Single-cell sequencing of the human midbrain reveals glial activation and a neuronal state specific to Parkinson’s disease.
Smajic S, Prada-Medina CA, Landoulsi Z, Dietrich C, Jarazo J, Henck J, Balachandran S, Pachchek S, Morris CM, Antony P, Timmermann B, Sauer S, Schwamborn JC, May P, Grunewald A, Spielmann M.
Neurology; 2020 Sep. doi:10.1101/2020.09.28.20202812

Integrated analysis of Xist upregulation and gene silencing at the onset of random X-chromosome inactivation at high temporal and allelic resolution.
Pacini G, Dunkel I, Mages N, Mutzel V, Timmermann B, Marsico A, Schulz EG.
bioRxiv 2020.07.20.211573; Genomics; 2020 Juli. doi:10.1101/2020.07.20.211573

A CRISPR-Cas9-engineered mouse model for GPI anchor deficiency mirrors human phenotype and shows hippocampal synaptic dysfunctions.
de los Santos MR, Rivalan M, David FS, Knaus A, Stumpf A, Velasquez LM, Voigt A, Mattei D, Long M, Vogt G, Wittler L, Timmermann B, Robinson PN, Horn D, Mundlos S, Kornak U, Schmitz D, Winter Y, Krawitz PM.
bioRxiv 2020.04.20.050591; Neuroscience; 2020 Apr. doi:10.1101/2020.04.20.050591

Peer-reviewed Papers
Mouse embryonic stem cells self-organize into trunk-like structures with neural tube and somites.
Veenvliet JV, Bolondi A, Kretzmer H, Haut L, Scholze-Wittler M, Schifferl D, Koch F, Pustet M, Heimann S, Buschow R, Wittler L, Timmermann B, Meissner A, Herrmann BG.
Science. 2020 [accepted]

Non-coding deletions uncover Maenli lncRNA transcription as a major regulator of En1 during limb development.
Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL , Speck-Martins CE , Carvalho D, Farage L, Lourenço C, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson M, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Gobert RP, Unger S, Bonafé L, Grote P, Rivolta C, Superti-Furga A, Mundlos S.
Nature. 2020 [accepted]

Alternative splicing coupled nonsense-mediated decay shapes the temperature-dependent transcriptome.
Neumann A, Meinke S, Goldammer G, Strauch M, Schubert D, Timmermann B, Heyd F, Preußner M.
EMBO reports. 2020 [accepted]

PWD/Ph-encoded genetic variants modulate the cellular Wnt/β-Catenin response to suppress ApcMin-triggered intestinal tumor formation.
Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka S, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M.
Cancer Res. 2020 [accepted]

Endocytosis-mediated replenishment of amino acids favors cancer cell proliferation and survival in chromophobe renal cell carcinoma.
Xiao Y, Rabien A, Buschow R, Amstislavskiy V, Busch J, Kilic E, Villegas SL, Timmermann B, Schütte M, Mielke T, Yaspo M-L, Jung K, Meierhofer D.
Cancer Research. 28. Oktober 2020;canres.1998.2020. doi:10.1158/0008-5472.CAN-20-1998

Cell autonomous requirement of neurofibromin (Nf1) for postnatal muscle hypertrophic growth and metabolic homeostasis.
Wei X, Franke J, Ost M, Wardelmann K, Börno S, Timmermann B, Meierhofer D, Kleinridders A, Klaus S, Stricker S.
J Cachexia Sarcopenia Muscle. 2020 Oct 19; doi:10.1002/jcsm.12632

Network integration and modelling of dynamic drug responses at multi-omics levels.
Selevsek N, Caiment F, Nudischer R, Gmuender H, Agarkova I, Atkinson FL, Bachmann I, Baier V, Barel G, Bauer C, Boerno S, Bosc N, Clayton O, Cordes H, Deeb S, Gotta S, Guye P, Hersey A, Hunter FMI, Kunz L, Lewalle A, Lienhard M, Merken J, Minguet J, Oliveira B, Pluess C, Sarkans U, Schrooders Y, Schuchhardt J, Smit I, Thiel C, Timmermann B, Verheijen M, Wittenberger T, Wolski W, Zerck A, Heymans S, Kuepfer L, Roth A, Schlapbach R, Niederer S, Herwig R, Kleinjans J.
Commun Biol. 2020 Oct 15;3(1):573. doi:10.1038/s42003-020-01302-8

The mole genome reveals regulatory rearrangements associated with adaptive intersexuality.
M Real F, Haas SA, Franchini P, Xiong P, Simakov O, Kuhl H, Schöpflin R, Heller D, Moeinzadeh MH, Heinrich V, Krannich T, Bressin A, Hartmann MF, Wudy SA, Dechmann DKN, Hurtado A, Barrionuevo FJ, Schindler M, Harabula I, Osterwalder M, Hiller M, Wittler L, Visel A, Timmermann B, Meyer A, Vingron M, Jiménez R, Mundlos S, Lupiáñez DG.
Science. 2020 Oct 9;370(6513):208-214. doi:doi: 10.1126/science.aaz2582

An unbiased molecular approach using 3’UTRs resolves the avian family-level tree of life.
Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M.
Mol Biol Evol. 2020 Aug 11; doi:10.1093/molbev/msaa191

Genomic evidence for sensorial adaptations to a nocturnal predatory lifestyle in owls.
Espíndola-Hernández P, Mueller JC, Carrete M, Boerno ST, Kempenaers B.
Genome Biol Evol. 2020 Aug 8; doi:10.1093/gbe/evaa166

Epigenetic regulator function through mouse gastrulation.
Grosswendt S*, Kretzmer H*, Smith ZD, Sampath Kumar A, Hetzel S, Wittler L, Klages S, Timmermann B, Mukherji S and Meissner A. * equal contribution
Nature. 2020 Aug;584(7819):102–8. doi:10.1038/s41586-020-2552-x

Decreased mitochondrial DNA content drives OXPHOS dysregulation in chromophobe renal cell carcinoma.
Xiao Y, Clima R, Busch J, Rabien A, Kilic E, Villegas SL, Timmermann B, Attimonelli M, Jung K, Meierhofer D.
Cancer Res. 2020 Jul 21; doi:10.1158/0008-5472.CAN-20-0754

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis.
Chua RL, Lukassen S, Trump S, Hennig BP, Wendisch D, Pott F, Debnath O, Thürmann L, Kurth F, Völker MT, Kazmierski J, Timmermann B, Twardziok S, Schneider S, Machleidt F, Müller-Redetzky H, Maier M, Krannich A, Schmidt S, Balzer F, Liebig J, Loske J, Suttorp N, Eils J, Ishaque N, Liebert UG, von Kalle C, Hocke A, Witzenrath M, Goffinet C, Drosten C, Laudi S, Lehmann I, Conrad C, Sander L-E, Eils R.
Nat Biotechnol. 2020 Jun 26. doi:10.1038/s41587-020-0602-4

Genes acting in synapses and neuron projections are early targets of selection during urban colonization.
Mueller JC, Carrete M, Boerno S, Kuhl H, Tella JL, Kempenaers B.
Mol Ecol. 2020 Apr 20; doi:10.1111/mec.15451

TCRs with segment TRAV9-2 or a CDR3 histidine are overrepresented among nickel-specific CD4+ T cells.
Aparicio-Soto M, Riedel F, Leddermann M, Bacher P, Scheffold A, Kuhl H, Timmermann B, Chudakov DM, Molin S, Worm M, Heine G, Thierse H-J, Luch A, Siewert K.
Allergy. 2020 Apr 16; doi:10.1111/all.14322

The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes.
Hogan JD, Keenan JL, Luo L, Ibn-Salem J, Lamba A, Schatzberg D, Piacentino ML, Zuch DT, Core AB, Blumberg C, Timmermann B, Grau JH, Speranza E, Andrade-Navarro MA, Irie N, Poustka AJ, Bradham CA.
Dev Biol. 2020 Apr 15;460(2):139-154; doi:10.1016/j.ydbio.2019.12.002

Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches.
Bratovič M, Fonfara I, Chylinski K, Gálvez E, Sullivan T, Börno S, Timmermann B, Boettcher M, Charpentier E.
Nat Chem Biol. 2020 Mar 2. doi:10.1038/s41589-020-0490-4

The zinc finger domains in U2AF26 and U2AF35 have diverse functionalities including a role in controlling translation.
Herdt O, Reich S, Medenbach J, Timmermann B, Olofsson D, Preußner M, Heyd F.
RNA Biol. 2020 Mar 1;1–14. doi:10.1080/15476286.2020.1732701

A Conserved Kinase-Based Body-Temperature Sensor Globally Controls Alternative Splicing and Gene Expression.
Haltenhof T, Kotte A, De Bortoli F, Schiefer S, Meinke S, Emmerichs A-K, Petermann KK, Timmermann B, Imhof P, Franz A, Loll B, Wahl MC, Preußner M, Heyd F.
Mol Cell. 2020 Feb 7; doi:10.1016/j.molcel.2020.01.028

Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication.
Kupke SY*, Ly L*, Börno S*, Ruff A, Timmermann B, Vingron M, Haas S, Reichl U. * equal contribution
Viruses. 2020 Jan 7;12(1):71. doi:10.3390/v12010071


Peer-reviewed Papers

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project.
Ernesto Lowy-Gallego, Susan Fairley, Xiangqun Zheng-Bradley, Magali Ruffier, Laura Clarke, Paul Flicek, 1000 Genomes Project Consortium.
Version 2. Wellcome Open Res. 2019 Dec 30 [revised 2019 Dec 30];4:50. doi:10.12688/wellcomeopenres.15126.2

Papillary Renal Cell Carcinomas Rewire Glutathione Metabolism and Are Deficient in Both Anabolic Glucose Synthesis and Oxidative Phosphorylation.
Al Ahmad A, Paffrath V, Clima R, Busch JF, Rabien A, Kilic E, Villegas S, Timmermann B, Attimonelli M, Jung K, Meierhofer D.
Cancers (Basel). 3. September 2019;11(9). doi:10.3390/cancers11091298

Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture.
Despang A, Schöpflin R, Franke M, Ali S, Jerkovic I, Paliou C, Chan WL, Timmermann B, Wittler L, Vingron M, Mundlos S, Ibrahim DM.
Nat Genet. 2019 Jul 29. doi:10.1038/s41588-019-0466-z

Iranome: A catalogue of genomic variations in the Iranian population.
Fattahi Z, Beheshtian M, Mohseni M, Poustchi H, Sellars E, Nezhadi H, Amini A, Arzhangi S, Jalalvand K, Jamali P, Mohammadi Z, Davarnia B, Nikuei P, Oladnabi M, Mohammadzadeh A, Zohrehvand E, Nejatizadeh A, Shekari M, Bagherzadeh M, Shamsi-Gooshki E, Börno S, Timmermann B, Haghdoost A, Najafipour R, Khorshid HRK, Kahrizi K, Malekzadeh R, Akbari MR, Najmabadi H.
Hum Mutat. 2019 Jul 25; doi:10.1002/humu.23880

Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium.
Brandt R, Sell T, Lüthen M, Uhlitz F, Klinger B, Riemer P, Giesecke-Thiel C, Schulze S, El-Shimy IA, Kunkel D, Fauler B, Mielke T, Mages N, Herrmann BG, Sers C, Blüthgen N, Morkel M.
Nat Commun. 2019 02;10(1):2919. doi:10.1038/s41467-019-10954-y

Differential IL2 transcription kinetics render mouse but not human T cells vulnerable to splicing inhibition early after activation.
Bose D, Neumann A, Timmermann B, Meinke S, Heyd F.
Mol Cell Biol. 2019 Jun 3; doi:10.1128/MCB.00035-19

Preformed Chromatin Topology Assists Transcriptional Robustness of Shh during Limb Development.
Paliou C, Guckelberger P, Schöpflin R, Heinrich V, Esposito A, Chiariello AM, Simona Bianco, Carlo Annunziatella, Johannes Helmuth, Stefan Haas, Ivana Jerković M, Brieske N, Wittler L, Timmermann B, Nicodemi M, Vingron M, Mundlos S, Andrey G.
Proc Natl Acad Sci USA. 2019 May 30; doi:10.1073/pnas.1900672116

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.
Gossmann TI​, Shanmugasundram A​, Börno S, Duvaux L, Lemaire C​, Kuhl​ H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C​, Mülleder M, Calvani E, Zelezniak A​, Griffin JL, Bork​ P, Allaine D, Cohas A, Welch JJ*, Timmermann B​*, RalserM*. *equal contribution
Curr Biol. 2019 May 20;29(10):1712-1720.e7.

Low catalytic activity is insufficient to induce disease pathology in triosephosphate isomerase (TPI) deficiency.
Segal J, Mülleder M, Krüger A, Adler T, Scholze-Wittler M, Becker L, Calzada-Wack J, Garrett L, Hölter SM, Rathkolb B, Rozman J, Racza I, Fischer R, Busch DH, Neff F, Klingenspor M, Klopstock T, Grüning NM, Michel S, Lukaszewska-McGreal B, Voigt I, Hartmann L, Timmermann B, Lehrach H, Wolf E, Wurst W, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Schrewe H, Yuneva M, and Ralser M.
J Inherit Metab Dis. 2019 May 20. doi:10.1002/jimd.12105

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.
Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas-Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ.
Curr Biol. 2019 May 10. pii: S0960-9822(19)30407-5. doi:10.1016/j.cub.2019.04.009

Increased versatility despite reduced molecular complexity – evolution, structure and function of metazoan splicing factor PRPF39.
De Bortoli F, Neumann A, Kotte A, Timmermann B, Schüler T, Wahl M, Loll B and Heyd F.
Nucleic Acids Res. 2019 Apr 5. pii: gkz243 doi:10.1093/nar/gkz243

DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro.
Verheijen M, Lienhard M, Schrooders Y, Clayton O, Nudischer R, Boerno ST, Timmermann B, Selevsek N, Schlapbach R, Gmuender H, Gotta S, Geraedts J, Herwig R, Kleinjans J and Caiment F.
Sci Rep. 2019 Mar 15;9(1):4641. doi:10.1038/s41598-019-40660-0

Serial Genomic Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations.
Kraft K, Magg A, Heinrich V, Riemenschneider C, Schöpflin R, Markowski J, Ibrahim DM, Acuna-Hidalgo R, Despang A, Andrey G, Wittler L, Timmermann B, Vingron M, Mundlos S.
Nat Cell Biol. 2019 Feb 11. doi:10.1038/s41556-019-0273-x

An integrative systems approach identifies novel candidates in Marfan syndrome-related pathophysiology.
Bhushan R, Altinbas L, Jäger M, Zaradzki M, Lehmann D, Timmermann B, Clayton N, Zhu Y, Kallenbach K, Kararigas G, Robinson PN.
J Cell Mol Med. 2019 Jan 24. doi:10.1111/jcmm.14137


Peer-reviewed Papers

Dynamic 3D chromatin architecture determines enhancer specificity and morphogenetic identity in limb development.
Kragesteen BK, Spielmann M, Paliou C, Heinrich V, Schoepflin R, Esposito A, Annunziatella C, Bianco S, Chiariello AM, Jerković I, Harabula I, Guckelberger P, Pechstein M, Wittler L, Chan WL, Franke M, Darío Lupiáñez G, Kraft K, Timmermann B, Vingron M, Visel A, Nicodemi M, Mundlos, Andrey G.
Nat Genet. 2018 Oct;50(10):1463-1473. doi:10.1038/s41588-018-0221-x

Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance.
Grasse S, Lienhard M, Freese S, Steinbach A, Grimm C, Hussong M, Rolff J, Becker M, Dreher F, Schirmer U, Boerno S, Ramisch A, Leschber G, Timmermann B, Odenthal M, Büttner R, Grohé C, Lüders H, Vingron M, Fichtner I, Kein S, Sültmann H, Lehrach H, Herwig R, Schweiger M.
Genome Med. 2018 Jul 20;10(1):55. doi:10.1186/s13073-018-0562-1

Esrrb unlocks silenced enhancers for reprogramming to naïve pluripotency.
Adachi K, Wolfgang Kopp W, Wu G, Heising S, Greber B, Stehling M, Araúzo-Bravo MJ, Boerno ST, Timmermann B, Vingron M, Schöler HR.
Cell Stem Cell. 2018 Jun 11; doi:10.1016/j.stem.2018.05.020

Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas.
Mueller JC, Kuhl H, Boerno S, Tella JL, Carrete M, Kempenaers B.
Proc Biol Sci. 2018 May 16;285(1878). doi:10.1098/rspb.2018.0206

Global delay in nascent strand DNA methylation.
Charlton J, Downing TL, Smith ZD, Gu H, Clement K, Pop R, Akopian V, Klages S, Santos DP, Tsankov AM, Timmermann B, Ziller MJ, Kiskinis E, Gnirke A, Meissner A.
Nat Struct Mol Biol. 2018 Mar 12; doi:10.1038/s41594-018-0046-4

Genome-wide strategies identify downstream target genes of connective tissue-associated transcription factors.
Orgeur M, Martens M, Leonte G, Nassari S, Bonnin M-A, Börno ST, Timmermann B, Hecht J, Duprez D, Stricker S.
Development. 2018 Mar 6; doi:10.1242/dev.161208

Genome-wide tracking of dCas9-methyltransferase footprints.
Galonska C, Charlton J, Mattei AL, Donaghey J, Clement K, Gu H, Mohammad AW, Stamenova EK, Cacchiarelli D, Klages S, Timmermann B, Cantz T, Schöler HR, Gnirke A, Ziller MJ, Meissner A.
Nat Commun. 2018 Feb 9;9(1):597. doi:10.1038/s41467-017-02708-5

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model.
Orgeur M, Martens M, Börno ST, Timmermann B, Duprez D, Stricker S.
Biol Open. 2018 Jan 17;7(1). doi:10.1242/bio.028498

Genetics of intellectual disability in consanguineous families.
Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers H-H, Najmabadi H.
Mol Psychiatry. 2018 Jan 4; doi:10.1038/s41380-017-0012-2



Peer-reviewed Papers

Odd skipped-related 1 identifies a population of embryonic fibro-adipogenic progenitors regulating myogenesis during limb development.
Vallecillo-García P, Orgeur M, Vom Hofe-Schneider S, Stumm J, Kappert V, Ibrahim DM, Börno ST, Hayashi S, Relaix F, Hildebrandt K, Sengle G, Koch M, Timmermann B, Marazzi G, Sassoon DA, Duprez D, Stricker S.
Nat Commun. 2017 Oct 31;8(1):1218 doi:10.1038/s41467-017-01120-3

Protein interaction perturbation profiling at amino-acid resolution.
Woodsmith J, Apelt L, Casado-Medrano V, Özkan Z, Timmermann B, Stelzl U.
Nat Methods. 2017 Oct 16; doi:10.1038/nmeth.4464

The cancer-associated U2AF35 470A>G (Q157R) mutation creates an in-frame alternative 5’ splice site that impacts on splicing regulation in Q157R patients.
Herdt O, Neumann A, Timmermann B, Heyd F.
RNA. 2017 Sep 11; doi:10.1261/rna.061432.117

LSD1 modulates the non-canonical integrin β3 signaling pathway in non-small cell lung carcinoma cells.
Lim S-Y, Macheleidt I, Dalvi P, Schäfer SC, Kerick M, Ozretić L, Ortiz-Cuaran S, George J, Merkelbach-Bruse S, Wolf J, Timmermann B, Thomas RK, Schweiger MR, Buettner R, Odenthal M.
Sci Rep. 2017 Aug 31;7(1):10292. doi:10.1038/s41598-017-09554-x

The Mobile Element Locator Tool (MELT): Population-scale mobile element discovery and biology.
Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project Consortium, Devine SE.
Genome Res. 2017 Aug 30; doi:10.1101/gr.218032.116

Haplotype-resolved sweet potato genome traces back its hexaploidization history.
Yang J, Moeinzadeh M-H, Kuhl H, Helmuth J, Xiao P, Haas S, Liu G, Zheng J, Sun Z, Fan W, Deng G, Wang H, Hu F, Zhao S, Fernie AR, Boerno S, Timmermann B, Zhang P, Vingron M.
Nat Plants. 2017 Aug 21; doi:10.1038/s41477-017-0002-z

Antagonistic Activities of Sox2 and Brachyury Control the Fate Choice of Neuro-Mesodermal Progenitors.
Koch F, Scholze M, Wittler L, Schifferl D, Sudheer S, Grote P, Timmermann B, Macura K, Herrmann BG.
Dev Cell. 2017 Aug 9; doi:10.1016/j.devcel.2017.07.021

Genomic and transcriptomic heterogeneity of colorectal tumors arising in Lynch Syndrome.
Binder H, Hopp L, Schweiger MR, Hoffmann S, Jühling F, Kerick M, Timmermann B, Siebert S, Grimm C, Nersisyan L, Arakelyan A, Herberg M, Buske P, Loeffler-Wirth H, Rosolowski M, Engel C, Przybilla J, Peifer M, Friedrichs N, Moeslein G, Odenthal M, Hussong M, Peters S, Holzapfel S, Nattermann J, Hueneburg R, Schmiegel W, Royer-Pokora B, Aretz S, Kloth M, Kloor M, Buettner R, Galle J, Loeffler M.
J Pathol. 2017 Jul 20; doi:10.1002/path.4948

Patterning and gastrulation defects caused by the tw18 lethal are due to loss of Ppp2r1a.
Lange L, Marks M, Liu J, Wittler L, Bauer H, Piehl S, Bläß G, Timmermann B, Herrmann BG
Biol Open. 2017 Jun 15;6(6):752–64. doi:10.1242/bio.023200

Wild tobacco genomes reveal the evolution of nicotine biosynthesis.
Xu S , Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, Baldwin IT
Proc Natl Acad Sci USA. 2017 May 23; doi:10.1073/pnas.1700073114

Alignment of 1000 Genomes Project Reads to Reference Assembly GRCh38.
Zheng-Bradley X, Streeter I, Fairley S, Richardson D, Clarke L, Flicek P, 1000 Genomes Project Consortium.
Gigascience. 2017 May 20; doi:10.1093/gigascience/gix038

Transcriptomic and proteomic insight into the effects of a defined European mistletoe extract in Ewing sarcoma cells reveals cellular stress responses.
Twardziok M, Meierhofer D, Börno S, Timmermann B, Jäger S, Boral S, Eggert A, Delebinski CI, Seifert G.
BMC Complement Altern Med. 2017 Apr 28;17(1):237. doi:10.1186/s12906-017-1715-2

QSEA – modelling of genome-wide DNA methylation from sequencing enrichment experiments.
Lienhard M, Grasse S, Rolff J, Frese S, Schirmer U, Becker M, Börno S, Timmermann B, Chavez L, Sültmann H, Leschber G, Fichtner I, Schweiger M, Herwig R.
Nucleic Acids Res. 2017 Apr 7;45(6):e44. doi:10.1093/nar/gkw1193

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding.
Andrey G, Schöpflin R, Jerković I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S.
Genome Res. 2017 Feb;27(2):223-233 doi:10.1101/gr.213066.116

The bromodomain protein BRD4 regulates splicing during heat shock.
Hussong M, Kaehler C, Kerick M, Grimm C, Franz A, Timmermann B, Welzel F, Isensee J, Hucho T, Krobitsch S, Schweiger MR.
Nucleic Acids Res. 2017 Jan 9;45(1):382–94. doi:10.1093/nar/gkw729



Peer-reviewed Papers

Formation of novel chromatin domains determines pathogenicity of genomic duplications.
Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan W-L, Spielmann M, Timmermann B, Wittler L, Kurth I, Cambiaso P, Zuffardi O, Houge G, Lambie L, Brancati F, Pombo A, Vingron M, Spitz F, Mundlos S.
Nature. 2016 Oct 5;538(7624):265–9. doi:10.1038/nature19800

A cancer specific hypermethylation signature of the TERT promoter predicts biochemical relapse in prostate cancer: A retrospective cohort study.
Castelo-Branco P, Leão R, Lipman T, Campbell B, Lee D, Price A, Zhang C, Heidari A, Stephens D, Boerno S, Coelho H, Gomes A, Domingos C, Apolonio JD, Schäfer G, Bristow RG, Schweiger MR, Hamilton R, Zlotta A, Figueiredo A, Klocker H, Sültmann H, Tabori U.
Oncotarget. 2016 Jul 16; doi:10.18632/oncotarget.10639

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, Ayub Q, McCarthy SA, Narechania A, Kashin S, Chen Y, Banerjee R, Rodriguez-Flores JL, Cerezo M, Shao H, Gymrek M, Malhotra A, Louzada S, Desalle R, Ritchie GRS, Cerveira E, Fitzgerald TW, Garrison E, Marcketta A, Mittelman D, Romanovitch M, Zhang C, Zheng-Bradley X, Abecasis GR, McCarroll SA, Flicek P, Underhill PA, Coin L, Zerbino DR, Yang F, Lee C, Clarke L, Auton A, Erlich Y, Handsaker RE, 1000 Genomes Project Consortium, Bustamante CD, Tyler-Smith C.
Nat Genet. 2016 Jun;48(6):593–9. doi:10.1038/ng.3559

Transcriptional signature induced by a C-terminal c-Src mutant in a human breast cell line.
Broecker F, Hardt C, Herwig R, Timmermann B, Kerick M, Wunderlich A, Schweiger M, Borsig L, Heikenwalder M, Lehrach H, Moelling K.
FEBS J. 2016 May;283(9):1669–88. doi:10.1111/febs.13694

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRS, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin C-S, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O’Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.
PLoS Genet. 2016 Apr;12(4):e1005954; doi:10.1371/journal.pgen.1005954

Characterization and refinement of growth related quantitative trait loci in European sea bass (Dicentrarchus labrax) using a comparative approach.
Louro B, Kuhl H, Tine M, de Koning D-J, Batargias C, Volckaert FAM, Reinhardt R, Canario AVM, Power DM.
Aquaculture. 2016 Mar;455:8–21; doi:10.1016/j.aquaculture.2016.01.004

Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals.
Mueller JC, Kuhl H, Timmermann B, Kempenaers B.
Mol Ecol Resour. 2016 Mar;16(2):549–61. doi:10.1111/1755-0998.12450

The metabolic background is a global player in Saccharomyces gene expression epistasis.
Alam MT, Zelezniak A, Mülleder M , Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M.
Nature Microbiology. 2016 Feb 1;15030. doi:10.1038/nmicrobiol.2015.30

Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis.
Spier I, Kerick M, Drichel D, Horpaopan S, Altmüller J, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Holinski-Feder E, Perner S, Thiele H, Nöthen MM, Hoffmann P, Timmermann B, Schweiger MR, Aretz S.
Fam Cancer. 2016 Jan 16; doi:10.1007/s10689-016-9870-z

Low-level APC mutational mosaicism is the underlying cause in a substantial fraction of unexplained colorectal adenomatous polyposis cases.
Spier I, Drichel D, Kerick M, Kirfel J, Horpaopan S, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Perner S, Hoffmann P, Kristiansen G, Timmermann B, Nöthen MM, Holinski-Feder E, Schweiger MR, Aretz S.
J Med Genet. 2016 Mar;53(3):172-9 doi:10.1136/jmedgenet-2015-103468



Peer-reviewed Papers

Combined ultra-low input mRNA and whole-genome sequencing of human embryonic stem cells.
Mertes F, Lichtner B, Kuhl H, Blattner M, Otte J, Wruck W, Timmermann B, Lehrach H, Adjaye J.
BMC Genomics. 2015;16(1):925. doi:10.1186/s12864-015-2025-z

Allele frequencies of BRAFV600 mutations in primary melanomas and matched metastases and their relevance for BRAF inhibitor therapy in metastatic melanoma.
Satzger I, Marks L, Kerick M, Klages S, Berking C, Herbst R, Kapp A, Völker B, Schacht V, Timmermann B, Gutzmer R.
Oncotarget. 2015 Oct 16; doi:10.18632/oncotarget.5634

A global reference for human genetic variation.
The 1000 Genomes Project Consortium [MPI contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Davydov AN, Herwig R, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML, and Lehrach H].
Nature. 2015 Oct 1;526(7571):68–74. doi:10.1038/nature15393

An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer E-W, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.
Nature. 2015 Oct 1;526(7571):75–81. doi:10.1038/nature15394

miR-22 and miR-29a are members of the androgen receptor cistrome modulating LAMC1 and Mcl-1 in prostate cancer.
Pasqualini L, Bu H, Puhr M, Narisu N, Rainer J, Schlick B, Schäfer G, Angelova M, Trajanoski Z, Börno ST, Schweiger MR, Fuchsberger C, Klocker H.
Mol Endocrinol. 2015 Jul;29(7):1037–54. doi:10.1210/me.2014-1358

Effects of different oocyte retrieval and in vitro maturation systems on bovine embryo development and quality.
Ulloa SMB, Heinzmann J, Herrmann D, Timmermann B, Baulain U, Großfeld R, Diederich M, Lucas-Hahn A, Niemann H.
Zygote. 2015 Jun;23(3):367–77. doi:10.1017/S0967199413000658

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions.
Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S.
Cell. 2015 May 21;161(5):1012-25. doi:10.1016/j.cell.2015.04.004

The CatSper channel controls chemosensation in sea urchin sperm.
Seifert R, Flick M, Bönigk W, Alvarez L, Trötschel C, Poetsch A, Müller A, Goodwin N, Pelzer P, Kashikar ND, Kremmer E, Jikeli J, Timmermann B, Kuhl H, Fridman D, Windler F, Kaupp UB, Strünker T.
EMBO J. 2015 Feb 3;34(3):379-92. doi:10.15252/embj.201489376

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.
Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira E, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M.
Genome Biol. 2015 Jan 29;16(1):19. doi:10.1186/s13059-014-0578-9



Peer-reviewed Papers

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation.
Tine M, Kuhl H, Gagnaire P-A, Louro B, Desmarais E, Martins RST, Hecht J, Knaust F, Belkhir K, Klages S, Dieterich R, Stueber K, Piferrer F, Guinand B, Bierne N, Volckaert FAM, Bargelloni L, Power DM, Bonhomme F, Canario AVM, Reinhardt R.
Nat Commun. 2014 Dec 23;5:5770. doi: 10.1038/ncomms6770. doi:10.1038/ncomms6770

The landscape of human STR variation.
Willems T, Gymrek M, Highnam G, The 1000 Genomes Project Consortium, Mittelman D, Erlich Y.
Genome Res. 2014 Nov;24(11):1894-904. doi:10.1101/gr.177774.114

Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome.
Krawitz PM, Schiska D, Krüger U, Appelt S, Heinrich V, Parkhomchuk D, Timmermann B, Millan JM, Robinson PN, Mundlos S, Hecht J, Gross M.
Mol Genet Genomic Med. 2014 Sep;2(5):393–401 doi:10.1002/mgg3.92

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium [MPIMG contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M and Lehrach H].
Genome Biol. 2014 June 30;15(6):R88. doi:10.1186/gb-2014-15-6-r88

Rare and Private Variations in Neural Crest, Apoptosis and Sarcomere Genes Define the Polygenic Background of Isolated Tetralogy of Fallot.
Grunert M, Dorn C, Schueler M, Dunkel I, Schlesinger J, Mebus S, Alexi-Meskishvili V, Perrot A, Wassilew K, Timmermann B, Hetzer R, Berger F, Sperling SR.
Hum Mol Genet. 2014 Jun 15;23(12):3115-28. doi:10.1093/hmg/ddu021

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Delaneau O, Marchini J & 1000 Genomes Project Consortium [MPIMG contributors: Lehrach H, Sudbrak R, Amstislavskiy VS, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML, Herwig R]
Nat Commun. 2014 Jun 13; 5: 3934. doi:10.1038/ncomms4934

The tissue-specific transcriptomic landscape of the mid-gestational mouse embryo.
Werber M, Wittler L, Timmermann B, Grote P, Herrmann BG.
Development. 2014 Jun;141(11):2325-30. doi:10.1242/dev.105858

Classic bladder exstrophy: Frequent 22q11.21 duplications and definition of a 414 kb phenocritical region: 22Q11.21 Duplications in Bladder Exstrophy.
Draaken M, Baudisch F, Timmermann B, Kuhl H, Kerick M, Proske J, Wittler L, Pennimpede T, Ebert A-K, Rösch W, Stein R, Bartels E, von Lowtzow C, Boemers TM, Herms S, Gearhart JP, Lakshmanan Y, Kockum CC, Holmdahl G, Läckgren G, Nordenskjöld A, Boyadjiev SA, Herrmann BG, Nöthen MM, Ludwig M, Reutter H.
Birth Defects Res Part A Clin Mol Teratol. 2014 Jun;100(6):512-7. doi:10.1002/bdra.23249

The bromodomain protein BRD4 regulates the KEAP1/NRF2 dependent oxidative stress response.
Hussong M, Börno S, Kerick M, Wunderlich A, Franz A, Sültmann H, Timmermann B, Lehrach H, Hirsch-Kauffmann M, Schweiger MR.
Cell Death Dis. 2014 Apr 24;5:e1195. doi:10.1038/cddis.2014.157



Peer-reviewed Papers

Reconstructing Native American migrations from whole-genome and whole-exome data.
Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G, 1000 Genomes Project Consortium, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD.
PLoS Genet. 2013;9(12):e1004023. doi:10.1371/journal.pgen.1004023

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.
Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, 1000 Genomes Project Consortium, Lee C, Gerstein M.
Genome Res. 2013 Dec;23(12):2042–52. doi:10.1101/gr.154625.113

Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum).
Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK.
BMC Genomics. 2013 Nov 14;14(1):793. doi:10.1186/1471-2164-14-793

Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium [MPI contributors: Lehrach H, Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML], Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, McVean GA.
Science. 2013 Oct 4;342(6154):1235587.

Distinct global shifts in genomic binding profiles of limb malformation associated HOXD13 mutations.
Ibrahim DM, Hansen P, Rödelsperger C, Stiege AC, Dölken S, Horn D, Jäger M, Janetzki C, Krawitz P, Leschik G, Wagner F, Scheuer T, Schmidt-von Kegler M, Seemann P, Timmermann B, Robinson PN, Mundlos S, Hecht J.
Genome Res. 2013 Dec;23(12):2091-102.

Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni M-E, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lünsdorf H, Fernández M, Juárez S, Ciordia S, Singer A, Kagan O, Egorova O, Alain Petit P, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martínez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN.
Nat Commun. 2013 Jul 23;4:2156.

High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications.
Röhr C, Kerick M, Fischer A, Kühn A, Kashofer K, Timmermann B, Daskalaki A, Meinel T, Drichel D, Börno ST, Nowka A, Krobitsch S, McHardy AC, Kratsch C, Becker T, Wunderlich A, Barmeyer C, Viertler C, Zatloukal K, Wierling C, Lehrach H, Schweiger MR.
PLoS ONE. 2013 Jul;8(7):e67461.

Genomics and epigenomics: new promises of personalized medicine for cancer patients.
Schweiger M-R, Barmeyer C, Timmermann B.
Brief Funct Genomics. 2013 Sep;12(5):411–21.

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.
Montgomery SB, Goode DL, Kvikstad E, Albers CA, Zhang ZD, Mu XJ, Ananda G, Howie B, Karczewski KJ, Smith KS, Anaya V, Richardson R, Davis J, 1000 Genomes Project Consortium, MacArthur DG, Sidow A, Duret L, Gerstein M, Makova KD, Marchini J, McVean G, Lunter G.
Genome Res. 2013 May;23(5):749–61.

A Y2H-seq approach defines the human protein methyltransferase interactome.
Weimann M, Grossmann A, Woodsmith J, Özkan Z, Birth P, Meierhofer D, Benlasfer N, Valovka T, Timmermann B, Wanker EE, Sauer S, Stelzl U.
Nat Methods. 2013 Apr;10(4):339–42.

Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells.
Feldmann R, Fischer C, Kodelja V, Behrens S, Haas S, Vingron M, Timmermann B, Geikowski A, Sauer S.
Nucleic Acids Res. 2013 Apr 1;41(6):3518–31.

Anterior gradient 2 and 3--two prototype androgen-responsive genes transcriptionally upregulated by androgens and by oestrogens in prostate cancer cells.
Bu H, Schweiger MR, Manke T, Wunderlich A, Timmermann B, Kerick M, Pasqualini L, Shehu E, Fuchsberger C, Cato ACB, Klocker H.
FEBS J. 2013 Mar;280(5):1249–66.

DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer.
Grimm C, Chavez L, Vilardell M, Farrall AL, Tierling S, Böhm JW, Grote P, Lienhard M, Dietrich J, Timmermann B, Walter J, Schweiger MR, Lehrach H, Herwig R, Herrmann BG, Morkel M.
PLoS Genet. 2013 Feb;9(2):e1003250.

The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse.
Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M, Herrmann BG.
Dev Cell. 2013 Jan 28;24(2):206–14.



Peer-reviewed Papers

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.
Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, 1000 Genomes Project Consortium.
Am J Hum Genet. 2012 Dec 7;91(6):1022–32.

Mutations of the EPHB6 receptor tyrosine kinase induce a pro-metastatic phenotype in non-small cell lung cancer.
Bulk E, Yu J, Hascher A, Koschmieder S, Wiewrodt R, Krug U, Timmermann B, Marra A, Hillejan L, Wiebe K, Berdel WE, Schwab A, Müller-Tidow C.
PLoS ONE. 2012 Dec;7(12):e44591.

Involvement of the MLL gene in adult T-lymphoblastic leukemia.
Türkmen S, Timmermann B, Bartels G, Gröger D, Meyer C, Schwartz S, Haferlach C, Rieder H, Gökbuget N, Hoelzer D, Marschalek R, Burmeister T.
Genes Chromosomes Cancer. 2012 Dec;51(12):1114–24.

Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation.
Börno ST, Fischer A, Kerick M, Fälth M, Laible M, Brase JC, Kuner R, Dahl A, Grimm C, Sayanjali B, Isau M, Röhr C, Wunderlich A, Timmermann B, Claus R, Plass C, Graefen M, Simon R, Demichelis F, Rubin MA, Sauter G, Schlomm T, Sültmann H, Lehrach H, Schweiger MR.
Cancer Discov. 2012 Nov;2(11):1024–35.

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium [MPI contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Davydov AN, Herwig R, Lienhard M, Mertes F, Sultan M, Timmermann B, Yaspo ML, and Lehrach H].
Nature. 2012 Nov 1;491(7422):56–65.

Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus.
Spielmann M, Brancati F, Krawitz PM, Robinson PN, Ibrahim DM, Franke M, Hecht J, Lohan S, Dathe K, Nardone AM, Ferrari P, Landi A, Wittler L, Timmermann B, Chan D, Mennen U, Klopocki E, Mundlos S.
Am J Hum Genet. 2012 Oct 5;91(4):629–35.

The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt.
Ralser M, Kuhl H, Ralser M, Werber M, Lehrach H, Breitenbach M, Timmermann B.
Open Biol. 2012 Aug;2(8):120093.

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, 1000 Genomes Project Consortium [MPI contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M, and Lehrach H].
Nat Methods. 2012 May;9(5):459–62.

Characteristics of fads2 gene expression and putative promoter in European sea bass (Dicentrarchus labrax): comparison with salmonid species and analysis of CpG methylation.
Geay F, Zambonino-Infante J, Reinhardt R, Kuhl H, Santigosa E, Cahu C, Mazurais D.
Mar Genomics. 2012 Mar;5:7–13.

A systematic survey of loss-of-function variants in human protein-coding genes.
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner M-M, Hunt T, Barnes IHA, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium [MPI contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M, and Lehrach H], Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C.
Science. 2012 Feb 17;335(6070):823–8.

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.

Long-term survival of hydrated resting eggs from Brachionus plicatilis.
Clark MS, Denekamp NY, Thorne MAS, Reinhardt R, Drungowski M, Albrecht MW, Klages S, Beck A, Kube M, Lubzens E.
PLoS ONE. 2012 Jan 9;7(1):e29365.

Public Relations

Genomanalyse von Modellorganismen: Saccharomyces cerevisiae.
Ralser M, Timmermann B.
BIOspektrum. 2012 Aug 28;18(5):504–7.



Peer-reviewed Papers

The Interlaboratory RObustness of Next-generation sequencing (IRON) study: a deep sequencing investigation of TET2, CBL and KRAS mutations by an international consortium involving 10 laboratories.
Kohlmann A, Klein H-U, Weissmann S, Bresolin S, Chaplin T, Cuppens H, Haschke-Becher E, Garicochea B, Grossmann V, Hanczaruk B, Hebestreit K, Gabriel C, Iacobucci I, Jansen JH, te Kronnie G, van de Locht L, Martinelli G, McGowan K, Schweiger MR, Timmermann B, Vandenberghe P, Young BD, Dugas M, Haferlach T.
Leukemia. 2011 Dec;25(12):1840–8.

Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development.
Göke J, Jung M, Behrens S, Chavez L, O’Keeffe S, Timmermann B, Lehrach H, Adjaye J, Vingron M.
PLoS Comput Biol. 2011 Dec;7(12):e1002304.

Novel correlations between the genotype and the phenotype of hypertrophic and dilated cardiomyopathy: results from the German Competence Network Heart Failure.
Waldmüller S, Erdmann J, Binner P, Gelbrich G, Pankuweit S, Geier C, Timmermann B, Haremza J, Perrot A, Scheer S, Wachter R, Schulze-Waltrup N, Dermintzoglou A, Schönberger J, Zeh W, Jurmann B, Brodherr T, Börgel J, Farr M, Milting H, Blankenfeldt W, Reinhardt R, Özcelik C, Osterziel K-J, Loeffler M, Maisch B, Regitz-Zagrosek V, Schunkert H, Scheffold T, German Competence Network Heart Failure.
Eur J Heart Fail. 2011 Nov;13(11):1185–92.

The genome sequence of Atlantic cod reveals a unique immune system.
Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel J-H, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO, Moum T, Skage M, Berg PR, Gjøen T, Kuhl H, Thorsen J, Malde K, Reinhardt R, Du L, Johansen SD, Searle S, Lien S, Nilsen F, Jonassen I, Omholt SW, Stenseth NC, Jakobsen KS.
Nature. 2011 Sep 8;477(7363):207–10.

Human induced pluripotent stem cells harbor homoplasmic and heteroplasmic mitochondrial DNA mutations while maintaining human embryonic stem cell-like metabolic reprogramming.
Prigione A, Lichtner B, Kuhl H, Struys EA, Wamelink M, Lehrach H, Ralser M, Timmermann B, Adjaye J.
Stem Cells. 2011 Sep;29(9):1338–48.

The functional spectrum of low-frequency coding variation.
Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project [MPIMG contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M and Lehrach H].
Genome Biol. 2011 Sep;12(9):R84.

Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones.
Kuhl H, Tine M, Beck A, Timmermann B, Kodira C, Reinhardt R.
Genomics. 2011 Sep;98(3):202–12.

Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
Kerick M, Isau M, Timmermann B, Sültmann H, Herwig R, Krobitsch S, Schaefer G, Verdorfer I, Bartsch G, Klocker H, Lehrach H, Schweiger MR.
BMC Med Genomics. 2011 Sep;4:68.

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group [MPIMG contributors: Sudbrak R, Amstislavskiy VS, Borodina TA, Dahl A, Herwig R, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, and Lehrach H].
Bioinformatics. 2011 Aug 1;27(15):2156–8.

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, 1000 Genomes Project [MPIMG contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M and Lehrach H], Bustamante CD.
Proc Natl Acad Sci USA. 2011 Jul 19;108(29):11983–8.

Variation in genome-wide mutation rates within and between human families.
Conrad DF, Keebler JEM, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project [MPIMG contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M and Lehrach H].
Nat Genet. 2011 Jul;43(7):712–4.

The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations.
Schweiger MR, Kerick M, Timmermann B, Isau M.
Cancer Metastasis Rev. 2011 Jun;30(2):199–210.

Genome of Streptococcus oralis strain Uo5.
Reichmann P, Nuhn M, Denapaite D, Brückner R, Henrich B, Maurer P, Rieger M, Klages S, Reinhard R, Hakenbeck R.
J Bacteriol. 2011 Jun;193(11):2888–9.

Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.
Jones AC, Monroe EA, Podell S, Hess WR, Klages S, Esquenazi E, Niessen S, Hoover H, Rothmann M, Lasken RS, Yates JR 3rd, Reinhardt R, Kube M, Burkart MD, Allen EE, Dorrestein PC, Gerwick WH, Gerwick L.
Proc Natl Acad Sci USA. 2011 May 24;108(21):8815–20.

Benchmarking of mutation diagnostics in clinical lung cancer specimens.
Querings S, Altmüller J, Ansén S, Zander T, Seidel D, Gabler F, Peifer M, Markert E, Stemshorn K, Timmermann B, Saal B, Klose S, Ernestus K, Scheffler M, Engel-Riedel W, Stoelben E, Brambilla E, Wolf J, Nürnberg P, Thomas RK.
PLoS ONE. 2011 May;6(5):e19601.

Natural history of SLC11 genes in vertebrates: tales from the fish world.
Neves JV, Wilson JM, Kuhl H, Reinhardt R, Castro LFC, Rodrigues PNS.
BMC Evol Biol. 2011 Apr 18;11:106.

Identification of genes essential for prey-independent growth of Bdellovibrio bacteriovorus HD100.
Roschanski N, Klages S, Reinhardt R, Linscheid M, Strauch E.
J Bacteriol. 2011 Apr;193(7):1745–56.

Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite.
De Gregoris TB, Rupp O, Klages S, Knaust F, Bekel T, Kube M, Burgess JG, Arnone MI, Goesmann A, Reinhardt R, Clare AS.
Biofouling. 2011 Apr;27(4):367–74.

Comparative genomic analysis of fruiting body formation in Myxococcales.
Huntley S, Hamann N, Wegener-Feldbrügge S, Treuner-Lange A, Kube M, Reinhardt R, Klages S, Müller R, Ronning CM, Nierman WC, Søgaard-Andersen L.
Mol Biol Evol. 2011 Feb;28(2):1083–97.

Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HYK, Leng J, Li R, Li Y, Lin C-Y, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project [MPI contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M and Lehrach H].
Nature. 2011 Feb 3;470(7332):59–65.

Book Chapters

Genomics and Cancer Risk Assessment.
Schweiger MR, Timmermann B.
In: Obe G, Jandrig B, Marchant GE, Schütz H, Wiedemann PM, editors. Cancer Risk Evaluation [Internet].
Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA; 2011 [cited 2013 Sep 17]. p. 175–93.



Peer-reviewed Papers

Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.
Timmermann B, Kerick M, Roehr C, Fischer A, Isau M, Boerno ST, Wunderlich A, Barmeyer C, Seemann P, Koenig J, Lappe M, Kuss AW, Garshasbi M, Bertram L, Trappe K, Werber M, Herrmann BG, Zatloukal K, Lehrach H, Schweiger MR.
PLoS ONE. 2010 Dec 22;5(12):e15661.

Diversity of human copy number variation and multicopy genes.
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project [MPI contributors: Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Sudbrak R, Timmermann B, Tolzmann M and Lehrach H], Eichler EE.
Science. 2010 Oct 29;330(6004):641–6.

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.
Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, Lehrach H, Herwig R, Adjaye J.
Genome Res. 2010 Oct;20(10):1441–50.

A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium [MPI contributors: Sudbrak R, Albrecht MW, Amstislavskiy VS, Borodina TA, Dahl A, Davydov AN, Herwig R, Marquardt P, Mertes F, Nietfeld W, Parkhomchuk DV, Soldatov AV, Timmermann B, Tolzmann M, and Lehrach H].
Nature. 2010 Oct 28;467(7319):1061–73.

A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging.
Timmermann B, Jarolim S, Russmayer H, Kerick M, Michel S, Krüger A, Bluemlein K, Laun P, Grillari J, Lehrach H, Breitenbach M, Ralser M.
Aging (Albany NY). 2010 Aug;2(8):475–86.

   2nd generation DNA sequencing meets functional genomics.
   Gut IG.
   Aging (Albany NY). 2010 Sep;2(9):541.

   Revisiting the free radical theory using next-generation sequencing technology.
   Burhans WC, Weinberger M.
   Aging (Albany NY). 2010 Aug;2(8):459–60.

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.

High-throughput sequencing of microdissected chromosomal regions.
Weise A, Timmermann B, Grabherr M, Werber M, Heyn P, Kosyakova N, Liehr T, Neitzel H, Konrat K, Bommer C, Dietrich C, Rajab A, Reinhardt R, Mundlos S, Lindner TH, Hoffmann K.
Eur J Hum Genet. 2010 Apr;18(4):457–62.

Translation of next-generation sequencing (NGS) into molecular diagnostics.
Kotschote S, Wagner C, Marschall C, Mayer K, Hirv K, Kerick M, Timmermann B, Klein H-G.
LaboratoriumsMedizin. 2010 Jan 1;34(6):311–8.

Public Relations

[High-throughput sequencing of frozen and paraffin-embedded tumor and normal tissue].
Kerick M, Timmermann B, Schweiger M-R.
Pathologe. 2010 Oct;31 Suppl 2:255–7.

Hochdurchsatzsequenzierung: Vom Forschungslabor in die Diagnostik.
Timmermann B.
Diagnostik im Dialog. 2010 Aug;29:17–8.

Auf dem Weg zur Next Generation Diagnostik.
Timmermann B.
Trillium Report. 2010 Aug;8(2):114–5.



Peer-reviewed Papers

Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.
Schweiger MR, Kerick M, Timmermann B, Albrecht MW, Borodina T, Parkhomchuk D, Zatloukal K, Lehrach H.
PLoS ONE. 2009;4(5):e5548.

Public Relations

Systematische Analyse der genetischen Variabilität des Menschen: Report 1000 Genomes Project.
Timmermann B, Albrecht MW, Amstislavskiy V, Borodina T, Dahl A, Herwig R, Nietfeld W, Parkhomchuk D, Soldatov A, Sudbrak R, Lehrach H.
Laborwelt. 2009 May;3:8–10.

Chemical-genetic profiling mittels Next Generation Sequencing.
Ralser M, Lehrach H, Timmermann B.
Laborwelt. 2009 May;3:16–7.



Peer-reviewed Papers

Sequencing and genotypic analysis of the triosephosphate isomerase (TPI1) locus in a large sample of long-lived Germans.
Ralser M, Nebel A, Kleindorp R, Krobitsch S, Lehrach H, Schreiber S, Reinhardt R, Timmermann B.
BMC Genet. 2008;9:38.

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