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Archiv-Übersicht     Angebot Nr. 12908

Angebotsdatum: 26. Juni 2018
Art der Stelle: Doktorarbeit
Fachgebiet: Informatik > Bioinformatik
Titel des Themas: Understanding molecular pathways of neuroregeneration and neurodegeneration

Institut: Boston Children's Hospital
Herr Christoph Schlaffner
3 Blackfan Circle
02115 Boston
Tel.:    Fax.:
Homepage: http://www.childrenshospital.org/Research/Labs/steen-laboratory
E-Mail Kontakt: mail

Beschreibung: The Laboratories of Dr. Judith Steen, Associate Professor of Neurology, and Dr. Hanno Steen, Associate Professor of Pathology, are joint multidisciplinary laboratories working to understand neuroregeneration and neurodegenerative disease using systems biology approaches. The laboratory develops novel qualitative and quantitative methodologies in mass spectrometry and at the interface of proteomics and transcriptomics with emphasis on computational proteomics approaches.

These novel qualitative and quantitative methods and bioinformatics tools developed in our group are being applied to understand the biology of regeneration and neurodegeneration in mouse models, stem cells and human tissues. The research is aimed to identify biomarkers of the neurodegenerative process and to find molecular targets for therapeutics. Further functional studies using biochemical, molecular and cell biology approaches are used to verify and understand the role of biomarkers and targets in the context of injury and disease. The goal of our research is to use molecular information provided by our quantitative proteomics measurements and transcriptomics information to ameliorate neurodegeneration and promote regeneration.

We are looking for highly motivated individuals with a Master’s degree or equivalent in Computer Science or Bioinformatics who are interested in neurobiology, biomarker discovery and/or bioinformatics to join the lab as PhD students. Applicants should have an excellent track record alongside very good English communication skills. Previous training and experience in proteomcis or transcriptomics is beneficial.

We offer a position with specialization in bioinformatics in proteomics, transcriptomics and neurobiology with challenging projects. Our group is integrated in the vibrant, stimulating and multidisciplinary research environment of the F.M. Kirby Center for Neurobiology at Boston Children’s Hospital and Harvard Medical School with affiliation with Harvard University. A successful candidate will be involved in method development in transcriptomics and proteomics and the integration of both and work closely with lab-based and bioinformatics post-doctoral fellows in the group.

Doctoral students generally complete their research in our lab within 4 years while being registered at the University of Berlin for their graduate degree. The annual income of a doctoral student is $34,000US.

Boston Children’s Hospital and Harvard University are equal opportunity employers. Full applications should include a brief statement on research interests, a CV, list of publications (if applicable), and contact information for two referees. These should be compiled into a single pdf file and sent to Christoph Schlaffner (christoph.schlaffner@childrens.harvard.edu). For further information please contact Christoph Schlaffner or visit our website http://www.childrenshospital.org/Research/Labs/steen-laboratory.
Methoden: Biochemistry (protein purification, interaction studies)
Cell Biology and Molecular Biology (TC, assay development, flow cytometry, microscopy, cloning, phage display)
Quantitative mass spectrometry (multiplexed quantification, label free quantification, interaction proteomics, MRM/PRM method development)
Virology (recombinant viruses, virus production, infection experiments)
Transcriptomics (Next generation sequencing, single cell sequencing)
Computer Science (algorithm development, machine learning, and data analytics)
Anfangsdatum: 1. August 2018
Geschätzte Dauer: 4 years
Bezahlung: $34,000US
Papers: Bennike TB, Bellin MD, Xuan Y, Stensballe A, Møller FT, Beilman GJ, Levy O, Cruz-Monserrate Z, Andersen V, Steen J, Conwell DL, Steen H. A Cost-Effective High-Throughput Plasma and Serum Proteomics Workflow Enables Mapping of the Molecular Impact of Total Pancreatectomy with Islet Autotransplantation. J Proteome Res. 2018 May 4;17(5):1983-1992. doi: 10.1021/acs.jproteome.8b00111. Epub 2018 Apr 19. PubMed PMID: 29641209.

Bennike TB, Steen H. High-Throughput Parallel Proteomic Sample Preparation Using 96-Well Polyvinylidene Fluoride (PVDF) Membranes and C18 Purification Plates. Methods Mol Biol. 2017;1619:395-402. doi: 10.1007/978-1-4939-7057-5_27. PubMed PMID: 28674899.

Tang S, Hemberg M, Cansizoglu E, Belin S, Kosik K, Kreiman G, Steen H, Steen J. f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome. Nucleic Acids Res. 2016 Jun 2;44(10):e97. doi: 10.1093/nar/gkw157. Epub 2016 Mar 14. PubMed PMID: 26980280; PubMed Central PMCID: PMC4889934.

Mair W, Muntel J, Tepper K, Tang S, Biernat J, Seeley WW, Kosik KS, Mandelkow E, Steen H, Steen JA. FLEXITau: Quantifying Post-translational Modifications of Tau Protein in Vitro and in Human Disease. Anal Chem. 2016 Apr 5;88(7):3704-14. doi: 10.1021/acs.analchem.5b04509. Epub 2016 Mar 7. PubMed PMID: 26877193; PubMed Central PMCID: PMC5808556.

Belin S, Nawabi H, Wang C, Tang S, Latremoliere A, Warren P, Schorle H, Uncu C, Woolf CJ, He Z, Steen JA. Injury-induced decline of intrinsic regenerative ability revealed by quantitative proteomics. Neuron. 2015 May 20;86(4):1000-1014. doi: 10.1016/j.neuron.2015.03.060. Epub 2015 Apr 30. PubMed PMID: 25937169; PubMed Central PMCID: PMC4551425.

Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA. Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun. 2014 Nov 18;5:5429. doi: 10.1038/ncomms6429. PubMed PMID: 25403355; PubMed Central PMCID: PMC4416701.

Serang O, Cansizoglu AE, Käll L, Steen H, Steen JA. Nonparametric Bayesian evaluation of differential protein quantification. J Proteome Res. 2013 Oct 4;12(10):4556-65. doi: 10.1021/pr400678m. Epub 2013 Sep 11. PubMed PMID: 24024742; PubMed Central PMCID: PMC3824391.
Sonstiges: Actual start date can be discussed.