Dr Roland Arnold

Dr Roland Arnold

Institute of Cancer and Genomic Sciences
Research Fellow

Contact details

Address
Institute of Cancer and Genomic Sciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT

Dr. Roland Arnold is a group leader at the Institute for Cancer and Genomic Sciences and joined the institute in 2017 to build up a research group dedicated to bioinformatics for cancer and diseases.

He is interested in developing and applying methods that help us to bridge the gap between genomic alterations, especially in cancer, and cellular phenotypes by novel data analysis methods and by data-integration. While having experience in a wide range of methods and different high-throughput data types, his special interest is in methods that allow us to look at gene expression data in sophisticated ways and to deduce biologically relevant information that otherwise would have been overlooked.

Qualifications

  •  PhD in Bioinformatics, Technical University Munich (Dr. rer. nat), 2010
  • Diplom Bioinformatics, joint curriculum Technical University and Ludwig-Maximillians University, Munich, 2005

Biography

Roland started his scientific career as a student assistant in Munich working on biological database systems. In Munich, he finished his PhD under the supervision of Prof. Dr.  Mewes and Dr. Thomas Rattei where he analysed bacterial virulence, especially on the Type III secretion apparatus which is used by certain bacteria to transport proteins into host cells.

His post-doctoral training was at the Donnelly Centre for Cellular and Biomolecular Research in Toronto with Prof. Philip Kim. During this time, he worked on diverse projects including analyses of genetic and physical interaction screens in bacteria and cancer, and on the design and analysis of specialised phage-display experiments designed to detect certain protein interactions, especially in signalling pathways.

This worked inspired him to switch his focus completely to cancer and he took on a second post-doc with Prof. Adam Shlien at the Hospital for Sick Children in Toronto, focussing on the analysis of next-generation sequencing data, especially RNA, in childhood and other cancers. He then took on a position as senior bioinformatician at the Wellcome Trust Centre for Human Genetics in Oxford, working with Prof. Ian Tomlinson on colorectal cancer. He joined the Institute of Cancer and Genomic Science in September 2017 as an independent group leader.

Teaching

  • MSc in Genomics Omics module (lecture on RNA-sequencing)
  • Teaching history:

              - co-supervision of bachelor and master students (University of Toronto)

              - supervision of student projects and internships (Munich, Toronto, and Oxford)

              - teaching assistant “programming for biologists” (Toronto)

Interested in an internship, Bachelor, Master, or PhD in cancer related bioinformatics and expression analysis? Please contact r.arnold.2@bham.ac.uk

Postgraduate supervision

Interested in doing a PhD in cancer related bioinformatics and expression analysis? Please contact r.arnold.2@bham.ac.uk

Research

Roland’s current main research interest is mainly on cancer related topics and covers following topics:

  • Novel transcriptional events and unusual iso-form usage. Application to cancer stratification and for biological insights.
  • Advanced understanding of gene expression experiments by data-integration and signal deconvolution.
  • Reconstruction of cancer specific interaction networks from expression data.
  • Development of cancer with special focus on colorectal cancer and the adenoma, carcinoma, metastasis sequence. Identification of factors that drive progression.
  • Cancer and pre-cursor classification based on transcriptional events and signatures.
  • Tailor-made methods and analysis for CRISPR and shRNA based activation or essentiality screens.

Research Groups and Centres:

https://www.birmingham.ac.uk/research/activity/cancer-genomics/index.aspx

www.rolilab.net

Other activities

Reviewer for several scientific journals.

Publications

(* indicates joint first authors)

Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA.  In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering. Nat Commun. 2017 Dec 13;8(1):2109. doi: 10.1038/s41467-017-00686-2. PMID: 29235467

Sundell GN, Arnold R, Ali M, Orts J, Guentert P, Chi CN, Ivarsson Y.  Proteome-wide analysis of phospho-regulated PDZ domain interactions through phosphomimetic proteomic peptide phage display.  Biorxiv, 211250

Shlien A, Rain K, Fuligni F, Arnold R, Nik-Zainal S, Dronov S, Mamanova L, Rosic A, Seok Ju Y, Cooke SL, Ramakrishna M, Papaemmanuil M, Davie HRs, Tarpey PS, Van Loo P, Wedge DC, Jones DR, Martin S, Marshall J, Anderson E, Hardy C, Barbashina V, Aparicio SAJR, Sauer, T Garred Ø, Vincent-Salomon A, Mariani O,, Boyault S, Fatima A, Langerød A, Borg A, Thomas G, Richardson AL, Børresen-Dale AL, Polyak K, Stratton MR, Campbell PJ, ICGC Breast Cancer Working Group, Oslo Breast Cancer Research Consortium.  Direct transcriptional consequences of somatic mutation in breast cancer. Cell reports 16 (7), 2032-2046. PMID: 27498871

J Jeon*, R Arnold*, F Singh, J Teyra, T Braun, PM Kim PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies. BMC bioinformatics 17 (1), 150 PMID: 27039071

Garrido-Urbani S*, Garg P*, Ghossoub R*, Arnold R*, Lembo F, Sundell GN, Kim PK, Lopez M, Zimmermann P, Sidhu SS, Ivarsson Y.  Proteomic peptide phage display uncovers novel interactions of the PDZ1-2 supramodule of syntenin. FEBS Lett. 2016 Jan;590(1):3-12. doi: 10.1002/1873-3468.12037. Epub 2016 Jan 8. PMID: 26787460

Eichinger V, Nussbaumer T, Platzer A, Jehl MA, Arnold R, Rattei T. EffectiveDB—updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems.  Nucleic Acids Res. 2015 Nov 20. pii: gkv1269. [Epub ahead of print], PMID 26590402

Shlien A, Campbell BB, de Borja R, Alexandrov LB, Merico D, Wedge D, Van Loo P, Tarpey PS, Coupland P, Behjati S, Pollett A, Lipman T, Heidari A, Deshmukh S, Avitzur N, Meier B, Gerstung M, Hong Y, Merino DM, Ramakrishna M, Remke M, Arnold R, Panigrahi GB, Thakkar NP, Hodel KP, Henninger EE, Göksenin AY, Bakry D, Charames GS, Druker H, Lerner-Ellis J, Mistry M, Dvir R, Grant R, Elhasid R, Farah R, Taylor GP, Nathan PC, Alexander S, Ben-Shachar S, Ling SC, Gallinger S, Constantini S, Dirks P, Huang A, Scherer SW, Grundy RG, Durno C, Aronson M, Gartner A, Meyn MS, Taylor MD, Pursell ZF, Pearson CE, Malkin D, Futreal PA, Stratton MR, Bouffet E, Hawkins C, Campbell PJ, Tabori U; Biallelic Mismatch Repair Deficiency Consortium. Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers. Nat Genet. 2015 Mar;47(3):257-62. doi: 10.1038/ng.3202. Epub 2015 Feb 2, PMID    25642631

Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A,  Deineko V,  Kumar A, Leung E, Rizzolo  K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry,W Emili A, Morris Q, Bader G, Babu M. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics. 2015 Feb 1;31(3):306-10. doi: 10.1093/bioinformatics/btu671. Epub 2014 Oct, PMID 25316676

Babu M*, Arnold R*, Bundalovic-Torma C*, Gagarinova A*, Wong KS, Kumar A, Stewart,G, Samanfar B, Aoki H, Wagih O, Vlasblom J, Phanse S, Lad K, Yeou Hsiung Yu A, Graham C, Jin K, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J,Houry WA, Parkinson J, Emili (* joint first authors) A Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLoS Genet. 2014 Feb 20;10(2):e1004120, eCollection 2014 Feb. PMID: 24586182

Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Häuser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P. The binary protein-protein interaction landscape of Escherichia coli. Nat Biotechnology 2014 Feb 23 [Epub aheadof print] PubMed PMID: 24561554.

Ivarsson Y, Arnold R, McLaughlin M, Nim S, Joshi R, Ray D, Liu B, Teyra J, Pawson T, Moffat J, Li SS, Sidhu SS, Kim PM. Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phagepe ptidomes. Proc Natl Acad Sci USA. 2014 Feb 18;111(7):2542-7.Epub 2014 Feb 3 PMID: 24550280

Arnold R, Goldenberg F, Mewes HW, Rattei T. SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. Nucleic Acids Res. 2014 Jan;42(Database issue):D279-84. doi: 10.1093/nar/gkt970. Epub 2013 Oct 27. PubMed PMID: 24165881

Vizeacoumar FJ*, Arnold R*, Vizeacoumar FS, Chandrashekhar M, Buzina A, YoungJT, Kwan JH, Sayad A, Mero P, Lawo S, Tanaka H, Brown KR, Baryshnikova A, Mak AB, Fedyshyn Y, Wang Y, Brito GC, Kasimer D, Makhnevych T, Ketela T, Datti A, Babu M, Emili A, Pelletier L, Wrana J, Wainberg Z, Kim PM, Rottapel R, O'Brien CA, Andrews B, Boone C, Moffat J. A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Mol Syst Biol. 2013 Oct, 8;9:696, doi: 10.1038/msb.2013.54 PMID: 24104479

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P., eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9.  Epub 2011 Nov 16. PMID: 22096231

Arnold  R*, Boonen K*, Sun MGF, Kim PM (Review) Computational analysis of interactomes; current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. Methods. 2012 Aug;57(4):508-18.   Epub 2012 Jun 28 PMID: 22750305 (* joint first author)

Babu M, Díaz-Mejía JJ, Vlasblom J, Gagarinova A, Phanse S, Graham C, Yousif F, Ding H, Xiong X, Nazarians-Armavil A, Alamgir M, Ali M, Pogoutse O, Pe'er A, Arnold R, Michaut M, Parkinson J, Golshani A, Whitfield C, Wodak SJ, Moreno-Hagelsieb G, Greenblatt JF, Emili A. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. PLoS Genet. 2011 Nov;7(11):e1002377. Epub 2011 Nov 17. PMID: 22125496

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways
PLoS Genet. 2011 Nov;7(11):e1002377. Epub 2011 Nov 17. PMID: 22125496

Nuk MR, Reisner A, Neuwirth M, Schilcher K, Arnold R, Jehl A, Rattei T, Zechner EL., Functional analysis of the finO distal region of plasmid R1. Plasmid.  2010 Dec 08. [Epub ahead of print]  PMID: 21145347

Jehl MA, Arnold R, Rattei T., Effective--a database of predicted secreted bacterial proteins. Nucleic Acids Res. 2011 Jan;39(Database issue):D591-5.  Epub 2010 Nov 11. PMID: 21071416

Lang S, Gruber K, Mihajlovic S, Arnold R, Gruber CJ, Steinlechner S, Jehl MA, Rattei T, Fröhlich KU, Zechner EL.,
Molecular recognition determinants for type IV secretion of diverse families of conjugative relaxases.
Mol Microbiol. 2010 Dec;78(6):1539-55. Epub 2010 Oct 15. PMID: 21143323

Arnold R, Jehl MA, Rattei T. Targeting effectors: the molecular recognition of Type III secreted proteins (Review)
Microbes  Infect. 2010 Feb 21. [Epub ahead of print] PMID: 20178857

Schmitz-Esser S, Tischler P, Arnold R, Montanaro J, Wagner M, Rattei T, Horn M., The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria. J Bacteriol. 2010 Feb;192(4):1045-57. Epub 2009 Dec 18. PMID: 20023027

Rattei T, Tischler P, Götz S, Jehl MA, Hoser J, Arnold R, Conesa A, Mewes HW;  SIMAP – a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res. 2010 Jasn;38(Database issue):D223-6.  Epub 2009 Nov 11. PMID:19906725

Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T.,
Sequence-based prediction of type III secreted proteins. Plos Pathogens  2009 Apr;5(4); PMID: 19390696

Highlight of this article:

Grynberg M, Godzik A (2009) The Signal for Signaling, Found. PLoS  Pathog 5(4): e1000398. i:10.1371/journal.ppat.1000398

Walter MC, Rattei T, Arnold R, Güldener U, Münsterkötter M, Nenova K, Kastenmüller G, Tischler P, Wölling A, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D. PEDANT covers all RefSeq genomes Nucleic Acids Res. 2009 Jan;37(Database issue):D408-PMID: 18940859

Loy A, Arnold R, Tischler P, Rattei T, Wagner M, Horn M. probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity. Environ  Microbiol. 2008 Oct;10(10):2894-8; PMID: 18647333

Rattei T, Tischler P, Arnold R, Hamberger F, Krebs J, Krumsiek J, Wachinger B, Stümpflen V, Mewes W.
SIMAP--structuring the network of protein similarities. Nucleic Acids  Res. 2008, Jan;36(Database issue):D289-92.  PMID: 18037617

Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale.
Bioinformatics. 2007 Feb 19; PMID: 17309896

Rattei T, Arnold R, Tischler P, Lindner D, Stumpflen V, Mewes HW. SIMAP: the similarity matrix of proteins.
Nucleic Acids  Res. 2006 Jan 1;34(Database issue):D252-6.  PMID: 16381858

Rattei T, Walter M, Arnold R, Anderson DP, Mewes W. Using public resource computing and systematic precalculation for large scale sequence analysis. International Workshop Distributed, High- Performance and Grid Computing in Computational Biology (GCCB 2006) at the ECCB 2006 Lecture Notes in Bioinformatics

Arnold R*, Rattei T*, Tischler P, Truong MD, Stumpflen V, Mewes W. SIMAP--The similarity matrix of proteins
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii42-ii46.  PMID: 16204123 (* joint first author)

Mewes HW, Amid C, Arnold R, Frishman D, Guldener U, Mannhaupt G, Munsterkotter M, Pagel P, Strack N, Stumpflen V, Warfsmann J, Ruepp A. MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids  Res. 2004 Jan 1;32(Database issue):D41-4.PMID: 14681354

Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KF.
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res. 2002 Jan 1;30(1):91-3. PMID:11752263

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