The Guide to GCB 2016 · 5 III. Lunch Opportunities and Mensa Cards Lunch at GCB is self-organized. On the map above you find some suggested places. At FU Mensa you have to pay using

The Guide to

GCB 2016 12 – 15 September 2016 in Berlin

Updates on https://twitter.com/MPI_MolGen #GCB2016

Contact through [email protected]

All information on www.gcb2016.de

2

Guide Contents

I. German Conference on Bioinformatics and FaBI .............................................. 2

II. The Venue ......................................................................................................... 3

III. Lunch Opportunities and Mensa Cards ............................................................. 6

IV. The Program ...................................................................................................... 7

i. Workshops on Day 1, Monday, 12. 9. 2016 ......................................... 7

ii. Conference Schedule ........................................................................... 9

iii. Presentations ..................................................................................... 13

iv. Posters ................................................................................................ 13

V. In the End…. ..................................................................................................... 19

The online version of this booklet is followed by the proceeding collection and the poster

abstracts.

I. German Conference on Bioinformatics and FaBI

The German Conference on Bioinformatics

(GCB) is an annual, international conference

devoted to all areas of bioinformatics.

Recent meetings attracted a multinational

audience with 250 – 300 participants each

year. The meeting is open to all fields of

bioinformatics and is meant as a platform

for the German and European

bioinformatics community.

The upcoming GCB will be chaired by Knut

Reinert, Professor at the Institute for

Bioinformatics at Freie Universität Berlin. It

will focus on computation in the academic

natural sciences and aims to showcase

applications and opportunities beyond.

Spearheading scientists will be presenting

along with young researchers and industry

representatives.

To jointly promote and direct the

development of the field of

Bioinformatics, the associations GI

(Gesellschaft für Informatik e.V.),

DECHEMA (Gesellschaft für Chemische

Technik und Biotechnologie e.V.), GBM

(Gesellschaft für Biochemie und

Molekularbiologie e.V.) and GDCh

(Gesellschaft Deutscher Chemiker e.V.)

founded the expert group for

bioinformatics (Fachgruppe Bioinfor-

matik) in September 2014. In September

2015, GMDS (Deutsche Gesellschaft für

Medizinische Informatik, Biometrie und

Epidemiologie e.V.) joint. Since then the

group unites interests of academia and

industry in the field. The GCB is the

conference of FaBI.

More information on www.gcb2016.de

or www.bioinformatik.de.

3

II. The Venue

Conference

Seminaris CampusHotel Berlin Takustr. 39 14195 Berlin

Workshops

Freie Universität Berlin Institut für Informatik Takustr. 9 14195 Berlin

For more information to get there and about see www.gcb2016.de/venue_travel.

4

Floor plan:

5

III. Lunch Opportunities and Mensa Cards

Lunch at GCB is self-organized. On the map above you find some suggested

places. At FU Mensa you have to pay using a Mensa card. If you have not

ordered it at the registration check-out, you can obtain one directly at the

canteen. There is a deposit on the card. Please make sure to return the card to

the Mensa administration at the end of GCB yourself. We cannot refund the

deposit ourselves.

Open with a map app

6

IV. The Program

i. Workshops on Day 1, Monday, 12. 9. 2016

10.00 Registration

11.30-14.30 WS 1 OpenMS

WS 2 Cloud

Computing

BIH

Core Facility WS

at Seminaris 14.30-15.00 Coffee Break

15.00-17.00 WS 1 OpenMS

WS 2 Cloud

Computing

WS 3 Shotgun

Sequencing

17.00 Welcome Reception with beer and BBQ Conference registration is open

How to find the Workshops:

7

8

ii. Conference Schedule

All events take place in Seminaris Campus

Hotel, Domus Conference Room, 2nd floor,

unless announced otherwise.

Tuesday, 13. 9. 2016 - Day 2

8.00 Registration opens

9.00 Opening by Prof Knut Reinert, Organizer of GCB2016

and Professor Peter-André Alt, President of FU Berlin

9.30 Rare genetic variants and the onset of multiple tumours Francesca Ciccarelli, King's College London, UK, Keynote 1

Ch

air:

Kn

ut

Rei

ner

t

10.10 MARCARviz: Interactive web-platform for exploratory analysis of toxicogenomics data for nongenotoxic hepatocarcinogenesis Michael Römer, Talk 1

10.30 An Integrative Computational Framework for Personalized Detection of Tumor Epitopes in Melanoma Immunotherapy Tanushree Jaitly, Talk 2

10.50 Coffee Break

11.30 Prediction of amyloidogenicity based on the n-gram analysis Synthetases Michal Burdukiewicz, Talk 3

Ch

air:

Ber

nh

ard

Ren

ard

11.50 Binding Mode Characterization of Class II Aminoacyl tRNA Synthetases Florian Kaiser, Talk 4 (Highlight)

12.10 Computational molecular design with focus on protein-protein interactions, privileged scaffolds and recurring folding patterns in proteins. Synthetases Oliver Koch, Talk 5 (Junior Research)

12.30 Lunch break at Mensa

14.00 AliTV – interactive visualization of whole genome comparisons Sonja Hohlfeld, Talk 6

Ch

air:

Mar

cel

Sch

ulz

Ch

air:

Mar

cel

Sch

ulz

14.20 BIH Award for Women in Bioinformatics: Award ceremony Laudatio and talk by the winner

9

15.00 How gene regulation networks change during development: network inference from single cell data Michael Stumpf, Imperial College London, UK, Keynote 2

Ch

air:

Mar

cel S

chu

lz

15.40 Coffee Break

16.00 tmod: an R package for general and multivariate enrichment analysis January Weiner, Talk 7

16.20 Poster Pitch

16.40 Poster Session in the lobby of Seminaris Campus Hotel, ground floor

19.00 BIH Award for Women in Bioinformatic: Celebration get-together in the lobby of Seminaris Campus Hotel, ground floor

Wednesday, 14. 9. 2016 - Day 3

8.00 Registration

9.00 Modeling cancer evolution from genomic data Niko Beerenwinkel, ETH, Switzerland, Keynote 3

C

hai

r: M

. Vin

gro

n

& I.

Ko

ch

9.40 Exploring and exploiting interspecific interactions Marie-France Sagot, Université Claude Bernard Lyon, France, Keynote 4

1 Coffee Break

10.40 Intel R&D Session Opening and chair by Lena Prochnow from Berlin Partner

sponsored by

10.50 Intel’s activities in software for life sciences Pascal Costanza, Intel, R&D Talk 1

11.20 Science for a Better Life: what is the purpose of my research? Bertram Weiss, Bayer, R&D Talk 2

11.50 Distilling experimental data into actionable drug discovery Daniel Ziemek, Pfizer, R&D Talk 3

10

at Seminaris lobby, ground floor

12.20 R&D Session Impulse Talks

13.00 Open R&D Session with finger food lunch,

supported by

13.00 Scientific Posters are still on display in parallel in the lobby of Seminaris Campus Hotel, 1st floor

at Domus Conference Room, 2nd floor

15.00 Open FaBI meeting

15.30 Social event: Wannsee boat cruise w/ coffee A bus shuttle is organized and leaves at 15.30 sharp in front of Seminaris, Takustr 39

19.00 Program Committee Dinner (invited guests only) at Loretta am Wannsee

19.00 alternatively: Berlin Night out

(plan individually!)

Thursday, 15. 9. 2016 - Day 4

8.00 Registration

9.00 Computational Biology to understand RNA regulatory mechanisms Uwe Ohler, MDC, Berlin, Keynote 5

Ch

air:

Ulf

Les

er 9.40 Predicting enhancers using a small subset of high confidence examples and

co-training Matthew Huska, Talk 8

10.00 FUCHS - Full circle characterization using RNAseq Franziska Metge, Talk 9

10.20 A statistical model for epigenetic control of miRNAs Lisa Barros de Andrade e Sousa, Talk 10

10.40 Coffee Break

11

11.00 AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences Jan Grau, Talk 11 (Highlight)

Ch

air:

Oliv

er K

oh

lbac

her

11.20 Computational Biology and Evolutionary Genomics Michael Hiller, Talk 12 (Junior Research)

11.40 Multitask regression for context-specific prioritization of miRNA targets in transcripts Azim Dehghani Amirabad, Talk 13

12.00 PaPrBaG: A random forest approach for the detection of novel pathogens from NGS data Carlus Deneke, Talk 14

12.30 Lunch break at Mensa

13.30 Systems BioMedicine using high-throughput screening – From RNAi, CRISPER/cas9, miRNA and drug screens to targeting signaling pathways Jan Baumbach, Talk 15 (Highlight)

Ch

air:

Dan

iel H

uso

n

& K

nu

t R

ein

ert

13.50 de.NBI - German Network for Bioinformatics Infrastructure Alfred Pühler, Talk 16, Report

14.30 Bioinformatics support for the Tübiom community gut microbiome project Sina Beieri, Talk 17

14.50 SLIMM: Species Level Identification of Microorganisms from Metagenomes Temesgen Dadi, Talk 18

15.10 Coffee Break

15.20 Monolithic Multiparameter Diagnostics, from Molecules to Applied Statistical Bioinformatics Stefan Rödiger, Talk 19 (Junior Research)

Ch

air:

Jan

Bau

mb

ach

15.40 RGFA: powerful and convenient handling of assembly graphs Giorgio Gonnella, Talk 20

16.10 Improving ancient DNA genome assembly Alexander Seitz, Talk 21

16.30 GCB 2016 Poster Award by Tim Conrad

16.50 Closing words by Prof Knut Reinert

12

iii. Presentations

The proceedings are available online as a collection published by PeerJ on

https://peerj.com/collections/41-german-conference-bioinformatics-2016.

The online version of this booklet is followed by the proceeding collection.

Keynotes

Contributed Talks

Talk 1 MARCARviz: Interactive web-platform for exploratory analysis of toxicogenomics data for nongenotoxic hepatocarcinogenesis

Michael Römer

Talk 2 An Integrative Computational Framework for Personalized Detection of Tumor Epitopes in Melanoma Immunotherapy

Tanushree Jaitly

Talk 3 Prediction of amyloidogenicity based on the n-gram analysis Synthetases

Michal Burdukiewicz

Talk 6 AliTV – interactive visualization of whole genome comparisons

Sonja Hohlfeld

Talk 7 tmod: an R package for general and multivariate enrichment analysis

January Weiner

Talk 8 Predicting enhancers using a small subset of high confidence examples and co-training

Matthew Huska

Talk 9 FUCHS - Full circle characterization using RNAseq Franziska Metge

Talk 10 A statistical model for epigenetic control of miRNAs Lisa Barros de Andrade e Sousa

Talk 13 Multitask regression for context-specific prioritization of miRNA targets in transcripts

Azim Dehghani Amirabad

Talk 14 PaPrBaG: A random forest approach for the detection of novel pathogens from NGS data

Carlus Deneke

Talk 16 (Report)

de.NBI and ELIXIR Alfred Pühler

13

Talk 17 Bioinformatics support for the Tübiom community gut microbiome project

Sina Beier

Talk 18 SLIMM: Species Level Identification of Microorganisms from Metagenomes

Temesgen Dadi

Talk 20 RGFA: powerful and convenient handling of assembly graphs

Giorgio Gonnella

Talk 21 Improving ancient DNA genome assembly Alexander Seitz

Highlights

Talk 4 Binding Mode Characterization of Class II Aminoacyl tRNA Synthetases

Florian Kaiser

Talk 11 AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Jan Grau

Talk 15 Systems BioMedicine using high-throughput screening – From RNAi, CRISPER/cas9, miRNA and drug screens to targeting signaling pathways

Jan Baumbach

Junior Research

Talk 5 Computational molecular design with focus on protein-protein interactions, privileged scaffolds and recurring folding patterns in proteins. Synthetases

Oliver Koch

Talk 12 Computational Biology and Evolutionary Genomics Michael Hiller

Talk 19 Monolithic Multiparameter Diagnostics, from Molecules to Applied Statistical Bioinformatics

Stefan Rödiger

Post Pitch Flash Talks (1 minute, 1 slide)

Poster 90 Fully reproducible workflows with Snakemake and Bioconda

Johannes Koester

Poster 91 A Bayesian model for singlecell transcript expression analysis on MERFISH data

Johannes Koester

Poster 42 Variant frequency-based tree reconstruction for single-cell data

Jochen Singer

Poster 130 Bistability analysis of the gut metabolome interactions in view of dysregulation leading to inflammatory and other altered pathological states

Gunter Neumann

Poster 20 SimLoRD: Simulation of Long Read Data Bianca Stöcker

Poster 88 Simulating ddRADseq reads with RAGE Henning Timm

Poster 66 TBro - a transcriptome browser for de novo RNA-sequencing experiments

Markus J. Ankenbrand

Poster 84 Complex inversions in the human genome Sascha Meiers

Poster 65 Fast Multiple Sequence Alignment Fabian Klötzl

Poster 22 Rapid construction of synthetic supergenomes Christine Jandrasits

14

Poster 62 Measuring Local Complexity in Genomes Bernhard Haubold

Poster 37 Privacy protection in NGS procedures using a realtime read filtering approach

Tobias P. Loka

Poster 40 A novel Framework for tracking neutrophiles in live cell imaging data

Thomas Temme

Poster 70 reper - find, classify and quantify repeats without a genome assembly

Niklas Terhoeven

Poster 48 Bayesian Reverse Engineering of Gene Regulatory Networks in Heart Development

Eleonora Lippolis

Poster 60 `kmerPyramid': an interactive visualization R-package for k-mer distributions

Klaus Jung

iv. Posters

The abstract booklet for the posters presented at GCB 2016 are available online on

www.gcb2016.de/download/GCB_Poster.pdf. The online version of this booklet is

followed by the the poster abstracts.

Posters 1-60 plus the Poster of the BIH Award winner are on

display at Session 1, Posters 61-102 and all additional ones

are on display at Session 2.

Posters at Session 1, Tuesday, 13 September

1 Seyed Ziaeddin Alborzi, Marie-Dominique Devignes and David Ritchie

Associating Gene Ontology Terms with Protein Domains

2 Simon Tausch, Bernhard Renard, Andreas Nitsche and Piotr Wojciech Dabrowski

Separation of foreground and background reads in mixed NGS datasets

3 Andreas Andrusch, Piotr Wojciech Dabrowski, Jeanette Klenner and Andreas Nitsche

Identification of pathogen sequences in NGS datasets

4 Daniel Arend, Astrid Junker, Danuta Schüler, Matthias Lange and Uwe Scholz

PGP Repository: A Plant Phenomics and Genomics Data Publication Infrastructure

5 Vasanthi Priyadarshini Gaddi and Lars Kaderali AN INTEGRATIVE NETWORK APPROACH FOR GLIOBLASTOMA

6 Diogo Marinho Almeida, Artur Silva, Fabio Vandin, Qihua Tan, Richard Röttger and Jan Baumbach

DiMmeR: Discovery of Multiple Differentially Methylated Regions

7 Raik Otto, Christine Sers and Ulf Leser Robust In-Silico identification of sequenced Cancer Cell Lines

8 Ursula Neumann and Dominik Heider EFS: An ensemble of feature selection methods for binary classification

15

9 Theresia Conrad, Olaf Kniemeyer, Thomas Krueger, Sebastian G Henkel, Axel Brakhage, Reinhard Guthke and Jörg Linde

Transcriptomic and proteomic response of Aspergillus fumigatus to caspofungin

10 Norma J Wendel, Jochen Schmid, Volker Sieber and Dominik Heider

Synthetic Biology Approach for the Development of Customized Polysaccharides

11 Sascha Daniel Krauß, Hesham Yosef, Samir El-Mashtoly, Klaus Gerwert and Axel Mosig

Automatic distinction between healthy cells and cancer cells in urine samples using Raman microscopy

12 Michael Seifert, Betty Friedrich and Andreas Beyer Importance of rare gene copy number alterations for personalized tumor characterization

13 Annika Röhl and Alexander Bockmayr Fast Minimal Network Finder

14 Alexandra Reimers, Henning Knoop, Alexander Bockmayr and Ralf Steuer

Evaluating the stoichiometric and energetic constraints of cyanobacterial diurnal growth

15 Paweł Błażej, Małgorzata Wnętrzak, Dorota Mackiewicz and Paweł Mackiewicz

Selection at the amino acid level as one of the forces behind the synonymous codons usage bias

16 Anke Heit, Wenhu Cao, Erik Stricker, Martin Löchelt and Agnes Hotz-Wagenblatt

In silico investigations of bovine foamy virus microRNA

17 Stephanie Schaarschmidt Combined statistical analysis of metabolite profiles from 49 natural accessions of Arabidopsis thaliana grown under three different experimental conditions to investigate cold acclimation

18 Himanshu Manchanda, Nora Seidel, Markus Blaess, Ralf Claus, Joerg Linde, Andreas Saurbrei, Reinhard Guthke and Michaela Schmidtke

Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus

19 Martina Cantone, Martin Eberhardt, Melanie Küspert, Simone Reiprich, Michael Wegner and Julio Vera

The Oligodendrocyte Differentiation Network: a Systems Biology Approach

20 Bianca K Stöcker, Johannes Köster and Sven Rahmann

SimLoRD: Simulation of Long Read Data

21 Julianus Pfeuffer, Knut Reinert and Oliver Kohlbacher

OpenMS: Efficient tools and workflows for computational mass spectrometry

22 Christine Jandrasits and Bernhard Y Renard Rapid construction of synthetic super-genomes

23 Dirk Walther The orientation of transcription factor binding site motifs in gene promoter regions: does it matter?

24 Paula Korkuc and Dirk Walther The regulatory role of protein phosphorylation on compound binding

25 Laura Perlaza and Dirk Walther Using synchronous genomic sequence mutations to discern macromolecular interactions in Arabidopsis

26 Antje M Thamm, Marlene Taja, Svetlana Y Gerdes and Andrew D Hanson

Using comparative genomics to find functions for unknown genes, and genes for missing enzyme functions

27 Truong Khanh Linh Dang, Cornelia Meckbach, Rebecca Tacke, Stephan Waack and Mehmet Gültas

A novel sequence based feature for the identification of DNA-binding sites in proteins using Jensen-Shannon divergence

28 Nils Petersen and Andrew Torda RNA secondary structure prediction with 3D constraints

29 Khadija El Amrani, Nancy Mah and Andreas Kurtz CLASSIFICATION OF KIDNEY DISEASE CELL TYPES USING WHOLE-GENOME EXPRESSION PROFILES

30 Carsten Kemena, Tristan Bitard-Feildel, Nicolas Terrapon, Andrew Moore and Erich Bornberg-Bauer

DomainWorld: A pipeline to analyze domain arrangements

16

31 Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch and Dominik Heider

eccCL: an optimized GPU implementation of ensemble classifier chains

32 Elias Dohmen, Carsten Kemena, Lukas Kremer and Erich Bornberg-Bauer

DOGMA: domain-based transcriptome and proteome quality assessment

33 Heiko Giese, Joerg Ackermann, Ilka Wittig, Ulrich Brandt and Ina Koch

PULSAR: a software for batch pre-processing of complexome profiling data

34 Teresa Domaszewska, Lisa Scheuermann, Anca Dorhoi, Stefan Kaufmann and January Weiner

Novel data integration approach identifies concordant and discordant immune responses between mice and humans

35 Jens Keilwagen, Michael Wenk, Jan Grau, Jessica Erickson, Martin Schattat and Frank Hartung

Using intron position conservation for homology-based gene prediction

36 Sandra Appelt, Marcel Grunert and Silke Rickert-Sperling

miRNome Analysis of Next-Generation Sequencing Data From Patients with Tetralogy of Fallot

37 Tobias P Loka, Simon H Tausch, Piotr Wojciech Dabrowski and Bernhard Y Renard

Privacy protection in NGS procedures using a real-time read filtering approach

38 Sven Giese, Adam Belsom and Juri Rappsilber Optimized Fragmentation Regime for Cross-Linked Peptides

39 Carolin Kosiol Ancestral and Recent Population Genomics

40 Thomas Temme, Thomas Irmer, Laura Struensee, Michael Blachetta, Anthony Squire, Nina Schulze, Marc Schuster, Matthias Gunzer and Axel Mosig

A novel Framework for tracking neutrophiles in live cell imaging data

41 Joerg Winkler and Stefan Kurtz GtSeedExtend -- an efficient and robust implementation of a seed-and-extend algorithm for computing local alignments of sequences with large differences

42 Jochen Singer, Jack Kuipers, Katharina Jahn and Niko Beerenwinkel

Variant frequency-based tree reconstruction for single-cell data

43 Milos Nikolic, Argyris Papantonis and Alvaro Rada-Iglesias

GARLIC: A Bioinformatic Toolkit for Etiologically Connecting Diseases and Cell Type-Specific Regulatory Maps

44 Thomas Huebsch, Ralf Herwig and Margret R Höhe Dissecting Diploidy: Cis and Trans Configurations of Mutations in 1092 Genomes

45 Julia Helmecke and Dietmar Schomburg Metabolic model of Sulfolobus acidocaldarius for lignocellulosic biofuel production

46 Benedikt Diewald, Eileen Socher and Heinrich Sticht Comparative Study of the Nuclear Egress Complexes of Several Herpes Viruses Using MD Simulations

47 Eileen Socher and Heinrich Sticht Molecular Dynamics Studies on the pH-Dependent Regulation of Proteins: From Viruses to Plants

48 Eleonora Lippolis, Marco Moraschini, Felix B Engel, Riccardo Bellazzi and Fulvia Ferrazzi

Bayesian Reverse Engineering of Gene Regulatory Networks in Heart Development

49 Cornelia Meckbach, Rebecca Tacke, Stephan Waack, Edgar Wingender and Mehmet Gültas

PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information

50 Matthias Lienhard, Sabrina Grasse, Jana Rolff, Steffen Frese, Uwe Schirmer, Michael Becker, Stefan Börno, Bernd Timmermann, Lukas Chavez, Holger Sültmann, Gunda Leschber, Iduna Fichtner, Michal Ruth Schweiger and Ralf Herwig

QSEA – modelling of genome-wide DNA methylation from sequencing enrichment experiments

51 Michael Menzel and Andreas Gogol-Döring Enhort: A Platform for Deep Analysis of Genomic Positions

52 Sandra Weissenborn and Dirk Walther Metabolic pathway assignment based on phylogenetic profiling

17

53 Maureen Smith, Redmond Smyth, Roland Marquet and Max von Kleist

MIMEAnTo – A bioinformatics tool to profile functional RNA in mutational interference mapping experiments

54 Joanna Ziobro, Paweł Błażej and Paweł Mackiewicz The model of immune system dynamics

55 Alan Beccati, Jan Gerken, Christian Quast, Pelin Yilmaz, Alireza Rezaei Mahdiraji, Jörg Peplies and Frank Oliver Glöckner

Exploring the SILVA phylogenetic tree in your Web Browser

56 Jens Kunze Multi sample single cell analytics - Advantages of reproducibility

57 Marcus Ulbrich and Dietmar Schomburg EnzymeDetector: Enhancements in 2016 to delineate connections between an enzyme pool of an organism and diverse microbial characteristics

58 Sandra Placzek, Dietmar Schomburg, Antje Chang, Lisa Jeske, Ida Schomburg, Jana Tillack and Marcus Ulbrich

New Perspectives and new Tools in BRENDA

59 Anna Kuhn Modified Ampli1[TM] WGA products enable improved genome coverage for single cells

60 Jochen Kruppa and Klaus Jung `kmerPyramid': an interactive visualization R-package for k-mer distributions

Posters at Session 2, Tuesday, 13 September

61 Martin Eisenacher, Michael Kohl, Martin Hofmann-Apitius, Stefan Rüping, Harald P Mathis, Lars Böckmann, Jens Habermann, Christian Stephan and Christina Schröder

i:DSem - Verbundprojekt: Electronic Patient Path (EPP)

62 Anton Pirogov and Bernhard Haubold Measuring Local Complexity in Genomes

63 Sabine Stübler, Charlotte Kloft and Wilhelm Huisinga Towards a systems biology model for inflammatory bowel disease

64 Marcus Vollmer Arrhythmia Classification in Long-Term Electrocardiography Data using the Return Map of RR Intervals

65 Fabian Klötzl and Bernhard Haubold Fast Multiple Sequence Alignment

66 Markus Ankenbrand, Lorenz Weber, Dirk Becker, Frank Förster and Felix Bemm

TBro - a transcriptome browser for de novo RNA-sequencing experiments

67 Hannes Hauswedell, Rene Rahn, Temesgen Dadi, Jongkyu Kim, Christopher Pockrandt, Marcel Ehrhardt, Svenja Mehringer and Knut Reinert

SeqAn: the sequence analysis library

68 Sulav Duwal, Vikram Sunkara and Max von Kleist Multi-Scale System Pharmacology Modelling Pipeline To Assess The Prophylactic Efficacy of NRTIs Against HIV-1

69 Stefan Budach, Matthias Heinig and Annalisa Marsico Characterization of microRNA Regulation Using Expression Quantitative Trait Loci

70 Niklas Terhoeven, Thomas Hackl, Jörg Schultz and Rainer Hedrich

reper - find, classify and quantify repeats without a genome assembly

71 Jonas Ibn-Salem and Miguel A Andrade Prediction of three-dimensional chromatin looping from sequence motifs and protein

18

binding signals

72 Saskia Trescher, Jannes Münchmeyer, Christopher Schiefer and Ulf Leser

In-silico Approaches for Estimating Transcription Factor Activity from Transcriptome Data

73 Max Schubach, Matteo Re, Peter N Robinson and Giorgio Valentini

Variant relevance prediction in extremely imbalanced training sets

74 Kirsten Thobe, Christina Kuznia, Christine Sers and Heike Siebert

Identifying Cell Line Specific Crosstalk in Renal Cancer by Applying High-Throughput Proteomics to Model Pools

75 Arne Peter Raulf, Sarah Kasimir, Anke Reinacher-Schick, Andrea Tannapfel and Mosig Axel

Association rule mining for identifying cancer specific gene sets in genomic cancer sequencing data

76 Christoph Baldow, Sebastian Salentin, Lars Thielecke, Michael Schroeder and Ingmar Glauche

Multiplexing Clonality with MAGPIE

77 Stefanie Kasielke, Rainald Ehrig and Röblitz Susanna Parameter identification for curli fiber expression models

78 Sabrina Krakau, Hugues Richard and Annalisa Marsico Capturing protein-RNA interaction footprints from iCLIP-seq data

79 Annett Erkes, Jens Boch and Jan Grau Evolution of Transcription Activator-Like Effectors

80 Chris Lauber, Barbara Klink and Michael Seifert Comparative analysis of oligodendrogliomas reveals molecular characteristics of tumor subtypes

81 Jens Rieser, Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Christian Behrends, Ivan Dikic and Ina Koch

Protein-protein interaction networks for time-resolved Ubiquitinome data of Salmonella-infected cells

82 İlhan Erkin Acar, Rüçhan Ekren and Jens Allmer Detection of Alternative Explanations for Cancer Causes in Publicly Available Next Generation Sequencing Data

83 Florian Auer Bringing Pathway Knowledge to Systems Medicine Approaches

84 Sascha Meiers, Tobias Rausch, Markus Hsi-Yang Fritz, Adrian Stütz and Jan Korbel

Complex inversions in the human genome

85 Christian-Alexander Dudek, Henning Dannheim and Dietmar Schomburg

BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation

86 Gunther Neumann, Rebecca Wall, Ignacio Rangel, Tatjana Marques and Dirk Repsilber

Bistability analysis of the gut metabolome interactions in view of dysregulation leading to inflammatory and other altered pathological states

87 Juliane C Dohm, Alexandrina Bodrug, Philipp Peters, Nikolaus Zwickl and Heinz Himmelbauer

Approaches for improved contiguity of genome assemblies

88 Henning Timm, Hannah Weigand, Martina Weiss, Florian Leese and Sven Rahmann

Simulating ddRADseq reads with RAGE

89 Usman Saeed and Dmitrij Frishman Investigating the Fold Space in Membrane Proteins

90 Johannes Köster Fully reproducible workflows with Snakemake and Bioconda

91 Johannes Köster A Bayesian model for single-cell transcript expression analysis on MERFISH data

92 Michal Burdukiewicz, Piotr Sobczyk, Pawel Blazej and Paweł Mackiewicz

Prediction of malarial signal peptides

93 Richard A Schäfer and Björn Voß VisualGraphX - Interactive Graph Visualization within Galaxy

19

94 Marc Bonin-Andresen, Sascha Johannes, Pascal Schendel, Biljana Smiljanovic, Till Sörensen, Andreas Grützkau, Bruno Stuhlmueller and Thomas Häupl

BioRetis - An online tool to analyse geneexpression profiles, miRNA data, DNA methylation and NGS data

95 Biljana Smiljanovic, Till Sörensen, Marc Bonin-Andresen, Bruno Stuhlmueller, Gerd-Rüdiger Burmester, Andreas Grützkau and Thomas Häupl

Gene expression profiling and cytometry analysis from bone marrow monocytes, blood and synovial fluid from rheumatoid and osteoarthritis patients

96 Till Sörensen, Marc Bonin-Andresen, Ursula Schulte-Wrede, Sandra Hermann, Andreas Grützkau and Thomas Häupl

ImmunoClust - An automated pipeline to analyse cytometric profiles in synovial fluid compared to peripheral blood cells in rheumatoid arthritis

97 Bruno Stuhlmueller, Marc Bonin-Andresen, Biljana Smiljanovic, Till Sörensen, Pascal Schendel, Gerd-Rüdiger Burmester and Thomas Häupl

Genomic stratification by HLA-DRB4 expression - A strategy to identify predictors of methotrexate response in early rheumatoid arthritis

98 Maria Metsger, Cornelius Fischer, Sophia Bauch and Sascha Sauer

Deciphering gene regulatory networks from single-cell transcriptomics data in macrophage metabolic stress responce

99 Leon Kuchenbecker, Knut Reinert and Peter Robinson Functional T cell receptor beta-chain gene sequence discrimination using SVMs

100 A. Al-Dilaimi, T. Dammann-Kalinowski, A. Pühler, F. Sprengel, A. Tauch, D. Wibberg

de.NBI - German Network for Bioinformatics Infrastructure

101 Azim Dehghani Amirabad Multitask regression for condition-specific prioritization of miRNA targets in transcripts

102 Alina Munteanu and Uwe Ohler Sequence-structure motif identification for RNA-binding proteins

20

V. In the End….

We hope you enjoyed the German Conference on Bioinformatics 2016 and took home valuable

insights and ideas for future work and collaborations. We are very happy to have had you as our

guests.

Some things from our side before you go:

Please return your name tags to the reception desk; they will be put to good use at the

next event

Autumn is coming! Take one of our give-away umbrellas as a souvenir.

Please use our feedback form on

https://goo.gl/forms/Lm6kkksJimw0bjox2 to tell us what you liked

about this year’s GCB, and what you did not. We appreciate your

feedback to make the next conference experience even better!

We thank our Partners

…and hope to see you again at GCB2017 in Tübingen!

Your GCB team