura, H and Murakami, K and Murata, M and Ninomiya, N and Nishiyori, H and Noma, S and Ogawa, C and Sano, T and Simon, C and Tagami, M and Takahashi, Y and Kawai, J and Hayashizaki, Y
Nature Genetics 41 (5): 553-562. May 2009

Transcriptional features of genomic regulatory blocks.
Akalin, A. and Fredman, D. and Arner, E and Dong, X and Bryne, JC and Suzuki, H. and Daub, CO and Hayashizaki, Y and Lenhard, B
Genome Biology 10 (4): R38. 19 April 2009


Differential evolution of the 13 Atlantic salmon Hox clusters.
Mungpakdee, S. and Seo, H.C. and Angotzi, A.R. and Dong, X. and Akalin, A. and Chourrout, D.
Molecular Biology and Evolution 25 (7): 1333-1343. July 2008


Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates.
Kikuta, H. and Laplante, M. and Navratilova, P. and Komisarczuk, A.Z. and Engstroem, P.G. and Fredman, D. and Akalin, A. and Caccamo, M. and Sealy, I. and Howe, K. and Ghislain, J. and Pezeron, G. and Mourrain, P. and Ellingsen, S. and Oates, A.C. and Thisse, C. and Thisse, B. and Foucher, I. and Adolf, B. and Geling, A. and Lenhard, B. and Becker, T.S.
Genome Research 17 (5): 545-555. May 2007


Predicting the binding affinity of MHC class II peptides.
Altiparmak, F. and Akalin, A. and Ferhatosmanoglu, H.
Computational Systems Bioinformatics 2006 : 331-334. August 2006

Complex loci in human and mouse genomes.
Engstroem, P.G. and Suzuki, H. and Ninomiya, N. and Akalin, A. and Sessa, L. and Lavorgna, G. and Brozzi, A. and Luzi, L. and Tan, S.L. and Yang, L. and Kunarso, G. and Ng, E.L.C. and Batalov, S. and Wahlestedt, C. and Kai, C. and Kawai, J. and Carninci, P. and Hayashizaki, Y. and Wells, C. and Bajic, V.B. and Orlando, V. and Reid, J.F. and Lenhard, B. and Lipovich, L.
PLoS Genetics 2 (4): 564-577. 28 April 2006

This list was generated on Wed Nov 14 02:21:07 2018 CET.
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