Bioinformatics Core

The Bioinformatics Core offers a wide range of bioinformatics services for researchers at the UKE and related institutions. The main focus is on the analysis of high-throughput sequencing data. Services offered include data analysis, consulting, software development, and training.

Services

  • For many data analysis tasks standardized workflows, following published best-practices, are established at the Bioinformatics Core. For solving tasks were these workflows do not suffice, customized and integrative solutions are provided. In both cases the facility operates with a high degree of transparency, explaining and documenting analysis strategies and assessing results jointly with clients.

    Examples of applications for which bioinformatical solutions are provided:

    • RNA-Seq (differential and absolute expression, fusion genes, small RNAs)
    • Genotyping
    • ChIP-Seq
    • Metagenomics and Metatranscriptomics
    • Assemblies
    • Gene Prediction
    • Ribo-Seq
    • MeDIP-Seq
    • Bisulfite Sequencing
    • and many other applications

  • The facility provides bioinformatical consulting on various aspects of sequencing and sequence data analysis. Many research projects are supported over their whole live cycle. This includes initial project planning, official support for grant applications and documentation of bioinformatical methods for publications.
    Additionally the Bioinformatics Core gives advice on hardware and software solutions for workgroups who plan to carry out some or all analyzes by themselves.

  • The Bioinformatics Core has substantial expertise in developing custom software and workflows for sequence data analysis. Software development, however, is a time consuming process and thus the facility is forced to carefully evaluate the feasibility of proposed projects.

  • Regularly two workshops are held: “Applied Bioinformatics”, focuses on bioinformatics techniques for laboratory use and “An Introduction to Scientific Programming” aims to teach basic programming skills to attendees without substantial programming experience. The Bioinformatics Core is open for suggestions on other bioinformatical topics.

Contact

Malik Alawi
Malik Alawi
M. Sc.
  • Core manager
Location

W34, 1st Floor, Room number 116
Daniela Börnigen (derzeit in Elternzeit)
Dr.
Daniela Börnigen (derzeit in Elternzeit)
  • Bioinformatics Facility
Location

W34, 1st Floor, Room number 117.1
Mohammed Imtiaz
Mohammed Aslam Imtiaz
M. Sc.
  • Bioinformatics Facility
Location

W34, 1st Floor, Room number 117
Sebastian Kral
Sebastian Kral
M. Sc.
  • Bioinformatics Facility
Contact

Location

W34, 1st Floor, Room number 117
Minyue Qi
Minyue Qi
M. Sc.
  • Bioinformatics Facility
Contact

Location

W34, 1st Floor, Room number 117.1

References / Publications

isTab: true
Zurück
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
Vor

TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease
Neelagandan N, Gonnella G, Dang S, Janiesch P, Miller K, Küchler K, Marques R, Indenbirken D, Alawi M, Grundhoff A, Kurtz S, Duncan K
NUCLEIC ACIDS RES. 2019;47(1):341-361.

Next-generation sequencing of 32 genes associated with hereditary aortopathies and related disorders of connective tissue in a cohort of 199 patients
Renner S, Schüler H, Alawi M, Kolbe V, Rybczynski M, Woitschach R, Sheikhzadeh S, Stark V, Olfe J, Roser E, Seggewies F, Mahlmann A, Hempel M, Hartmann M, Hillebrand M, Wieczorek D, Volk A, Kloth K, Koch-Hogrebe M, Abou Jamra R, Mitter D, Altmüller J, Wey-Fabrizius A, Petersen C, Rau I, Borck G, Kubisch C, Mir T, von Kodolitsch Y, Kutsche K, Rosenberger G
GENET MED. 2019 [Epub ahead of print].

Lineage-specific control of TFIIH by MITF determines transcriptional homeostasis and DNA repair
Seoane M, Buhs S, Iglesias P, Strauss J, Puller A, Müller J, Gerull H, Feldhaus S, Alawi M, Brandner J, Eggert D, Du J, Thomale J, Wild P, Zimmermann M, Sternsdorf T, Schumacher U, Nollau P, Fisher D, Horstmann M
ONCOGENE. 2019;38(19):3616-3635.

T-lymphocyte-specific knockout of IKK-2 or NEMO induces T17 cells in an experimental nephrotoxic nephritis mouse model
Guo L, Huang J, Chen M, Piotrowski E, Song N, Zahner G, Paust H, Alawi M, Geffers R, Thaiss F
FASEB J. 2018 [Epub ahead of print];fj201800485RR.

The novel RAF1 mutation p.(Gly361Ala) located outside the kinase domain of the CR3 region in two patients with Noonan syndrome, including one with a rare brain tumor
Harms F, Alawi M, Amor D, Tan T, Cuturilo G, Lissewski C, Brinkmann J, Schanze D, Kutsche K, Zenker M
AM J MED GENET A. 2018;176(2):470-476.

Elsahy-Waters syndrome is caused by biallelic mutations in CDH11
Harms F, Nampoothiri S, Anazi S, Yesodharan D, Alawi M, Kutsche K, Alkuraya F
AM J MED GENET A. 2018;176(2):477-482.

Coinheritance of biallelic SLURP1 and SLC39A4 mutations cause a severe genodermatosis with skin peeling and hair loss all over the body
Harms F, Nampoothiri S, Kortüm F, Thomas J, Panicker V, Alawi M, Altmüller J, Yesodharan D, Kutsche K
BRIT J DERMATOL. 2018;179(5):1192-1194.

Clinical and genetic spectrum of AMPD2-related pontocerebellar hypoplasia type 9
Kortüm F, Jamra R, Alawi M, Berry S, Borck G, Helbig K, Tang S, Huhle D, Korenke G, Hebbar M, Shukla A, Girisha K, Steinlin M, Waldmeier-Wilhelm S, Montomoli M, Guerrini R, Lemke J, Kutsche K
EUR J HUM GENET. 2018;26(5):695-708.

Reply: ATAD1 encephalopathy and stiff baby syndrome: a recognizable clinical presentation
Piard J, Essien Umanah G, Harms F, Abalde-Atristain L, Amram D, Chang M, Chen R, Alawi M, Salpietro V, Rees M, Chung S, Houlden H, Verloes A, Dawson T, Dawson V, Van Maldergem L, Kutsche K
BRAIN. 2018;141(6):e50.

A homozygous ATAD1 mutation impairs postsynaptic AMPA receptor trafficking and causes a lethal encephalopathy
Piard J, Umanah G, Harms F, Abalde-Atristain L, Amram D, Chang M, Chen R, Alawi M, Salpietro V, Rees M, Chung S, Houlden H, Verloes A, Dawson T, Dawson V, Van Maldergem L, Kutsche K
BRAIN. 2018;141(3):651-661.

Comparative study of whole genome amplification and next generation sequencing performance of single cancer cells
Babayan A, Alawi M, Gormley M, Müller V, Wikman H, McMullin R, Smirnov D, Li W, Geffken M, Pantel K, Joosse S
ONCOTARGET. 2017;8(34):56066-56080.

Novel poly-uridine insertion in the 3'UTR and E2 amino acid substitutions in a low virulent classical swine fever virus
Coronado L, Liniger M, Muñoz-González S, Postel A, Pérez L, Pérez-Simó M, Perera C, Frías-Lepoureau M, Rosell R, Grundhoff A, Indenbirken D, Alawi M, Fischer N, Becher P, Ruggli N, Ganges L
VET MICROBIOL. 2017;201:103-112.

Pregnancy-Related Immune Adaptation Promotes the Emergence of Highly Virulent H1N1 Influenza Virus Strains in Allogenically Pregnant Mice
Engels G, Hierweger A, Hoffmann J, Thieme R, Thiele S, Bertram S, Dreier C, Resa-Infante P, Jacobsen H, Thiele K, Alawi M, Indenbirken D, Grundhoff A, Siebels S, Fischer N, Stojanovska V, Muzzio D, Jensen F, Karimi K, Mittrücker H, Arck P, Gabriel G
CELL HOST MICROBE. 2017;21(3):321-333.

Recovery of the first full-length genome sequence of a parapoxvirus directly from a clinical sample
Günther T, Haas L, Alawi M, Wohlsein P, Marks J, Grundhoff A, Becher P, Fischer N
SCI REP-UK. 2017;7(1):3734.

Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism
Harms F, Girisha K, Hardigan A, Kortüm F, Shukla A, Alawi M, Dalal A, Brady L, Tarnopolsky M, Bird L, Ceulemans S, Bebin M, Bowling K, Hiatt S, Lose E, Primiano M, Chung W, Juusola J, Akdemir Z, Bainbridge M, Charng W, Drummond-Borg M, Eldomery M, El-Hattab A, Saleh M, Bézieau S, Cogné B, Isidor B, Küry S, Lupski J, Myers R, Cooper G, Kutsche K
AM J HUM GENET. 2017;100(1):117-127.

Optimization of design and production strategies for novel adeno-associated viral display peptide libraries
Körbelin J, Hunger A, Alawi M, Sieber T, Binder M, Trepel M
GENE THER. 2017;24(8):470-481.

Acute Liver Failure Meets SOPH Syndrome: A Case Report on an Intermediate Phenotype
Kortüm F, Marquardt I, Alawi M, Korenke G, Spranger S, Meinecke P, Kutsche K
PEDIATRICS. 2017;139(1):pii: e20160550.

Long-term CD38 saturation by daratumumab interferes with diagnostic myeloma cell detection
Oberle A, Brandt A, Alawi M, Langebrake C, Janjetovic S, Wolschke C, Schütze K, Bannas P, Kröger N, Koch-Nolte F, Bokemeyer C, Binder M
HAEMATOLOGICA. 2017;102(9):e368-e370.

Monitoring multiple myeloma by next-generation sequencing of V(D)J rearrangements from circulating myeloma cells and cell-free myeloma DNA
Oberle A, Brandt A, Voigtländer M, Thiele B, Radloff J, Schulenkorf A, Alawi M, Akyüz N, März M, Ford C, Krohn-Grimberghe A, Binder M
HAEMATOLOGICA. 2017;102(6):1105-1111.

Mutational landscape reflects the biological continuum of plasma cell dyscrasias
Rossi A, Voigtländer M, Janjetovic S, Thiele B, Alawi M, März M, Brandt A, Hansen T, Radloff J, Schön G, Hegenbart U, Schönland S, Langer C, Bokemeyer C, Binder M
BLOOD CANCER J. 2017;7(2):e537.

Pegivirus Infection in Domestic Pigs, Germany
Baechlein C, Grundhoff A, Fischer N, Alawi M, Hoeltig D, Waldmann K, Becher P
EMERG INFECT DIS. 2016;22(7):1312-4.

Runx1 downregulates stem cell and megakaryocytic transcription programs that support niche interactions
Behrens K, Triviai I, Schwieger M, Tekin N, Alawi M, Spohn M, Indenbirken D, Ziegler M, Müller U, Alexander W, Stocking C
BLOOD. 2016;127(26):3369-81.

Immunosuppressive Yersinia Effector YopM Binds DEAD Box Helicase DDX3 to Control Ribosomal S6 Kinase in the Nucleus of Host Cells
Berneking L, Schnapp M, Rumm A, Trasak C, Ruckdeschel K, Alawi M, Grundhoff A, Kikhney A, Nolte F, Buck F, Perbandt M, Betzel C, Svergun D, Hentschke M, Aepfelbacher M
PLOS PATHOG. 2016;12(6):e1005660.

Correlation of somatic mutations with outcome after FLAMSA-busulfan sequential conditioning and allogeneic stem cell transplantation in patients with MDS
Christopeit M, Badbaran A, Alawi M, Zabelina T, Zeck G, Wolschke C, Ayuketang F, Kröger N
EUR J HAEMATOL. 2016;97(3):288-96.

Indication of Horizontal DNA Gene Transfer by Extracellular Vesicles
Fischer S, Cornils K, Speiseder T, Badbaran A, Reimer R, Indenbirken D, Grundhoff A, Brunswig-Spickenheier B, Alawi M, Lange C
PLOS ONE. 2016;11(9):e0163665.

A novel multiple joint dislocation syndrome associated with a homozygous nonsense variant in the EXOC6B gene
Girisha K, Kortüm F, Shah H, Alawi M, Dalal A, Bhavani G, Kutsche K
EUR J HUM GENET. 2016;24(8):1206-10.

Essential control of early B-cell development by Mef2 transcription factors
Herglotz J, Unrau L, Hauschildt F, Fischer M, Kriebitzsch N, Alawi M, Indenbirken D, Spohn M, Müller U, Ziegler M, Schuh W, Jäck H, Stocking C
BLOOD. 2016;127(5):572-81.

Pulmonary Targeting of Adeno-associated Viral Vectors by Next-generation Sequencing-guided Screening of Random Capsid Displayed Peptide Libraries
Körbelin J, Sieber T, Michelfelder S, Lunding L, Spies E, Hunger A, Alawi M, Rapti K, Indenbirken D, Müller O, Pasqualini R, Arap W, Kleinschmidt J, Trepel M
MOL THER. 2016;24(6):1050-61.

Presence of atypical porcine pestivirus (APPV) genomes in newborn piglets correlates with congenital tremor
Postel A, Hansmann F, Baechlein C, Fischer N, Alawi M, Grundhoff A, Derking S, Tenhündfeld J, Pfankuche V, Herder V, Baumgärtner W, Wendt M, Becher P
SCI REP-UK. 2016;6:27735.

Versatility of Biofilm Matrix Molecules in Staphylococcus epidermidis Clinical Isolates and Importance of Polysaccharide Intercellular Adhesin Expression during High Shear Stress
Schaeffer C, Hoang T, Sudbeck C, Alawi M, Tolo I, Robinson D, Horswill A, Rohde H, Fey P
mSphere. 2016;1(5):e00165-16..

A transplant “immunome” screening platform defines a targetable epitope fingerprint of multiple myeloma
Schieferdecker A, Oberle A, Thiele B, Hofmann F, Göthel M, Miethe S, Hust M, Braig F, Voigt M, Pein U, Nolte F, Haag F, Alawi M, Indenbirken D, Grundhoff A, Bokemeyer C, Bacher U, Kröger N, Binder M
BLOOD. 2016;127(25):3202-14.

Functional dissection of an alternatively spliced herpesvirus gene by splice site mutagenesis
Schommartz T, Loroch S, Alawi M, Grundhoff A, Sickmann A, Brune W
J VIROL. 2016;90(9):4626-36.

De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype
Shashi V, Pena L, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin H, Cho M, Stong N, Hickey S, Shuss C, , Freemark M, Bellet J, Keels M, Bonner M, El-Dairi M, Butler M, Kranz P, Stumpel C, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki M, Hoischen A, Need A, Goldstein D, Kortüm F
AM J HUM GENET. 2016;99(4):991-999.

Rapid Capture Next-Generation Sequencing in Clinical Diagnostics of Kinase Pathway Aberrations in B-Cell Precursor ALL
Stadt U, Escherich G, Indenbirken D, Alawi M, Adao M, Horstmann M
PEDIATR BLOOD CANCER. 2016;63(7):1283-6.

Homozygous HOXB1 loss-of-function mutation in a large family with hereditary congenital facial paresis
Vogel M, Velleuer E, Schmidt-Jiménez L, Mayatepek E, Borkhardt A, Alawi M, Kutsche K, Kortüm F
AM J MED GENET A. 2016;170(7):1813-9.

An AP4B1 frameshift mutation in siblings with intellectual disability and spastic tetraplegia further delineates the AP-4 deficiency syndrome
Abdollahpour H, Alawi M, Kortüm F, Beckstette M, Seemanova E, Komárek V, Rosenberger G, Kutsche K
EUR J HUM GENET. 2015;23(2):256-259.

Epidermal growth factor receptor mutation mediates cross-resistance to panitumumab and cetuximab in gastrointestinal cancer
Braig F, März M, Schieferdecker A, Schulte A, Voigt M, Stein A, Grob T, Alawi M, Indenbirken D, Kriegs M, Engel E, Vanhoefer U, Grundhoff A, Loges S, Riecken K, Fehse B, Bokemeyer C, Binder M
ONCOTARGET. 2015;6(14):12035-47.

SCNT-derived ESCs with mismatched mitochondria trigger an immune response in allogeneic hosts
Deuse T, Wang D, Stubbendorff M, Itagaki R, Grabosch A, Greaves L, Alawi M, Grünewald A, Hu X, Hua X, Velden J, Reichenspurner H, Robbins R, Jaenisch R, Weissman I, Schrepfer S
CELL STEM CELL. 2015;16(1):33-8.

Identification of a Novel Hepacivirus in Domestic Cattle from Germany
Fischer N, Baechlein C, Grundhoff A, Alawi M, Indenbirken D, Postel A, Baron A, Offinger J, Becker K, Beineke A, Rehage J, Becher P
J VIROL. 2015;89(14):7007-15.

Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples
Fischer N, Indenbirken D, Meyer T, Lütgehetmann M, Lellek H, Spohn M, Aepfelbacher M, Alawi M, Grundhoff A
J CLIN MICROBIOL. 2015;53(7):2238-50.

Deciphering the microRNA signature of pathological cardiac hypertrophy by engineered heart tissue- and sequencing-technology
Hirt M, Werner T, Indenbirken D, Alawi M, Demin P, Kunze A, Stenzig J, Starbatty J, Hansen A, Fiedler J, Thum T, Eschenhagen T
J MOL CELL CARDIOL. 2015;81:1-9.

Mutations in KCNH1 and ATP6V1B2 cause Zimmermann-Laband syndrome
Kortüm F, Caputo V, Bauer C, Stella L, Ciolfi A, Alawi M, Bocchinfuso G, Flex E, Paolacci S, Dentici M, Grammatico P, Korenke G, Leuzzi V, Mowat D, Nair L, Nguyen T, Thierry P, White S, Dallapiccola B, Pizzuti A, Campeau P, Tartaglia M, Kutsche K
NAT GENET. 2015;47(6):661-7.

Emergence of daptomycin non-susceptibility in colonizing vancomycin-resistant Enterococcus faecium isolates during daptomycin therapy
Lellek H, Franke G, Ruckert C, Wolters M, Wolschke C, Christner M, Büttner H, Alawi M, Kröger N, Rohde H
INT J MED MICROBIOL. 2015;305(8):902-909.

Close relationship of ruminant pestiviruses and classical Swine Fever virus
Postel A, Schmeiser S, Oguzoglu T, Indenbirken D, Alawi M, Fischer N, Grundhoff A, Becher P
EMERG INFECT DIS. 2015;21(4):668-72.

A Comprehensive Analysis of Replicating Merkel Cell Polyomavirus Genomes Delineates the Viral Transcription Program and Suggests a Role for mcv-miR-M1 in Episomal Persistence
Theiss J, Günther T, Alawi M, Neumann F, Tessmer U, Fischer N, Grundhoff A
PLOS PATHOG. 2015;11(7):e1004974.

Mutations in NDUFB11, Encoding a Complex I Component of the Mitochondrial Respiratory Chain, Cause Microphthalmia with Linear Skin Defects Syndrome
van Rahden V, Fernandez-Vizarra E, Alawi M, Brand K, Fellmann F, Horn D, Zeviani M, Kutsche K
AM J HUM GENET. 2015;96(4):640-50.

Rapid Metagenomic Diagnostics for Suspected Outbreak of Severe Pneumonia
Fischer N, Rohde H, Indenbirken D, Günther T, Reumann K, Lütgehetmann M, Meyer T, Kluge S, Aepfelbacher M, Alawi M, Grundhoff A
EMERG INFECT DIS. 2014;20(6):1072-5.

Exom-Sequenzierung zur Identifizierung von Krankheitsgenen für seltene Syndrome: Erfahrungen aus Hamburg
Kortüm F, Abdollahpour H, Alawi M, Korenke G, Seemanova E, Tinschert S, Zenker M, Rosenberger G, Kutsche K
MED GENET-BERLIN. 2014;26:246-254.

Bromodomain protein BRD4 is required for estrogen receptor-dependent enhancer activation and gene transcription
Nagarajan S, Hossan T, Alawi M, Najafova Z, Indenbirken D, Bedi U, Taipaleenmäki H, Ben-Batalla I, Scheller M, Loges S, Knapp S, Hesse E, Chiang C, Grundhoff A, Johnsen S
CELL REP. 2014;8(2):459-468.

Next-generation sequencing of peripheral B-lineage cells pinpoints the circulating clonotypic cell pool in multiple myeloma
Thiele B, Kloster M, Alawi M, Indenbirken D, Trepel M, Grundhoff A, Binder M
BLOOD. 2014;123(23):3618-21.

Dual roles of the transcription factor grainyhead-like 2 (GRHL2) in breast cancer
Werner S, Frey S, Riethdorf S, Schulze C, Alawi M, Kling L, Vafaizadeh V, Sauter G, Terracciano L, Schumacher U, Pantel K, Assmann V
J BIOL CHEM. 2013;288(32):22993-3008.

Letzte Aktualisierung aus dem FIS: 24.06.2019 - 04:49 Uhr