Deep Sequencing - Publications

2018

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes

Solimena M et al.

Diabetologia. 2018 Mar;61(3):641-657

Insm1 Induces Neural Progenitor Delamination in Developing Neocortex via Downregulation of the Adherens Junction Belt-Specific Protein Plekha7

Stefania Tavano, Elena Taverna, Nereo Kalebic, Christiane Haffner, Takashi Namba, Andreas Dahl, Michaela Wilsch-Br€auninger, Judith T.M.L. Paridaen and Wieland B. Huttner

Neuron. 2018 Feb 19. pii: S0896-6273(18)30077-1

The axolotl genome and the evolution of key tissue formation regulators

Nowoshilow S, Schloissnig S, Fei JF, Dahl A, Pang AWC, Pippel M, Winkler S, Hastie AR, Young G, Roscito JG, Falcon F, Knapp D, Powell S, Cruz A, Cao H, Habermann B, Hiller M, Tanaka EM, Myers EW

Nature. 2018 Feb 1;554(7690):50-55

The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms

Grohme MA, Schloissnig S, Rozanski A, Pippel M, Young GR, Winkler S, Brandl H, Henry I, Dahl A, Powell S, Hiller M, Myers E, Rink JC

Nature. 2018 Feb 1;554(7690):56-61

Whole exome sequencing identifies mTOR and KEAP1 as potential targets for radiosensitization of HNSCC cells refractory to EGFR and β1 integrin inhibition

Erik Klapproth, Ellen Dickreuter, Falk Zakrzewski, Michael Seifert, Andreas Petzold, Andreas Dahl, Evelin Schröck, Barbara Klink and Nils Cordes

Oncotarget 2018 Jan 18, Online ISSN: 1949-2553

Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity

Mitroulis I at al.

Cell. 2018 Jan 11;172(1-2):147-161.e12

SETD1A protects HSCs from activation-induced functional decline in vivo

Arndt K, Kranz A, Fohgrub J, Jolly A, Bledau AS, Di Virgilio M, Lesche M, Dahl A, Höfer T, Stewart AF, Waskow C

Blood. 2018 Jan 18. pii: blood-2017-09-806844

The complete and fully assembled genome sequence of Aeromonas salmonicida subsp. pectinolytica and its comparative analysis with other Aeromonas species: investigation of the mobilome in environmental and pathogenic strains

Pfeiffer F, Zamora-Lagos MA, Blettinger M, Yeroslaviz A, Dahl A, Gruber S, Habermann BH

BMC Genomics. 2018 Jan 5;19(1):20

Although Abundant in Tumor Tissue, Mast Cells Have No Effect on Immunological Micro-milieu or Growth of HPV-Induced or Transplanted Tumors

Ghouse SM, Polikarpova A, Muhandes L, Dudeck J, Tantcheva-Poór I, Hartmann K, Lesche M, Dahl A, Eming S, Müller W, Behrendt R, Roers A

Cell Rep. 2018 Jan 2;22(1):27-35

2017

Setd1b, encoding a histone 3 lysine 4 methyltransferase, is a maternal effect gene required for the oogenic gene expression program

Brici D, Zhang Q, Reinhardt S, Dahl A, Hartmann H, Schmidt K, Goveas N, Huang J, Gahurova L, Kelsey G, Anastassiadis K, Stewart AF, Kranz A

Development. 2017 Jul 15;144(14):2606-2617

Zebrafish In-Vivo Screening for Compounds Amplifying Hematopoietic Stem and Progenitor Cells: - Preclinical Validation in Human CD34+ Stem and Progenitor Cells

Arulmozhivarman G et al.

Sci Rep. 2017 Sep 21;7(1):12084

Primary Spinal OPC Culture System from Adult Zebrafish to Study Oligodendrocyte Differentiation In Vitro

Kroehne V, Tsata V, Marrone L, Froeb C, Reinhardt S, Gompf A, Dahl A, Sterneckert J, Reimer MM

Front Cell Neurosci. 2017 Sep 14;11:284

Neurotrophin Receptor p75NTR Regulates Immune Function of Plasmacytoid Dendritic Cells

Bandola J, Richter C, Ryser M, Jamal A, Ashton MP, von Bonin M, Kuhn M, Dorschner B, Alexopoulou D, Navratiel K, Roeder I, Dahl A, Hedrich CM, Bonifacio E, Brenner S, Thieme S

Front Immunol. 2017 Aug 17;8:981

Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion

Cornils K, Thielecke L, Winkelmann D, Aranyossy T, Lesche M, Dahl A, Roeder I, Fehse B, Glauche I

Mol Cancer. 2017 Jul 14;16(1):120

Analyses of clonality of BcrAbl-induced leukemia by Genetic Barcodes

K Cornils , L Thielecke , D Winkelmann , M Lesche , T Aranyossy , A Dahl , I Roeder , B Fehse , I Glauche

Klin Padiatr 2017; 229(03): 182-195

Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles

Albrecht V, Zweiniger C, Surendranath V, Lang K, Schöfl G, Dahl A, Winkler S, Lange V, Böhme I, Schmidt AH

HLA. 2017 Aug;90(2):79-87

Donor cell leukemia: evidence for multiple preleukemic clones and parallel long term clonal evolution in donor and recipient

Herold S, Kuhn M, Bonin MV, Stange T, Platzbecker U, Radke J, Lange T, Sockel K, Gutsche K, Schetelig J, Röllig C, Schuster C, Roeder I, Dahl A, Mohr B, Serve H, Brandts C, Ehninger G, Bornhäuser M, Thiede C

Leukemia. 2017 Jul;31(7):1637-1640

An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity

Zhang W, Fu J, Liu J, Wang H, Schiwon M, Janz S, Schaffarczyk L, von der Goltz L, Ehrke-Schulz E, Dörner J, Solanki M, Boehme P, Bergmann T, Lieber A, Lauber C, Dahl A, Petzold A, Zhang Y, Stewart AF, Ehrhardt A

Cell Rep. 2017 May 23;19(8):1698-1709

CD8+ T cells specific for the islet autoantigen IGRP are restricted in their T cell receptor chain usage

Fuchs YF, Eugster A, Dietz S, Sebelefsky C, Kühn D, Wilhelm C, Lindner A, Gavrisan A, Knoop J, Dahl A, Ziegler AG, Bonifacio E

Sci Rep. 2017 Mar 16;7:44661

Assessment of the T cell receptor repertoire in long-term platelet donors by next generation sequencing

Link CS, Hölig K, Rücker-Braun E, Lang K, Kuhn M, Eugster A, Klesse C, Schmiedgen M, Heidenreich F, Oelschlägel U, Dahl A, Bornhäuser M, Bonifacio E, Schetelig J

Br J Haematol. 2017 Mar 8. doi: 10.1111/bjh.14576

TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes

Akpinar M, Lesche M, Fanourgakis G, Fu J, Anastassiadis K, Dahl A, Jessberger R

PLoS Genet. 2017 Mar 6;13(3):e1006660

Limitations and challenges of genetic barcode quantification

Thielecke L, Aranyossy T, Dahl A, Tiwari R, Roeder I, Geiger H, Fehse B, Glauche I, Cornils K

Sci Rep. 2017 Mar 3;7:43249

Pancreas lineage allocation and specification are regulated by sphingosine-1-phosphate signalling

Serafimidis I, Rodriguez-Aznar E, Lesche M, Yoshioka K, Takuwa Y, Dahl A, Pan D, Gavalas A

PLoS Biol. 2017 Mar 1;15(3):e2000949

2016

T cell receptor repertoires after adoptive transfer of expanded allogeneic regulatory T cells

Theil A, Wilhelm C, Kuhn M, Petzold A, Tuve S, Oelschlägel U, Dahl A, Bornhäuser M, Bonifacio E, Eugster A

Clin Exp Immunol. 2017 Feb;187(2):316-324

IL4/STAT6 Signaling Activates Neural Stem Cell Proliferation and Neurogenesis upon Amyloid-β42 Aggregation in Adult Zebrafish Brain

Bhattarai P, Thomas AK, Cosacak MI, Papadimitriou C, Mashkaryan V, Froc C, Reinhardt S, Kurth T, Dahl A, Zhang Y, Kizil C

Cell Rep. 2016 Oct 18;17(4):941-948

Loss of Trex1 in Dendritic Cells Is Sufficient To Trigger Systemic Autoimmunity

Peschke K et al.

J Immunol. 2016 Sep 15;197(6):2157-66

Abundant CMV reactive clonotypes in the CD8+ T cell receptor alpha repertoire following allogeneic transplantation

Cornelia Sibylle Link et al.

Clin Exp Immunol. 2016 Jun;184(3)

Chromatoid Body Protein TDRD6 Supports Long 3' UTR Triggered Nonsense Mediated mRNA Decay

Fanourgakis G, Lesche M, Akpinar M, Dahl A, Jessberger R.

PLoS Genet. 2016 May 5;12(5)

Identification of tox chromatin binding properties and downstream targets by DamID-seq

António Miguel de Jesus Domingues, Benedetta Artegiani, Andreas Dahl, Federico Calegari

Genom Data. 2016 Feb 3;7:264-8

Aldehyde dehydrogenase activity is necessary for beta cell development and functionality in mice

Anastasiou V, Ninou E, Alexopoulou D, Stertmann J, Müller A, Dahl A, Solimena M, Speier S, Serafimidis I, Gavalas A

Diabetologia. 2016 Jan;59(1):139-50

2015

Rapid Conversion of Fibroblasts into Functional Forebrain GABAergic Interneurons by Direct Genetic Reprogramming

Gaia Colasante et al.

Cell Stem Cell. 2015 Dec 3;17(6):719-34

CCND1-CDK4-mediated cell cycle progression provides a competitive advantage for human hematopoietic stem cells in vivo

Mende N, Kuchen EE, Lesche M, Grinenko T, Kokkaliaris KD, Hanenberg H, Lindemann D, Dahl A, Platz A, Höfer T, Calegari F, Waskow C

J Exp Med. 2015 Jul 27;212(8):1171-83

RNAi profiling of primary human AML cells identifies ROCK1 as a therapeutic target and nominates fasudil as an antileukemic drug

Wermke M, Camgoz A, Paszkowski-Rogacz M, Thieme S, von Bonin M, Dahl A, Platzbecker U, Theis M, Ehninger G, Brenner S, Bornhäuser M, Buchholz F

Blood. 2015 Jun 11;125(24):3760-8

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

Florio M, Albert M, Taverna E, Namba T, Brandl H, Lewitus E, Haffner C, Sykes A, Wong FK, Peters J, Guhr E, Klemroth S, Prüfer K, Kelso J, Naumann R, Nüsslein I, Dahl A, Lachmann R, Pääbo S, Huttner WB

Science. 2015 Mar 27;347(6229):1465-70

Regulation of liver metabolism by the endosomal GTPase Rab5

Zeigerer A, Bogorad RL, Sharma K, Gilleron J, Seifert S, Sales S, Berndt N, Bulik S, Marsico G, D'Souza RC, Lakshmanaperumal N, Meganathan Natarajan K, Sachinidis A, Dahl A, Holzhütter HG, Shevchenko A, Mann M, Koteliansky V, Zerial M.

Cell Rep. 2015 May 12;11(6):884-92

Identification and expression patterns of novel long non-coding RNAs in neural progenitors of the developing mammalian cortex

Julieta Aprea, Mathias Lesche, Simone Massalini, Silvia Prenninger, Dimitra Alexopoulou, Andreas Dahl, Michael Hiller & Federico Calegari

Neurogenesis Volume 2, Issue 1, 2015

TOX: a multifunctional transcription factor and novel regulator of mammalian corticogenesis

Artegiani B, de Jesus Domingues AM, Bragado Alonso S, Brandl E, Massalini S, Dahl A, Calegari F. Tox

EMBO J. 2015 Apr 1;34(7):896-910

High diversity in the TCR repertoire of GAD65 autoantigen-specific human CD4+ T cells

Eugster A, Lindner A, Catani M, Heninger AK, Dahl A, Klemroth S, Kühn D, Dietz S, Bickle M, Ziegler AG, Bonifacio E

J Immunol. 2015 Mar 15;194(6):2531-8

SAMHD1 prevents autoimmunity by maintaining genome stability

Kretschmer S, Wolf C, König N, Staroske W, Guck J, Häusler M, Luksch H, Nguyen LA, Kim B, Alexopoulou D, Dahl A, Rapp A, Cardoso MC, Shevchenko A, Lee-Kirsch MA

Ann Rheum Dis. 2015 Mar;74(3)

Defective removal of ribonucleotides from DNA promotes systemic autoimmunity

Günther C et al.

J Clin Invest. 2015 Jan 2; 125(1): 413–424

2014

Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack

Henderson D, Ogilvie LA, Hoyle N, Keilholz U, Lange B, Lehrach H; OncoTrack Consortium

Biotechnol J. 2014 Sep;9(9):1104-14.

The age and genomic integrity of neurons after cortical stroke in humans

Huttner HB et al.

Nat Neurosci. 2014 Jun;17(6):801-3

Clonal expansion capacity defines two consecutive developmental stages of long-term hematopoietic stem cells

Grinenko T, Arndt K, Portz M, Mende N, Günther M, Cosgun KN, Alexopoulou D, Lakshmanaperumal N, Henry I, Dahl A, Waskow C

J Exp Med. 2014 Feb 10;211(2):209-15

The earliest transcribed zygotic genes are short, newly evolved, and different across species

Heyn P, Kircher M, Dahl A, Kelso J, Tomancak P, Kalinka AT, Neugebauer KM

Cell Rep. 2014 Jan 30;6(2):285-92

Multiplexing clonality: combining RGB marking and genetic barcoding

Cornils K, Thielecke L, Hüser S, Forgber M, Thomaschewski M, Kleist N, Hussein K, Riecken K, Volz T, Gerdes S, Glauche I, Dahl A, Dandri M, Roeder I, Fehse B

Nucleic Acids Res. 2014 Apr;42(7)

2013

Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment

Aprea J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M, Dahl A, Groszer M, Hiller M, Calegari F

EMBO J. 2013 Dec 11;32(24):3145-60

Mouse SAMHD1 has antiretroviral activity and suppresses a spontaneous cell-intrinsic antiviral response

Behrendt R, Schumann T, Gerbaulet A, Nguyen LA, Schubert N, Alexopoulou D, Berka U, Lienenklaus S, Peschke K, Gibbert K, Wittmann S, Lindemann D, Weiss S, Dahl A, Naumann R, Dittmer U, Kim B, Mueller W, Gramberg T, Roers A

Cell Rep. 2013 Aug 29;4(4):689-96

Reactivating head regrowth in a regeneration-deficient planarian species

Liu SY, Selck C, Friedrich B, Lutz R, Vila-Farré M, Dahl A, Brandl H, Lakshmanaperumal N, Henry I, Rink JC

Nature. 2013 Aug 1;500(7460):81-4

The histone demethylase UTX regulates stem cell migration and hematopoiesis

Thieme S, Gyárfás T, Richter C, Özhan G, Fu J, Alexopoulou D, Muders MH, Michalk I, Jakob C, Dahl A, Klink B, Bandola J, Bachmann M, Schröck E, Buchholz F, Stewart AF, Weidinger G, Anastassiadis K, Brenner S

Blood. 2013 Mar 28;121(13)

2012

Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation

Börno ST et al.

Cancer Discov. 2012 Nov;2(11):1024-35

The 1000 Genomes Project: data management and community access

Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P

Nat Methods. 2012 Apr 27;9(5):459-62

MsLDR-creator: a web service to design msLDR assays

Bormann F, Dahl A, Sers C.

Mol Genet Genomics. 2012 Mar;287(3):273-4

Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics

Haupt A, Joberty G, Bantscheff M, Fröhlich H, Stehr H, Schweiger MR, Fischer A, Kerick M, Boerno ST, Dahl A, Lappe M, Lehrach H, Gonzalez C, Drewes G, Lange BM

BMC Cancer. 2012 Jan 25;12:38

2011

Methylation-specific ligation detection reaction (msLDR): a new approach for multiplex evaluation of methylation patterns

Bormann F, Sers C, Seliger B, Handke D, Bergmann T, Seibt S, Lehrach H, Dahl A

Mol Genet Genomics. 2011 Oct;286(3-4):279-91

Demographic history and rare allele sharing among human populations

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8

Mapping copy number variation by population-scale genome sequencing

Mills RE et al.

Nature. 2011 Feb 3;470(7332):59-65

2010

A map of human genome variation from population-scale sequencing

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA

Nature. 2010 Oct 28;467(7319):1061-73

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome

Krawitz PM et al.

Nat Genet. 2010 Oct;42(10):827-9

The application of massively parallel sequencing technologies in diagnostics

Dahl A, Mertes F, Timmermann B, Lehrach H

F1000 Biol Rep. 2010 Aug 9;2:59

1970

Regulatory T cell kinetics following adoptive transfer of expanded allogeneic regulatory T cells into patients with chronic graft-versus host disease

A. Fuchs (Theil) , C. Wilhelm , M. Kuhn , A. Petzold , S. Tuve , U. Oelschlägel , A. Dahl , M. Bornhäuser , E. Bonifacio , A. Eugster

Cytotherapy, 2017 May 23, 19(5):11