2013
2D meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction.
Lorenz R, Bernhart SH, Qin J, Honer Zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF.
IEEE/ACM Trans Comput Biol Bioinform. 2013
[Publisher's Page]
2012
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M.
Nature. 2012 Sep 6;489(7414):57-74
[Publisher's Page]
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R.
Genome Res. 2012 Sep;22(9):1775-89.
[Publisher's Page]
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.
Genome Res. 2012 Sep;22(9):1760-74
[Publisher's Page]
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.
Genome Res. 2012 Sep;22(9):1698-710.
[Publisher's Page]
Landscape of transcription in human cells
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.
Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.
[Publisher's Page]
The GENCODE pseudogene resource.
Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB.
Genome Biol. 2012 Sep 5;13(9):R51. [Epub ahead of print]
[Publisher's Page]
2011
Animal snoRNAs and scaRNAs with exceptional structures
Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.
RNA Biol. 2011 Nov-Dec;8(6):938-46. Epub 2011 Nov 1.
[Publisher's Page]
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. Epub 2011 Apr 19. [Publisher's Page]
2010
Nematode sbRNAs: homologs of vertebrate Y RNAs
Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan H. Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, Peter F. Stadler
J Mol Evol. 2010 Apr;70(4):346-58. Epub 2010 Mar 27
[Publisher's Page]
RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles
Rederstorff M, Bernhart SH, Tanzer A, Zywicki M, Perfler K, Lukasser M, Hofacker IL, Hüttenhofer A
Nucleic Acids Res. (2010) epub
[Publisher's Page]
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB
Nat Biotechnol. 2010 Jan;28(1):47-55. [Publisher's Page]
2009
Evolutionary Genomics of microRNAs and Their Relatives
Andrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin and Ivo L. Hofacker, and Peter F. Stadler
in: Evolutionary Genomics and Systems Biology, edited by Gustavo Caetano-Anolles, John Wiley & Sons. in print
Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens
Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler
Nucleic Acids Res. 37: 1602-1615 (2009)
[Abstract] [Supplement]
[Publisher's Page]
2008
Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals
Lynch VJ, Tanzer A, Wang Y, Leung FC, Gellersen B, Emera D, Wagner GP
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14928-33. Epub 2008 Sep 22
[Publisher's Page]
Folding Kinetics of Large RNAs
Michael Geis, Christoph Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler and Caroline Thurner
J Mol Biol. 2008 May 23; 379(1): 160-73
[Abstract] [Publisher's Page]
2007
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome.
Jan O. Korbel, Alexander Eckehart Urban, Jason P. Affourtit, Brian Godwin, Fabian Grubert, Jan Fredrik Simons, Philip M. Kim, Dean Palejev, Nicholas J. Carriero, Lei Du, Bruce E. Taillon, Zhoutao Chen, Andrea Tanzer, A. C. Eugenia Saunders, Jianxiang Chi, Fengtang Yang, Nigel P. Carter, Matthew E. Hurles, Sherman M. Weissman, Timothy T. Harkins, Mark B. Gerstein, Michael Egholm, Michael Snyder
Science. 2007 Oct 19; 318(5849): 420-6
[Publisher's Page]
Structured RNAs in the ENCODE selected regions of the human genome.
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF
Genome Res. 2007 Jun ; 17(6): 852-64
[Publisher's Page]
Preprint version: [abstract]
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium
Nature 447: 799-816 (2007)
[Publisher's Page]
RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
The Athanasius F. Bompfünewerer RNA Consortium: Rolf Backofen, Christoph Flamm, Claufia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will
J. Exp. Zool. B: Mol. Dev. Evol. 308B: 1-25 (2007).
[Publisher's page]
2006
Evolution of MicroRNAs
Andrea Tanzer, Peter F. Stadler
MicroRNA Protocols, Humana Press, Totowa, NJ, Methods in Molecular Biology 342: 335-350 (2006).
[Publisher's page]
The Expansion of the Metazoan MicroRNA Repertoire
Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried,
Andrea Tanzer, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler,
and The Students of Bioinformatics Computer Labs 2004 and 2005:
Sten Heinze, Alexander ''muppet'' Donath, Sven Findeß, Stephanie Keller, Kevin Peter,
Julian Jöris, Jokab Mühmel, Marco Dienelt (in Leipzig),
Martina Hödl, Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits,
Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor Neumayr,
Reinhard Wohlfart (in Vienna).
BMC Genomics, 7: 15 (2006).
[Publisher's page]
Preprint version: [abstract] [ps] [pdf]
[supplement]
2005
Evolutionary Patterns of Non-Coding RNAs
A.F. Bompfünewerer, Ch. Flamm, C. Fried, G. Fritzsch, I.L. Hofacker, J. Lehmann, K. Missal, A. Mosig, B. Müller, S.J. Prohaska, B.M.R. Stadler, P.F. Stadler, A. Tanzer, S. Washietl, Ch. Witwer
Th. Biosci. 123: 301-369 (2005).
[Publisher's Page]
Preprint version: [abstract] [ps] [pdf]
[supplement]
Comparative promoter region analysis powered by CORG
Christoph Dieterich, Steffen Grossmann, Andrea Tanzer,
Stefan Röpcke, Peter F Arndt, Peter F Stadler, Martin Vingron
BMC Genomics 6: 24 (2005).
[publisher's page]
Preprint version: [abstract] [pdf] [supplement]
Evolution of MicroRNAs Located Within Hox Gene Clusters
Andrea Tanzer, Chris T. Amemiya, Chang-Bae Kim, Peter F. Stadler
J.Exp.Zool.(Mol.Dev.Evol.) 304B: 75-85 (2005).
[Publisher's Page]
Preprint version: [abstract] [ps] [pdf]
[supplement]
2004
Molecular Evolution of a MicroRNA Cluster
Andrea Tanzer, Peter F. Stadler
J.Mol.Biol. 339: 327-335 (2004).
Preprint version: [abstract] [ps] [pdf]
[supplement]