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Fast mapping of short sequences with mismatches, insertions and deletions using index structures
Hoffmann, S., Otto, C., Kurtz, S., Sharma, C., Khaitovich, P., Stadler, P. F., Hackermüller, J.
PLoS Comput. Biol., 2009 Sep;5(9):e1000502

Non-Coding {RNA} Annotation of the Genome of Trichoplax adhaerens
Hertel, J., de Jong, D., Marz, M., Rose, D., Tafer, H., Tanzer, A., Schierwater, B., Stadler, P.F.
Nucleic Acids Res., 2009, 37, 1602-1615

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum
Copeland CC, Marz M, Rose D, Hertel J, Brindley PJ, Santana CB, Kehr S, Attolini CS, Stadler PF.
BMC Genomics. 2009 Oct 8;10:464.

Conserved Introns Reveal Novel Transcripts In Drosophila melanogaster
Hiller M., Findeiß S., Lein S., Marz M., Nickel C., Rose D., Schulz C., Backofen R., Prohaska S.J., Reuter G., Stadler P.F.
Genome Res. 2009 Jul;19(7):1289-300.

Mutate now, die later. Evolutionary dynamics with delayed selection.
Munteanu A, Stadler PF.
J Theor Biol. 2009 Oct 7;260(3):412-421.

Partition Function and Base Pairing Probabilities for RNA-RNA Interaction Prediction.
Huang FW, Qin J, Reidys CM, Stadler PF.
Bioinformatics. 2009 Oct 15;25(20):2646-54.

Mutations and lethality in simulated prebiotic networks
Aron Inger, Ariel Solomon, Barak Shenhav, Tsviya Olender, Doron Lancet
J Mol Evol. 2009 Sep 29.

Specialized or flexible feed-forward loop motifs: a question of topology.
Macia J, Widder S, Solé R
BMC Syst Biol. 2009 Aug 31;3:84.

Why are cellular switches Boolean? General conditions for multistable genetic circuits.
Macia J, Widder S, Solé R
J Theor Biol. 2009 Nov 7;261(1):126-35.

Chemoresistance acquisition induces a global shift of expression of aniogenesis-associated genes and increased pro-angogenic activity in neuroblastoma cells.
Michaelis M, Klassert D, Barth S, Suhan T, Breitling R, Mayer B, Hinsch N, Doerr HW, Cinatl J, Cinatl J Jr.
Mol Cancer. 2009 Sep 29;8:80.

Anti-cancer effects of artesunate in a panel of chemoresistant neuroblastoma cell lines.
Michaelis M, Kleinschmidt MC, Barth S, Rothweiler F, Geiler J, Breitling R, Mayer B, Deubzer H, Witt O, Kreuter J, Doerr HW, Cinatl J, Cinatl J Jr.
Biochem Pharmacol. 2009 Aug 19

Mutate now, die later – Evolutionary dynamics with delayed selection
A. Munteanu, P. F. Stadler
BIOINF 09-003 (Preprint 03/09)

GIFtS: Annotation Landscape Analysis with GeneCards
Arye Harel,, Aron Inger, Liora Strichman-Almashanu , Marilyn Safran and Doron Lancet
submitted to BMC bioinformatics 03/09

Genecards: Human Genome Paralog Hunter, Set distillation, Functional scoring and fast searches
Arye Harel , Gil Stelzer , Irina Dalah , Naomi Rosen , Justin Alexander, Michael Shmoish , Tsippi Iny Stein , Alexandra Sirota , Asaf Madi , Tsviya Olender , Aron Inger , Marilyn Safran , Doron Lancet
Presented at: The 12th Israeli Bioinformatics Symposium, 6Apr09, Weizmann Institute
 
Predicting Synthetic Lethality in the Human Protein Interaction Network
Aron Inger, Tsviya Olender and Doron Lancet
Presented at: The 12th Israeli Bioinformatics Symposium, 6Apr09, Weizmann Institute

Genedecks: Paralog hunting and gene-set distillation with Genecards annotation
Many authors...
Submitted to OMICS; 05-09

GeneCards tools for combinatorial annotation and dissemination of human genome information
Doron Lancet, Marilyn Safran, Tsviya Olender, Irina Dalah, Tsippi Iny Stein, Aron Inger, Arye Harel and Gil Stelzer
Departments of Molecular Genetics and Biological Services, the Weizmann Institute of Science
Presented at: General Integration of the Applications of Complexity in Science (GIACS) conference on “Data in Complex Systems”. Palermo, Italy, April 7-9 2008.

GeneCards: One stop site for human gene research
Gil Stelzer, Arye Harel, Irina Dalah, Naomi Rosen, Michael Shmoish, Tsippi Iny Stein, Alexandra Sirota, Asaf Madi, Marilyn Safran, Doron Lancet
Departments of Molecular Genetics and Biological Services, the Weizmann Institute of Science
Presented at: Congress of the Federation of the Israel Societies for Experimental Biology – FISEB (ILANIT), Eilat, Jan 28-31, 2008

GeneCards tools for HUMAN genome information: combinatorial annotation and functional scores
Arye Harel, Gil Stelzer, Irina Dalah, Naomi Rosen, Michael Shmoish, Tsippi Iny Stein, Alexandra Sirota, Asaf Madi, Yaron Solé, Tsviya Olender, Aron Inger, Marilyn Safran, Doron Lancet
Departments of Molecular Genetics and Biological Services, the Weizmann Institute of Science
Presented at: The 11th Israeli Bioinformatics Symposium (IBS). Tel Aviv University, April 27th, 2008.

Synthetic Lethality in Simulated Catalytic Networks
Aron Inger, Tsviya Olender, Doron Lancet
Department of Molecular genetics, Weizmann Institute of Science
Presented at: The 11th Israeli Bioinformatics Symposium (IBS).Tel-Aviv University, April 27th, 2008.

Human synthetic lethal interference from yeast experimental datasets
Núria Conde-Pueyo, Andreea Munteanu, Ricard V. Solé, Carlos Rodriguez-Caso
ICREA-Complex Systems Lab, Universitat Pompeu Fabra (GRIB-PRBB), Barcelona
Presented at: ESF Workshop Systems Biology in Medicine (SBM), Barcelona, May 8-10,2008.

Goals and pitfalls of gene-network interference methods: A comparative study from virtual microarrays and network dynamics
J. Goñi, C. Rodriguez-Caso, R.V. Solé, P. Villoslada, A. Munteanu
Presented at: Net-Works 2008, Pamplona, June 9-11, 2008.

Duplicated RNA genes in teleost fish genomes
Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF
J. Bioinf. and Comp. Biol. In press

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences
Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.
Genomics. 92:65-74. 2008.

Structural profiles of miRNA families from pairwise clustering
Kaczkowski B., Torarinsson E., Reiche K., Havgaard J. H., Stadler P. F., Gorodkin J.
Bioinformatics. in press.

“Genes“
Prohaska S. J., Stadler P.F.
Th. Biosci. in press

A story of Growing Confusion: Genes and Their Regulation
Prohaska S. J., Stadler P.F.
BIOMAT-2007: International Symposium on Mathematical and Computational Biology.   325-345 . Mondaini, Rubem P. and Dilao, Rui (editors). World Scientific. Singapore. 2008

Non-coding RNAs (Bookchapter)
Donath A, Findeiß S, Hertel J, Marz M, Otto W, Schulz C, Stadler PF, Wirth S.
Evolutionary Genomics. Gustavo Caetano-Annoles  (editor)

Identification of Stat3 controlled miRNAs involved in oncogenesis
Hackermüller J, Löffler D, Brocke-Heidrich K, Pfeifer G, Fried C, Kretzschmar AK, Ullmann K, Burger R, Gramatzki M, Blumert C, Bauer K, Cvijic H, Stadler PF,Horn F
RNA 2007 Twelfth annual meeting of the RNASociety, 2007, May 29 - June 3, Book of abstracts:176, Madison, WI, USA.

RNA-RNA interactions in living cells: Development of efficient high throughput methods to unhide the multiple targets of miRNAs
Kretzschmar AK, Michel M, Stadler PF, Horn PF, Kerstin U, Schulz C, Hackermüller J.
RNA 2007 Twelth annual meeting of the RNASociety, 2007, May 29 - June 3, Book of abstracts 321, Madison, WI, USA.

Development of methods to unhide the multiple targets of miRNAs
Kretzschmar AK, Michel M, Ullmann K, Schulz C, Stadler PF, Horn F, Hackermüller J.
Keystone Symposium “MicroRNA and Cancer”, June 8 - 12, Keystone, CO, USA.

Press release “Genetischer Müll als Ordnungshüter”, Fraunhofer Gesellschaft zur Förderung der angewandten Forschung e.V., München, 14.6.2007

Press conference “Genetischer Müll als Ordnungshüter“, Fraunhofer IZI, Leipzig, 19.6.2007

Interview: J. Hackermüller in „Wissen Hoch 12. Erkenntnisse und Themen die uns bewegen 2007/2008“. Frater H, Podbregar N, Lohmann D . Springer 2007.

Context Analysis of Differential Gene Expression Data (Poster)
P. Perco, A. Bernthaler, I. Mülberger, M. Haiduk, C. Stadler, R. Fechete, A. Lukas, R. Oberbauer, B. Mayer
Presented at the 2nd International Conference on Bioinformatics Research and Development. Vienna, Austria: Jul 7-9, 2008

Disease associated transcription factor modules (invited talk)
M. Wiesinger, P. Perco, J. Söllner, A. Lukas, B. Mayer
Presented at the 6th International Conference on Pathways, Networks, and Systems Medicine. Chania, Greece: Jun 16-21, 2008

A dependency graph approach for analyzing differential gene expression data of B-cell lymphomas
A. Bernthaler, I. Mühlberger, R. Fechete, P. Perco, A. Lukas and B. Mayer
Presented at the 6th International Conference on Pathways, Networks, and Systems Medicine. Chania, Greece: Jun 16-21, 2008

A dependency graph approach for analysis of differential gene expression profiles.
A. Bernthaler, I. Mühlberger, R. Fechete, P. Perco, A. Lukas and B. Mayer
Molecular Systems Biology, 5, 1720-1731 (2009).

Lateral inhibition in evo-devo. Minimal robust networks of development
Andreea Munteanu and Ricard V. Solé
Presented at the 9th International Conference on Systems Biology (ICSB). Gotheburg: Aug 22-28, 2008.

Neutrality and Robustness in evo-devo: emergence of lateral
Andreea Munteanu and Ricard V. Solé
PLoS Comput Biol 2008, 4(11): e1000226.

Evolution of vault RNAs
P. F. Stadler, J. J.-L. Chen, J. Hackermüller, S. Hoffmann, F. Horn, P. Khaitovich, A. Kretzschmar, A. Mosig, S. J. Prohaska, X. Qi, K. Schutt, K. Ullmann
(Submitted: 31th. October at J. Mol. Biol.)

Bioinformatic Analysis of gene expression profiles in chemosensitive and chemoresistant cancer cells to identify substances that overcome resistance
S. Barth, D. Klassert, K. Totz, C.Keller, B. Mayer, J. Cinatl, M. Michaelis
Presented at: 19th International Scientific Conference Mittweida, Germany: Nov. 05-06, 2008.
Published at: Scientific Reports (ISSN 1437-7624), Vol. 8 (2008), 23-26

Functional distance measure and reconstruction of context sensitivity in protein networks with dynamical hierarchies (Poster)
A. Bernthaler, P. Perco, R. Rapberger, J. Soellner, I. Mühlberger, M. Wiesinger, A. Lukas, R. Freund, M. Haiduk, B. Mayer
Presented at: Pacific Symposium on Biocomputing. Maui, Hawaii: Jan 4-8, 2008

Non-protein coding RNA – the dark matter of genomics (Talk; invited Seminar)
Hackermüller J.
Presented at: University Halle/Saale, Germany: September 20, 2007

Robustness of the interlinked dual-time positive feedback loops (Poster)
A. Munteanu, C. Rodríguez-Caso & R.V. Solé
ICREA-Complex Systems Lab, GRIB-Universitat Pompeu Fabra
Presented at: Congress of the Spanish Society of Biochemistry and Molecular Biology (SEBBM), Málaga, Spain: Sept 12-15, 2007
Link: http://complex.upf.es/~andreea/posters.html

Television interview: SWR3 “Service Gesundheit”, August 20, 2007; Hackermüller J.

NcDNAlign - a flexible and efficient package for the generation of non- protein coding multiple alignments from genomic sequences (Poster)
Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.
Presented at: 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)& 6th European Conference on Computational Biology (ECCB), Vienna, Austria: July 21-25, 2007

GeneDecks annotation combinatorics and unification for human genes
M. Safran, I.Dalah, S. Ron, M. Shmoish, T. Iny-Stein, N. Rosen, A. Madi, A. Sirota, G. Stelzer and D. Lancet;
Departments of Biological Services and Molecular Genetics – The Weitzmann Institute of Science
Presented at: 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)& 6th European Conference on Computational Biology (ECCB), Vienna, Austria: July 21-25

dynaNET: A novel computational framework for deriving functional context from omics data
A. Bernthaler, P. Perco, R. Rapberger, M. Haiduk, J. Söllner, C. Siehs, C. Pleban, M. Wiesinger, C. Stadler, A. Lukas and B. Mayer;
emergentec biodevelopment GmbH
Presented at: 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)& 6th European Conference on Computational Biology (ECCB), Vienna, Austria: July 21-25, 2007

Radio interview: RBB “Die Profis”, June 23, 2007; Hackermüller J.

Television interview: Leipzig Fernsehen; June 19, 2007; Hackermüller J.

Transcriptional control of a microRNA gene by Stat3 emerges as a major contribution to its oncogenicity (Talk; invited Seminar)
Hackermüller J.
Presented at: Osborne Memorial Laboratories, Yale University, New Haven, CT, USA: June 5, 2007

Nicht proteinkodierende RNA - die dunkle Materie der modernen Genomforschung (Talk; invited Seminar)
Hackermüller J.
Presented at: Bioinformatics meets Life Science: Leipzig, Germany: March 6, 2007