CMB

About CMB
Home Page
People
Publications
Dissertations
 
 
Imprint
 Stefan Haas

Stefan Haas's Home Page

Stefan Haas
MPI for Molecular Genetics
Computational Molecular Biology
Ihnestr. 73
D-14195 Berlin
Phone: + 49 + 30 8413 1164
Fax: + 49 + 30 8413 1152
Email: haas@molgen.mpg.de

Research Interests:

  • 2nd generation sequencing

  • tissue-specific gene regulation

  • alternative promoters (promotion)

  • alternative splicing (spliceNest)

  • EST clustering (GeneNest)

  • large scale primer design (PRIDE)

Short Vita:

  • 01/2001 - today: Project leader (Gene Structure & Array Design) at the Max-Planck-Institute for Molecular Genetics, Computational Molecular Biology, Berlin, Germany
  • 06/1999 - 12/2000: Postdoc at the German Cancer Research Center (DKFZ)

Degrees:

  • 1999: PhD in bioinformatics, Theoretical Bioinformatics, DKFZ, Heidelberg, Germany;
      supervisors: Annemarie Poustka, Martin Vingron, Eckhardt Fuchs

      Thesis: Automated design of oligodesoxynucleotide primers for high-throughput sequencing (in german)

  • 1995: Diploma in biology, University of Heidelberg, Germany;
      supervisor: Helmut Kettenmann

      Thesis: Electrophysiological analysis of ATP-receptors in isolated ameboid microglia derived from acute mouse brain slices (in german)

Publications

    Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA (2012) Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
    Bioinformatics, 28(7):1024-1025

    Huppke P, Brendel C, Kalscheuer V, Korenke GC, Marquardt I, Freisinger P, Christodoulou J, Pitelet G, Wilson C, Gruber-Sedlmayr U, Ullmann R, Haas S, Elpeleg O, Nürnberg U, Nürnberg P, Dad S, Moller LB, Kaler SG, Gärtner J. (2012) Mutations in SLC33A1 cause a lethal autosomal recessive disorder with congenital cataracts and hearing loss associated with low serum copper and ceruloplasmin.
    Am J Hum Genet., 90(1):61-68

    Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.
    Bioinformatics, 28(5):619-627

    Love MI, Mysicková A, Sun R, Kalscheuer V, Vingron M, Haas SA. (2011) Modeling Read Counts for CNV Detection in Exome Sequencing Data.
    Statistical Applications in Genetics and Molecular Biology, 10(1), Article 52

    Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P, Zecha A, Mohseni M, Puttmann L, Vahid LN, Jensen C, Moheb LA, Bienek M, Larti F, Mueller I, Weissmann R, Darvish H, Wrogemann K, Hadavi V, Lipkowitz B, Esmaeeli-Nieh S, Wieczorek D, Kariminejad R, Firouzabadi SG, Cohen M, Fattahi Z, Rost I, Mojahedi F, Hertzberg C, Dehghan A, Rajab A, Banavandi MJ, Hoffer J, Falah M, Musante L, Kalscheuer V, Ullmann R, Kuss AW, Tzschach A, Kahrizi K, Ropers HH. (2011) Deep sequencing reveals 50 novel genes for recessive cognitive disorders.
    Nature, 478(7367):57-63.

    Schraders M, Haas SA, Weegerink NJ, Oostrik J, Hu H, Hoefsloot LH, Kannan S, Huygen PL, Pennings RJ, Admiraal RJ, Kalscheuer VM, Kunst HP, Kremer H. (2011) Next-Generation Sequencing Identifies Mutations of SMPX, which Encodes the Small Muscle Protein, X-Linked, as a Cause of Progressive Hearing Impairment.
    Am J Hum Genet., 88:628-634

    Lin S, Haas S, Zemojtel T, Xiao P, Vingron M, Li R. (2011) Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators.
    Gene, 473(2):139-149

    Warnatz HJ, Querfurth R, Guerasimova A, Cheng X, Haas SA, Hufton AL, Manke T, Vanhecke D, Nietfeld W, Vingron M, Janitz M, Lehrach H, Yaspo ML. (2010) Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
    Nucleic Acids Res., 38(18):6112-6123

    Richard,H., Schulz,M.H., Sultan,M., Nürnberger,A., Schrinner,S., Balzereit,D., Dagand,E., Rasche,A., Lehrach,H., Vingron,M., Haas,S.A., Yaspo,M.L. (2010) Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
    Nucleic Acids Res., 38(10):e112

    Cheng,X., Guerasimova,A., Manke,T., Rosenstiel,P., Haas,S., Warnatz,H.J., Querfurth,R., Nietfeld,W., Vanhecke,D., Lehrach,H., Yaspo,M.L., Janitz,M. (2010) Screening of human gene promoter activities using transfected-cell arrays.
    Gene, 450(1-2):48-54

    Hu,H., Wrogemann,K., Kalscheuer,V., Tzschach,A., Richard,H., Haas,S.A., Menzel,C., Bienek,M., Froyen,G., Raynaud,M., Van Bokhoven,H., Chelly,J., Ropers,H.H., Chen,W. (2009) Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing.
    HUGO J., 3(1-4):41-49

    Roider,H.G., Lenhard,B., Kanhere,A., Haas,S.A., Vingron,M. (2009) CpG-depleted promoters harbor tissue-specific transcription factor binding signals - implications for motif overrepresentation analyses.
    Nucleic Acids Res., 37(19):6305-6315

    Baek,Y.S., Haas,S., Hackstein,H., Bein,G., Santana,M.H., Lehrach,H., Sauer,S. and Seitz,H. (2009) Identification of novel transcriptional regulators involved in macrophage differentiation and activation in U937 cells.
    BMC Immunology, 10:18

    Roider,H.G., Manke,T., O'Keeffe,S., Vingron,M., Haas,S.A. (2009) PASTAA: identifying transcription factors associated with sets of co-regulated genes.
    Bioinformatics, 25(4):435-442

    Sultan,M., Schulz,M.H., Richard,H., Magen,A., Klingenhoff,A., Scherf,M., Seifert,M., Borodina,T., Soldatov,A., Parkhomchuk,D., Schmidt,D., O'Keeffe,S., Haas,S., Vingron,M., Lehrach,H., Yaspo,M.L. (2008) A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome.
    Science, 321(5891):956-960

    Hain,T., Hossain,H., Chatterjee,S.S., Machata,S., Volk,U., Wagner,S., Brors,B., Haas,S., Kuenne,C.T., Billion,A.,Otten,S., Pane-Farre,J., Engelmann,S. and Chakraborty,T. (2008) Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e sigmaB regulon.
    BMC Microbiology, 8:20

    Beisel,C., Buness,A., Roustan-Espinosa,I.M., Koch,B., Schmitt,S., Haas,S.A., Hild,M., Katsuyama,T., Paro,R. (2007) Comparing active and repressed expression states of genes controlled by the Polycomb/Trithorax group proteins.
    Proc. Natl. Acad. Sci., 104(42):16615-16620

    Oberthuer,A., Berthold,F., Warnat,P., Hero,B., Kahlert,Y., Spitz,R., Ernestus,K., Koenig,R., Haas,S., Eils,R., Schwab,M., Brors,B., Westermann,F. and Fischer,M. (2006) Gene-expression based classification of neuroblastoma patients using a customized oligonucleotide-microarray outperforms current clinical risk stratification.
    J. Clin. Oncol., 24:5070-5078

    Hecht,H., Kuhl,H., Haas,S.A., Bauer,S., Poustka,A.J., Lienau,J., Schell,H., Stiege,V., Seitz,V., Reinhardt,R., Duda,G.N., Mundlos,S. and Robinson,P.N. (2006) Gene Identification and Analysis of Transcripts Differentially Regulated in Fracture Healing by EST Sequencing in the Domestic Sheep.
    BMC Genomics, 7:172

    Gupta,S., Vingron,M. and Haas,S.A. (2005) T-STAG: resource and web-interface for tissue-specific transcripts and genes.
    Nucleic Acids Res., 33(Web Server issue):W654-W658

    Belyakin,S.N., Christophides,G.K., Alekseyenko,A.A., Kriventseva,E.V., Belyaeva,E.S., Nanayev,R.A., Makunin,I.V., Heidelberg FlyArray Consortium, Kafatos,F.C., Zhimulev,I.F. (2005) Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories.
    PNAS, 102, 8269-8274

    Hui,J., Hung,L.H., Heiner,M., Schreiner,S., Neumuller,N., Reither,G., Haas,S.A., Bindereif,A. (2005) Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing.
    EMBO J., 24(11), 1988-1998

    Gupta,S., Zink,D., Korn,B., Vingron,M. and Haas,S.A. (2004) Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing.
    BMC Genomics, 5:72

    Gupta,S., Zink,D., Korn,B., Vingron,M. and Haas,S.A. (2004) Genome wide identification and classification of alternative splicing based on EST data.
    Bioinformatics, 20(16), 2579-2585

    Boutros,M., Kiger,A., Armknecht,S., Kerr,K., Hild,M., Koch,B., Haas,S.A., Heidelberg FlyArray, Paro,R. and Perrimon,N. (2004) Genome-wide RNAi Analysis of Cell Growth and Viability in Drosophila Cells.
    Science, 303 (5659), 832-835

    Xue-Franzen,Y., Haas,S.A., Brino,L., Gusnanto,A., Reimers,M., Talibi,D., Vingron,M., Ekwall,K. and Wright,A.P.H. (2004) A DNA microarray for fission yeast: minimal changes after a temperature shift to 36 C.
    Yeast, 21(1), 25-39

    Hild,M., Beckmann,B., Haas,S.A., Koch,B., Solovyev,V., Busold,C., Fellenberg,K., Boutros,M., Vingron,M., Sauer,F., Hoheisel,J.D. and Paro,R. (2003) An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.
    GenomeBiology, 5:R3

    Kalscheuer,V., Freude,K., Musante,L., Jensen,L.R., Yntema,H.G., Gecz,J., Sefiani,A., Hoffmann,K., Moser,B., Haas,S., Gurok,U., Haesler,S., Aranda,B., Nshedjan,A., Tzschach,A., Hartmann,N., Roloff,T.-C., Shoichet,S., Hagens,O., Tao,J., van Bokhoven,H., Turner,G., Chelly,J., Moraine,C., Fryns,J.-P., Nuber,U., Hoeltzenbein,M., Scharff,C., Scherthan,H., Lenzner,S., Hamel,B.C.J., Schweiger,S. and Ropers, H.-H. (2003) Mutations in the polyglutamine-binding protein 1 gene cause X-linked mental retardation.
    Nature Genet., 35 (4), 313-315

    Haas,S.A., Hild,M., Wright,A.P.H., Hain,T., Talibi,D., Vingron,M. (2003) Genome-scale design of PCR primers and long oligomers for DNA microarrays.
    Nucleic Acids Res., 31 (19), 5576-5581

    Coward,E., Haas,S.A. and Vingron,M. (2002) SpliceNest: visualization of gene structure and alternative splicing based on EST clusters.
    Trends Genet., 18 (1), 53-55

    Krause,A., Haas,S.A., Coward,E., Vingron,M. (2002) SYSTERS, GeneNest, SpliceNest: Exploring sequence space from genome to protein.
    Nucleic Acids Res., 30 (1), 299-300

    Boer,J.M., Huber,W., Sültmann,H., Wilmer,F., v.Heydebreck,A., Haas,S., Korn,B., Gunawan,B., Vente,A., Füzesi,L., Vingron,M., Poustka,A. (2001) Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500 element cDNA array.
    Genome Res., 11 (11), 1861-1870

    Petersohn,A., Brigulla,M., Haas,S., Hoheisel,J., Völker,U. and Hecker,M. (2001) Global analysis of the general stress response of Bacillus subtilis.
    J. Bacteriol., 183 (19), 5617-5631

    Haas,S.A., Beissbarth,T., Rivals,E., Krause,A. and Vingron,M. (2000) GeneNest: automated generation and visualization of gene indices.
    Trends Genet., 16 (11), 521-523

    Haas,S., Vingron,M., Poustka,A. and Wiemann,S. (1998) Primer design for large scale sequencing.
    Nucleic Acids Res., 26, 3006-3012

    Haas,S., Brockhaus,J., Verkhratsky, A. and Kettenmann, H. (1996) ATP-induced membrane currents in ameboid microglia acutely isolated from mouse brain slices.
    Neuroscience, 75, 257-261

    Freund,P. and Haas,S. (1995) Erfahrungen bei der Fuzzy-Regelung einer Destillationskolonne, In Fuzzy Logic 3 (ed. Altrock,v.C.), 205-230, Oldenbourg, Munich

Courses

Stefan Haas - Last Change: 12.08.03