Computer Science and Engineering
 Gothenburg University | Chalmers

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John Wiedenhoeft

Doctoral Student

Mailing address:
Department of Computer Science and Engineering
Chalmers | Gothenburg University
41296 Gothenburg, Sweden

Visiting address:
Department of Computer Science and Engineering
Chalmers | Gothenburg University
EDIT 6449
Rännvägen 6 B
41258 Göteborg, Sweden

Phone:
Fax:
E-mail: john.wiedenhoeft@chalmers.se

2017-pres: Postdoctoral Fellow, Chalmers University of Technology, Gothenburg, Sweden

2011-pres: Ph.D. student of Computer Science at Rutgers, The State University of New Jersey, Teaching Assistant for CS

2010-2011: Research assistant at Max Planck Institute for Molecular Genetics Berlin, Department of Computational Molecular Biology (Martin Vingron): phylogeny of multidomain proteins, biclustering of gene expression data

2010: Visiting scholar at Iowa State University, guest lecture at BCB faculty seminar

2009-2011: M.Sc. in Bioinformatics from Freie Universität Berlin and Charité

2009-2010: Splicing analysis for RNA-Seq in zebra finch genome project at Max Planck Institute for Molecular Genetics in Berlin

2008-2010: Research assistant at Freie Universität Berlin, Department of Animal Behaviour (Constanze Scharff): "Do birds tango? Biological origins of rhythm as a carrier of emotions" (Cluster of Excellence "Languages of Emotion")

2008: Research assistant at the Max Planck Institute for Evolutionary Anthropology (Mark Stoneking): Algorithms for human genomic diversity in population genetics (Marc Bauchet); Phylogenetic approaches towards the evolution of Bantu languages (Brigitte Pakendorf)

2007-2009: B.Sc. in Bioinformatics from Freie Universität Berlin and Charité

2004: Ethnomusicological field research with the Newār people in Bhaktapur, Kathmandu valley, Nepal (Gert-Matthias Wegner): "The role of the dhimay in ritual and processional music during biskaḥ jātrā"

2003-2006: Magister studies, majoring in musicology (Humboldt-Universität Berlin), ethnomusicology (Freie Universität Berlin) and communication research (Technische Universität Berlin)

2002: Civilian service at the home für speech and hearing impaired children in Chemnitz

Upcoming/Recent presentations

April 18, 2016. Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. Contributed Talk at RECOMB 2016, Santa Monica, CA

Recent publications

G.A. Bravo, A. Antonelli, C.D. Bacon, K. Bartoszek, M.P.K. Blom, S. Huynh, G. Jones, L.L. Knowles, S. Lamichhaney, T. Marcussen, H. Morlon, L.K. Nakhleh, B. Oxelman, B. Pfeil, A. Schliep, N. Wahlberg, F.P. Werneck, J. Wiedenhoeft, S. Willows-Munro and S.V. Edwards Embracing heterogeneity: building the Tree of Life and the future of phylogenomics. PeerJ 2018. Preprint, under review.

J. Wiedenhoeft and A. Schliep Using HaMMLET for Bayesian segmentation of WGS read-depth data. In Copy Number Variants: Methods and Protocols, Springer, 2018. To be published..

J. Wiedenhoeft, E. Brugel and A. Schliep Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. In Research in Computational Molecular Biology: 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings, Springer, 9649, 263, 2016.

J. Wiedenhoeft, E. Brugel and A. Schliep Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Computational Biology 2016, 12:5, e1004871.

J. Wiedenhoeft, E. Brugel and A. Schliep Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. biorXiv 2015.

Software lead

HaMMLET: Dynamically compressed Bayesian Hidden Markov Model using Haar Wavelet Shrinkage.