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.


  • 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.


Malik Alawi
Malik Alawi
M. Sc.
  • Core manager

W36 , Ground Floor, Room number 10
Ceren Saygi
Ceren Saygi
  • Bioinformatics Facility

W36 , Ground Floor, Room number 07
Christian Casar
Christian Casar
M. Sc.
  • Bioinformatics Facility

W36 , Ground Floor, Room number 08
Michael Spohn
Michael Spohn
M. Sc.
  • Bioinformatics Facility

W36 , Ground Floor, Room number 09

References / Publications

  • 2024
  • 2023
  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2011

New dienelactone hydrolase from microalgae bacterial community-Antibiofilm activity against fish pathogens and potential applications for aquaculture
Bergmann L, Balzer Le S, Hageskal G, Preuss L, Han Y, Astafyeva Y, Loevenich S, Emmann S, Perez-Garcia P, Indenbirken D, Katzowitsch E, Thümmler F, Alawi M, Wentzel A, Streit W, Krohn I
SCI REP-UK. 2024;14(1):377.

Intestinal epithelia and myeloid immune cells shape colitis severity and colorectal carcinogenesis via High-mobility group box protein 1
Foelsch K, Pelczar P, Zierz E, Kondratowicz S, Qi M, Müller C, Alawi M, Huebener S, Clauditz T, Gagliani N, Huber S, Huebener P
J CROHNS COLITIS. 2024 [Epub ahead of print].

Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome-1 in two new patients with the same homozygous TMCO1 variant and review of the literature
Abdelrazek I, Holling T, Harms F, Alawi M, Omar T, Abdalla E, Kutsche K
EUR J MED GENET. 2023;66(3):104715.

Stenotrophomonas maltophilia affects the gene expression profiles of the major pathogens Pseudomonas aeruginosa and Staphylococcus aureus in an in vitro multispecies biofilm model
Alio I, Moll R, Hoffmann T, Mamat U, Schaible U, Pappenfort K, Alawi M, Schie M, Thünauer R, Stamm J, Rohde H, Streit W
MICROBIOL SPECTR. 2023;11(6):.

Complete genome sequence of a Staphylococcus condimenti isolated from a port catheter-associated bloodstream infection
Berneking L, Büttner H, Qi M, Günther T, Lehnhoff D, Both A, Christner M, Wolters M, Alawi M, Aepfelbacher M, Rohde H

Midgut Volvulus Adds a Murine, Neutrophil-Driven Model of Septic Condition to the Experimental Toolbox
Elrod J, Kiwit A, Lenz M, Rohde H, Börnigen D, Alawi M, Mohr C, Pagerols Raluy L, Trochimiuk M, Knopf J, Reinshagen K, Herrmann M, Boettcher M
CELLS-BASEL. 2023;12(3):.

Murine scald models characterize the role of neutrophils and neutrophil extracellular traps in severe burns
Elrod J, Lenz M, Kiwit A, Armbrust L, Schönfeld L, Reinshagen K, Pagerols Raluy L, Mohr C, Saygi C, Alawi M, Rohde H, Herrmann M, Boettcher M
FRONT IMMUNOL. 2023;14:1113948.

Preclinical patient-derived modeling of castration-resistant prostate cancer facilitates individualized assessment of homologous recombination repair deficient disease
Elsesy M, Oh-Hohenhorst S, Oing C, Eckhardt A, Burdak-Rothkamm S, Alawi M, Müller C, Schüller U, Maurer T, von Amsberg G, Petersen C, Rothkamm K, Mansour W
MOL ONCOL. 2023;17(6):1129-1147.

A deep intronic variant in DNM1 in a patient with developmental and epileptic encephalopathy creates a splice acceptor site and affects only transcript variants including exon 10a
Harms F, Weiss D, Lisfeld J, Alawi M, Kutsche K
NEUROGENETICS. 2023;24(3):171-180.

INPP4A-related genetic and phenotypic spectrum and functional relevance of subcellular targeting of INPP4A isoforms
Hecher L, Harms F, Lisfeld J, Alawi M, Denecke J, Kutsche K
NEUROGENETICS. 2023;24(2):79-93.

Impact of AKT1 on cell invasion and radiosensitivity in a triple negative breast cancer cell line developing brain metastasis
Kempska J, Oliveira-Ferrer L, Grottke A, Qi M, Alawi M, Meyer F, Borgmann K, Hamester F, Eylmann K, Rossberg M, Smit D, Jücker M, Laakmann E, Witzel I, Schmalfeldt B, Müller V, Legler K
FRONT ONCOL. 2023;13:1129682.

Cardiofacioneurodevelopmental syndrome: Report of a novel patient and expansion of the phenotype
Abdalla E, Alawi M, Meinecke P, Kutsche K, Harms F
AM J MED GENET A. 2022;188(8):2448-2453.

Salvage Chemotherapy with Cisplatin, Ifosfamide, and Paclitaxel in Aggressive Variant of Metastatic Castration-Resistant Prostate Cancer
Amsberg G, Zilles M, Mansour W, Gild P, Alsdorf W, Kaune M, Böckelmann L, Hauschild J, Krisp C, Rohlfing T, Saygi C, Alawi M, Zielinski A, Langebrake C, Su X, Perner S, Tilki D, Schluter H, Graefen M, Dyshlovoy S, Bokemeyer C
INT J MOL SCI. 2022;23(23):.

Microalgae and Bacteria Interaction-Evidence for Division of Diligence in the Alga Microbiota
Astafyeva Y, Gurschke M, Qi M, Bergmann L, Indenbirken D, de Grahl I, Katzowitsch E, Reumann S, Hanelt D, Alawi M, Streit W, Krohn I
MICROBIOL SPECTR. 2022;10(4):.

Clinically Relevant KCNQ1 Variants Causing KCNQ1-KCNE2 Gain-of-Function Affect the Ca2+ Sensitivity of the Channel
Bauer C, Holling T, Horn D, Laço M, Abdalla E, Omar O, Alawi M, Kutsche K
INT J MOL SCI. 2022;23(17):.

Comprehensive profiling of myxopapillary ependymomas identifies a distinct molecular subtype with relapsing disease
Bockmayr M, Harnisch K, Pohl L, Schweizer L, Mohme T, Körner M, Alawi M, Suwala A, Dorostkar M, Monoranu C, Hasselblatt M, Wefers A, Capper D, Hench J, Frank S, Richardson T, Tran I, Liu E, Snuderl M, Engertsberger L, Benesch M, von Deimling A, Obrecht D, Mynarek M, Rutkowski S, Glatzel M, Neumann J, Schüller U
NEURO-ONCOLOGY. 2022;24(10):1689-1699.

Multiplexed mRNA analysis of brain-derived extracellular vesicles upon experimental stroke in mice reveals increased mRNA content with potential relevance to inflammation and recovery processes
Bub A, Brenna S, Alawi M, Kügler P, Gui Y, Kretz O, Altmeppen H, Magnus T, Puig B
CELL MOL LIFE SCI. 2022;79(6):329.

Novel biallelic variants expand the SLC5A6-related phenotypic spectrum
Holling T, Nampoothiri S, Tarhan B, Schneeberger P, Vinayan K, Yesodharan D, Roy A, Radhakrishnan P, Alawi M, Rhodes L, Girisha K, Kang P, Kutsche K
EUR J HUM GENET. 2022;30(4):439-449.

Characterization of IG-MYC-breakpoints and their application for quantitative minimal disease monitoring in high-risk pediatric Burkitt-lymphoma and -leukemia
Möker P, Zur Stadt U, Zimmermann M, Alawi M, Mueller S, Finger J, Knörr F, Riquelme A, Oschlies I, Klapper W, Bradtke J, Burkhardt B, Woessmann W, Damm-Welk C
LEUKEMIA. 2022;36(9):2343-2346.

Diagnostic potential of extracellular vesicles in meningioma patients
Ricklefs F, Maire C, Wollmann K, Dührsen L, Fita K, Sahm F, Herold-Mende C, von Deimling A, Kolbe K, Holz M, Bergmann L, Fuh M, Schlüter H, Alawi M, Reimer R, Sven P, Glatzel M, Westphal M, Lamszus K
NEURO-ONCOLOGY. 2022;24(12):2078-2090.

Pregnancy-induced maternal microchimerism shapes neurodevelopment and behavior in mice
Schepanski S, Chini M, Sternemann V, Urbschat C, Thiele K, Sun T, Zhao Y, Poburski M, Woestemeier A, Thieme M, Zazara D, Alawi M, Fischer N, Heeren J, Vladimirov N, Woehler A, Puelles V, Bonn S, Gagliani N, Hanganu-Opatz I, Arck P
NAT COMMUN. 2022;13(1):.

Biallelic FRA10AC1 variants cause a neurodevelopmental disorder with growth retardation
von Elsner L, Chai G, Schneeberger P, Harms F, Casar C, Qi M, Alawi M, Abdel-Salam G, Zaki M, Arndt F, Yang X, Stanley V, Hempel M, Gleeson J, Kutsche K
BRAIN. 2022;145(4):1551-1563.

Distinct clonal lineages and within-host diversification shape invasive Staphylococcus epidermidis populations
Both A, Huang J, Qi M, Lausmann C, Weißelberg S, Büttner H, Lezius S, Failla A, Christner M, Stegger M, Gehrke T, Baig S, Citak M, Alawi M, Aepfelbacher M, Rohde H
PLOS PATHOG. 2021;17(2):e1009304.

The SIRPα-CD47 immune checkpoint in NK cells
Deuse T, Hu X, Agbor-Enoh S, Jang M, Alawi M, Saygi C, Gravina A, Tediashvili G, Nguyen V, Liu Y, Valantine H, Lanier L, Schrepfer S
J EXP MED. 2021;218(3):.

Hypoimmune induced pluripotent stem cell-derived cell therapeutics treat cardiovascular and pulmonary diseases in immunocompetent allogeneic mice
Deuse T, Tediashvili G, Hu X, Gravina A, Tamenang A, Wang D, Connolly A, Mueller C, Mallavia B, Looney M, Alawi M, Lanier L, Schrepfer S
P NATL ACAD SCI USA. 2021;118(28):.

Deep (Meta)genomics and (Meta)transcriptome Analyses of Fungal and Bacteria Consortia From Aircraft Tanks and Kerosene Identify Key Genes in Fuel and Tank Corrosion
Krohn I, Bergmann L, Qi M, Indenbirken D, Han Y, Perez-Garcia P, Katzowitsch E, Hägele B, Lübcke T, Siry C, Riemann R, Alawi M, Streit W

Transcriptome Analysis in Vulvar Squamous Cell Cancer
Prieske K, Alawi M, Jaeger A, Wankner M, Eylmann K, Reuter S, Lebok P, Burandt E, Blessin N, Schmalfeldt B, Prieske K, Joosse S, Woelber L
CANCERS. 2021;13(24):.

Biallelic variants in VPS50 cause a neurodevelopmental disorder with neonatal cholestasis
Schneeberger P, Nampoothiri S, Holling T, Yesodharan D, Alawi M, Knisely A, Müller T, Plecko B, Janecke A, Kutsche K
BRAIN. 2021;2021(awab206):.

Vertically transferred maternal immune cells promote neonatal immunity against early life infections
Stelzer I, Urbschat C, Schepanski S, Thiele K, Triviai I, Wieczorek A, Alawi M, Ohnezeit D, Kottlau J, Huang J, Fischer N, Mittrücker H, Solano M, Fehse B, Diemert A, Stahl F, Arck P
NAT COMMUN. 2021;12(1):4706.

Pan-cancer analysis of whole genomes

NATURE. 2020;578(7793):82-93.

Draft Genome Sequence of the Green Alga Scenedesmus acuminatus SAG 38.81
Astafyeva Y, Alawi M, Indenbirken D, Danso D, Grundhoff A, Hanelt D, Streit W, Krohn I

Clonal Evolution after Allogeneic Hematopoietic Stem Cell Transplantation
Christopeit M, Badbaran A, Alawi M, Flach J, Fehse B, Kröger N
BIOL BLOOD MARROW TR. 2020;26(7):e167-e170.

High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms
Czech-Sioli M, Günther T, Therre M, Spohn M, Indenbirken D, Theiss J, Riethdorf S, Qi M, Alawi M, Wülbeck C, Fernandez-Cuesta I, Esmek F, Becker J, Grundhoff A, Fischer N
PLOS PATHOG. 2020;16(8):.

Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth
Harms F, Parthasarathy P, Zorndt D, Alawi M, Fuchs S, Halliday B, McKeown C, Sampaio H, Radhakrishnan N, Radhakrishnan S, Gorce M, Navet B, Ziegler A, Sachdev R, Robertson S, Nampoothiri S, Kutsche K
HUM MUTAT. 2020;41(9):1645-1661.

Glioma escape signature and clonal development under immune pressure
Maire C, Mohme M, Bockmayr M, Fita K, Riecken K, Börnigen D, Alawi M, Failla A, Kolbe K, Zapf S, Holz M, Neumann K, Dührsen L, Lange T, Fehse B, Westphal M, Lamszus K
J CLIN INVEST. 2020;130(10):5257-5271.

Deep amoA amplicon sequencing reveals community partitioning within ammonia-oxidizing bacteria in the environmentally dynamic estuary of the River Elbe
Malinowski M, Alawi M, Krohn I, Ruff S, Indenbirken D, Alawi M, Karrasch M, Lüschow R, Streit W, Timmermann G, Pommerening-Röser A
SCI REP-UK. 2020;10(1):.

Molecular profiling of an osseous metastasis in glioblastoma during checkpoint inhibition: potential mechanisms of immune escape
Mohme M, Maire C, Schliffke S, Joosse S, Alawi M, Matschke J, Schüller U, Dierlamm J, Martens T, Pantel K, Riethdorf S, Lamszus K, Westphal M

Genomic characterization of vulvar squamous cell carcinoma
Prieske K, Alawi M, Oliveira-Ferrer L, Jaeger A, Eylmann K, Burandt E, Schmalfeldt B, Joosse S, Woelber L
GYNECOL ONCOL. 2020;158(3):547-554.

Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage
Sauvigny T, Alawi M, Krause L, Renner S, Spohn M, Busch A, Kolbe V, Altmüller J, Löscher B, Franke A, Brockmann C, Lieb W, Westphal M, Schmidt N, Regelsberger J, Rosenberger G
J NEUROL. 2020;267(9):2533-2545.

Biallelic MADD variants cause a phenotypic spectrum ranging from developmental delay to a multisystem disorder
Schneeberger P, Kortüm F, Korenke G, Alawi M, Santer R, Woidy M, Buhas D, Fox S, Juusola J, Alfadhel M, Webb B, Coci E, Abou Jamra R, Siekmeyer M, Biskup S, Heller C, Maier E, Javaher-Haghighi P, Bedeschi M, Ajmone P, Iascone M, Peeters H, Ballon K, Jaeken J, Rodríguez Alonso A, Palomares-Bralo M, Santos-Simarro F, Meuwissen M, Beysen D, Kooy R, Houlden H, Murphy D, Doosti M, Karimiani E, Mojarrad M, Maroofian R, Noskova L, Kmoch S, Honzik T, Cope H, Sanchez-Valle A, , Gelb B, Kurth I, Hempel M, Kutsche K
BRAIN. 2020;143(8):2437-2453.

Bi-allelic Pathogenic Variants in HS2ST1 Cause a Syndrome Characterized by Developmental Delay and Corpus Callosum, Skeletal, and Renal Abnormalities
Schneeberger P, von Elsner L, Barker E, Meinecke P, Marquardt I, Alawi M, Steindl K, Joset P, Rauch A, Zwijnenburg P, Weiss M, Merry C, Kutsche K
AM J HUM GENET. 2020;107(6):1044-1061.

Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs
Spieck E, Spohn M, Wendt K, Bock E, Shively J, Frank J, Indenbirken D, Alawi M, Lücker S, Hüpeden J
ISME J. 2020;14(2):364-379.

Cellular Importin-α3 Expression Dynamics in the Lung Regulate Antiviral Response Pathways against Influenza A Virus Infection
Thiele S, Stanelle-Bertram S, Beck S, Kouassi N, Zickler M, Müller M, Tuku B, Resa-Infante P, van Riel D, Alawi M, Günther T, Rother F, Hügel S, Reimering S, McHardy A, Grundhoff A, Brune W, Osterhaus A, Bader M, Hartmann E, Gabriel G
CELL REP. 2020;31(3):.

Differential regulation of extracellular matrix proteins in three recurrent liver metastases of a single patient with colorectal cancer
Voß H, Wurlitzer M, Smit D, Ewald F, Alawi M, Spohn M, Indenbirken D, Omidi M, David K, Juhl H, Simon R, Sauter G, Fischer L, Izbicki J, Molloy M, Nashan B, Schlüter H, Jücker M
CLIN EXP METASTAS. 2020;37(6):649-656.

The landscape of viral associations in human cancers
Zapatka M, Borozan I, Brewer D, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H, Cooper C, Eils R, Ferretti V, Lichter P
NAT GENET. 2020;52(3):320-330.

A prenatally disrupted airway epithelium orchestrates the fetal origin of asthma in mice
Zazara-Giannou D, Wegmann M, Giannou A, Hierweger A, Alawi M, Thiele K, Huber S, Pincus M, Muntau A, Solano M, Arck P
J ALLERGY CLIN IMMUN. 2020;145(6):1641-1654.

DAMIAN an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples
Alawi M, Burkhardt L, Indenbirken D, Reumann K, Christopeit M, Kröger N, Lütgehetmann M, Aepfelbacher M, Fischer N, Grundhoff A
SCI REP-UK. 2019;9(1):16841.

De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans
Deuse T, Hu X, Agbor-Enoh S, Koch M, Spitzer M, Gravina A, Alawi M, Marishta A, Peters B, Kosaloglu-Yalcin Z, Yang Y, Rajalingam R, Wang D, Nashan B, Kiefmann R, Reichenspurner H, Valantine H, Weissman I, Schrepfer S
NAT BIOTECHNOL. 2019;37(10):1137-1144.

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. 2019;33(2):2359-2371.

Biallelic and De Novo Variants in DONSON Reveal a Clinical Spectrum of Cell Cycle-opathies with Microcephaly, Dwarfism and Skeletal Abnormalities
Karaca E, Posey J, Bostwick B, Liu P, Gezdirici A, Yesil G, Coban Akdemir Z, Bayram Y, Harms F, Meinecke P, Alawi M, Bacino C, Sutton V, Kortüm F, Lupski J
AM J MED GENET A. 2019;179(10):2056-2066.

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;21(8):1832-1841.

Alternative interaction sites in the influenza A virus nucleoprotein mediate viral escape from the importin-α7 mediated nuclear import pathway
Resa-Infante P, Bonet J, Thiele S, Alawi M, Stanelle-Bertram S, Tuku B, Beck S, Oliva B, Gabriel G
FEBS J. 2019;286(17):3374-3388.

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.

Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL
Zur Stadt U, Alawi M, Adao M, Indenbirken D, Escherich G, Horstmann M
BLOOD CANCER J. 2019;9(12):96.

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.

Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches
Krohn-Molt I, Alawi M, Förstner K, Wiegandt A, Burkhardt L, Indenbirken D, Thieß M, Grundhoff A, Kehr J, Tholey A, Streit W
FRONT MICROBIOL. 2017;8:1941.

BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells
Nagarajan S, Bedi U, Budida A, Hamdan F, Mishra V, Najafova Z, Xie W, Alawi M, Indenbirken D, Knapp S, Chiang C, Grundhoff A, Kari V, Scheel C, Wegwitz F, Johnsen S
NUCLEIC ACIDS RES. 2017;45(6):3130-3145.

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.

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies
Güllert S, Fischer M, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz R, Grundhoff A, Streit W

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):33-38.

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.

A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes
Ilmberger N, Güllert S, Dannenberg J, Rabausch U, Torres J, Wemheuer B, Alawi M, Poehlein A, Chow J, Turaev D, Rattei T, Schmeisser C, Salomon J, Olsen P, Daniel R, Grundhoff A, Borchert M, Streit W
PLOS ONE. 2014;9(9):e106707.

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.

Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors
Krohn-Molt I, Wemheuer B, Alawi M, Poehlein A, Güllert S, Schmeisser C, Pommerening-Röser A, Grundhoff A, Daniel R, Hanelt D, Streit W
APPL ENVIRON MICROB. 2013;79(20):6196-6206.

Runx1 is essential at two stages of early murine B-cell development
Niebuhr B, Kriebitzsch N, Fischer M, Behrens K, Günther T, Alawi M, Bergholz U, Müller U, Roscher S, Ziegler M, Buchholz F, Grundhoff A, Stocking C
BLOOD. 2013;122(3):413-23.

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.

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data
Alawi M, Kurtz S, Beckstette M
J INTEGR BIOINFORMAT. 2011;8(2):155.

Letzte Aktualisierung aus dem FIS: 18.07.2024 - 05:05 Uhr