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Jorg Hackermuller

Research Profile

Chemicals & Drugs

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Physiology

Transcription, Genetic

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K Boll; Friedemann Horn; K Kasack; Antje K Kretzschmar; N Mörbt; Kristin Reiche; J Schalken; J M Tomm; Gerald W Verhaegh; Martin von Bergen; Jorg Hackermuller
MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostate carcinoma.
Christian Otto; Kristin Reiche; Jorg Hackermuller
Detection of differentially expressed segments in tiling array data.
Dominic Rose; Katharina Schutt; Rolf Backofen; Jorg Hackermuller; Michael Hiller; Peter F Stadler
Computational discovery of human coding and non-coding transcripts with conserved splice sites.

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All Publications

2013: K Boll; Friedemann Horn; K Kasack; Antje K Kretzschmar; N Mörbt; Kristin Reiche; J Schalken; J M Tomm; Gerald W Verhaegh; Martin von Bergen; Jorg Hackermuller
MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostate carcinoma.
Oncogene 2013;32(3):277-85.
2012: Christian Otto; Kristin Reiche; Jorg Hackermuller
Detection of differentially expressed segments in tiling array data.
Bioinformatics (Oxford, England) 2012;28(11):1471-9.
2011: Dominic Rose; Katharina Schutt; Rolf Backofen; Jorg Hackermuller; Michael Hiller; Peter F Stadler
Computational discovery of human coding and non-coding transcripts with conserved splice sites.
Bioinformatics (Oxford, England) 2011;27(14):1894-900.
2011: Kristin Reiche; Katharina Schutt; Kerstin Boll; Friedemann Horn; Jorg Hackermuller
Bioinformatics for RNomics.
Methods in molecular biology (Clifton, N.J.) 2011;719():299-330.
2010: Cynthia M Sharma; Steve Hoffmann; Fabien Darfeuille; Jérémy Reignier; Sven Findeiss; Alexandra Sittka; Sandrine Chabas; Kristin Reiche; Jorg Hackermuller; Richard Reinhardt; Peter F Stadler; Jörg Vogel
The primary transcriptome of the major human pathogen Helicobacter pylori.
Nature 2010;464(7286):250-5.
2009: Steve Hoffmann; Christian Otto; Stefan Kurtz; Cynthia M Sharma; Philipp Khaitovich; Jörg Vogel; Peter F Stadler; Jorg Hackermuller
Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
PLoS computational biology 2009;5(9):e1000502.
2009: Peter F Stadler; Julian J-L Chen; Jorg Hackermuller; Steve Hoffmann; Friedemann Horn; Phillip Khaitovich; Antje K Kretzschmar; Axel Mosig; Sonja J Prohaska; Xiaodong Qi; Katharina Schutt; Kerstin Ullmann
Evolution of vault RNAs.
Molecular biology and evolution 2009;26(9):1975-91.
2008: Dominic Rose; Julian Jöris; Jorg Hackermuller; Kristin Reiche; Qiang Li; Peter F Stadler
Duplicated RNA genes in teleost fish genomes.
Journal of bioinformatics and computational biology 2008;6(6):1157-75.
2008: Elisabeth Sonnleitner; Theresa Sorger-Domenigg; Monika J Madej; Sven Findeiss; Jorg Hackermuller; Alexander Hüttenhofer; Peter F Stadler; Udo Bläsi; Isabella Moll
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.
Microbiology (Reading, England) 2008;154(Pt 10):3175-87.
2008: Steve Hoffmann; Sabine Cepok; Verena Grummel; Klaus Lehmann-Horn; Jorg Hackermuller; Jörg Hackermueller; Peter F Stadler; Hans-Peter Hartung; Achim Berthele; Florian Deisenhammer; Ralf Wassmuth; Ralf Wasmuth; Bernhard Hemmer
HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis.
American journal of human genetics 2008;83(2):219-27.
2008: Dominic Rose; Jana Hertel; Kristin Reiche; Peter F Stadler; Jorg Hackermuller
NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.
Genomics 2008;92(1):65-74.
2007: Dennis Löffler; Katja Brocke-Heidrich; Gabriele Pfeifer; Claudia Stocsits; Jorg Hackermuller; Antje K Kretzschmar; Renate Burger; Martin Gramatzki; Conny Blumert; Kay Bauer; Helena Cvijic; A Kerstin Ullmann; Peter F Stadler; Friedemann Horn
Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer.
Blood 2007;110(4):1330-3.
2007: Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason Dillon Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A. Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jorg Hackermuller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; piero carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos Antonarakis; Yutao Fu; Eric Green; Ulaş Karaöz; Adam Siepel; James TAYLOR; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Richmond Todd; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Goncalo Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature 2007;447(7146):799-816.
2007: Philipp Kapranov; Jill Cheng; Sujit Dike; David A Nix; Radharani Duttagupta; Aarron T Willingham; Peter F Stadler; Jana Hertel; Jorg Hackermuller; Ivo L Hofacker; Ian Bell; Evelyn Cheung; Jorg Drenkow; Erica Dumais; Sandeep Patel; Gregg Helt; Madhavan Ganesh; Srinka Ghosh; Antonio Piccolboni; Victor Sementchenko; Hari Tammana; Thomas Gingeras
RNA maps reveal new RNA classes and a possible function for pervasive transcription.
Science (New York, N.Y.) 2007;316(5830):1484-8.
2007: Stefan Washietl; Jakob S Pedersen; Jan O Korbel; Claudia Stocsits; Andreas R Gruber; Jorg Hackermuller; Jana Hertel; Manja Lindemeyer; Kristin Reiche; Andrea Tanzer; Catherine Ucla; Carine Wyss; Stylianos E Antonarakis; France Denoeud; Julien Lagarde; Jorg Drenkow; Philipp Kapranov; Thomas Gingeras; Roderic Guigó; Michael Snyder; Mark Gerstein; Alexandre Reymond; Ivo L Hofacker; Peter F Stadler
Structured RNAs in the ENCODE selected regions of the human genome.
Genome research 2007;17(6):852-64.
2007: Rolf Backofen; Stephan H Bernhart; Christoph Flamm; Claudia Fried; Guido Fritzsch; Jorg Hackermuller; Jana Hertel; Ivo L Hofacker; Kristin Missal; Axel Mosig; Sonja J Prohaska; Dominic Rose; Peter F Stadler; Andrea Tanzer; Stefan Washietl; Sebastian Will
RNAs everywhere: genome-wide annotation of structured RNAs.
Journal of experimental zoology. Part B, Molecular and developmental evolution 2007;308(1):1-25.
2007: Dominic Rose; Jorg Hackermuller; Stefan Washietl; Kristin Reiche; Jana Hertel; Sven Findeiss; Peter F Stadler; Sonja J Prohaska
Computational RNomics of drosophilids.
BMC genomics 2007;8():406.
2006: Ulrike Mückstein; Hakim Tafer; Jorg Hackermuller; Stephan H Bernhart; Peter F Stadler; Ivo L Hofacker
Thermodynamics of RNA-RNA binding.
Bioinformatics (Oxford, England) 2006;22(10):1177-82.
2005: Jorg Hackermuller; Nicole-Claudia Meisner; Manfred Auer; Markus Jaritz; Peter F Stadler
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model.
Gene 2005;345(1):3-12.
2004: Nicole-Claudia Meisner; Jorg Hackermuller; Volker Uhl; András Aszódi; Markus Jaritz; Manfred Auer
mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure.
Chembiochem : a European journal of chemical biology 2004;5(10):1432-47.