October 4–7 | Frankfurt, Germany

Accepted Papers

We have invited high-quality original full papers solicited on, but not limited to, the following topics:

. population genomics
. genome rearrangement
. comparative tools for genome assembly
. gene identification and/or annotation
. comparison of functional networks
. phylogenomics
. genome variation, diversity and dynamics
. comparative epigenomics
. genome evolution
. paleogenomics
. cancer evolution genomics

Please find below the list of accepted papers:

Title of the PaperAuthor(s)
  • Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
Ruth Davidson, Pranjal Vachaspati, Siavash Mirarab, Tandy Warnow
  • A comparative study of SVDquartets and other coalescent-based species tree estimation methods
Jed Chou, Ashu Gupta, Shashank Yaduvanshi, Ruth Davidson, Mike Nute, Siavash Mirarab, Tandy Warnow
  • ASTRID: Accurate Species TRees from Internode Distances
Pranjal Vachaspati, Tandy Warnow
  • Widespread signatures of local mRNA folding structure selection in four Dengue virus serotypes
Eli Goz, Tamir Tuller
  • A comparative genomics study on the effect of individual amino acids on ribosome stalling
Renana Sabi, Tamir Tuller
  • Efficient algorithms for reconciling gene trees and species networks via duplication and loss events
Thu-Hien To, Celine Scornavacca
  • Reconstruction of Composite Regulator-Target Splicing Networks from High-Throughput Transcriptome Data
Panagiotis Papasaikas, Arvind Rao, Peter Huggins, Juan Valcarcel, A. Javier Lopez
  • Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events
Chunfang Zheng, Daniella Santos Muñoz, Victor A. Albert, David Sankoff
  • Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence
Wandrille Duchemin, Vincent Daubin, Eric Tannier
  • A maximum pseudo-likelihood approach for phylogenetic networks
Yun Yu, Luay Nakhleh
  • Ancestral gene synteny reconstruction improves extant species scaffolding
Yoann Anselmetti, Vincent Berry, Cedric Chauve, Annie Chateau, Eric Tannier, Sèverine Bérard
  • Gene-Pseudogene Evolution: A Probabilistic Approach
Owais Mahmudi, Bengt Sennblad, Lars Arvestad, Katja Nowick, Jens Lagergren
  • Prediction of microbial phenotypes based on comparative genomics
Roman Feldbauer, Frederik Schulz, Matthias Horn, Thomas Rattei
  • Exact Approaches for Scaffolding
Mathias Weller, Annie Chateau, Rodolphe Giroudeau
  • Reconstruction of ancestral gene orders using intermediate genomes
Pedro Feijão
  • Reconstructing a SuperGeneTree minimizing reconciliation
Manuel Lafond, Aïda Ouangraoua, Nadia El-Mabrouk
  • Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies
Magali Semeria, Eric Tannier, Laurent Guéguen
  • Sampling and counting genome rearrangement scenarios
István Miklós, Heather Smith
  • Moments of genome evolution by Double Cut-and-Join
Priscila Biller, Laurent Guéguen, Eric Tannier
  • Event inference in multidomain families with phylogenetic reconciliation
Maureen Stolzer, Katherine Siewert, Minli Xu, Han Lai, Dannie Durand


Further Information:

Submitted papers must have not been published or be currently under the consideration for publication in any other journal or conference with formal proceedings. All accepted papers will have to be presented by one of the authors at the conference. Accepted papers will be published in one of two journal supplements, either to BMC Genomics or to BMC Bioinformatics. BMC will charge publication fees independently from the conference registration.

Detailed submission instructions can be found here.


The annual RECOMB-CG satellite conference brings together leading researchers in the mathematical, computational, and life sciences to discuss cutting edge research. Next to six invited keynote speakers and 20 contributed talks, the technical program also includes a vivid poster session.


We invite all participants to present their latest results that fall within the general scope of the conference as a poster. To do so, please submit a poster abstract in PDF format to

The abstract will be included into the Conference Program booklet, and must be limited to one A4 page (12 pt font) in length including all references and figures.

  • Poster Submission Deadline: Friday 28 August, 2015.
  • Notification of Acceptance: Tuesday 1 September, 2015.
  • We offer the possibility for late poster submission. However, we cannot guarantee that late poster abstracts are considered in the printed conference booklet.

The poster session is scheduled to the afternoon of Monday 5 October, but posters will be on display for the entire duration of the conference. The format will be A0 vertical (84cm=33.1″ wide, 118cm=46.8″ high). At least one author of each accepted poster is required to register for and attend the conference.

Please find below the list of accepted posters [updated daily]:

IDPoster TitleAuthor(s)
01Repeat- and Error-Aware Comparison of IndelsRoland Wittler, Svea Kokott, Tobias Marschall, Alexander Schönhuth, Veli Mäkinen
02Association between short peptides interaction strength with the ribosomal exit tunnel and their distribution in the proteomeRenana Sabi, Tamir Tuller
03Functional Analysis of a Pan-genomeTina Zekic, Jens Stoye
04Evidences of evolutionary selection for mutational robustness of local structural elements in HIV coding sequencesEli Goz, Tamir Tuller
05SecPred: predicting functional bacterial secretion systems based on machine learning techniquesValerie Eichinger, Roman Feldbauer, Thomas Rattei
06De novo Assembly and Comparative Genomics on Eukaryotic Species MixturesBastian Greshake, Andreas Blaumeiser, Simonida Zehr, Francesco Dal Grande, Anjuli Meiser, Imke Schmitt, Ingo Ebersberger
07Predicting the evolutionary traceability of proteins & pathwaysArpit Jain, Tina Köstler, Arndt von Haeseler, Ingo Ebersberger
08An integrative approach for tracing functional protein interaction networks using a ‘feature-aware’ phylogenetic profilingHolger Bergmann, Julian Dosch, Ingo Ebersberger
09Prediction of essential genes in pathogenic fungiJigisha Darbha, Geraldine Butler, Colm J. Ryan
10The four reversals conjectureIstván Miklós
11Reconstructing the Mutation History of a Tumor from Single Cell Sequencing DataKatharina Jahn, Jack Kuipers, Niko Beerenwinkel
12Genetic diversity and population structure of Bathymodiolus microbiotaAnne Kupczok, Rebecca Ansorge, Jillian Petersen, Nicole Dubilier, Tal Dagan
13Benchmarking Multiple Protein Sequence Alignments and the Effect of Guide-Tree TopologyFabian Sievers, Desmond G Higgins
14Compromise or optimize? The breakpoint anti-medianCaroline Anne Larlee, Alex Brandts, David Sankoff
15Small parsimony problem combining SCJ and prior given adjacency weightsNina Luhmann, Aïda Ouangraoua, Roland Wittler, Cedric Chauve
16Scoring Exons in a Multiple Genome Alignment for Comparative Gene PredictionLizzy Gerischer, Stefanie König, Lars Romoth, Mario Stanke
17A thorough comparision of alignment tools: BLAST, GHOSTX and DIAMONDJia Yu, Jochen Blom, Alexander Goesmann
18Comparative Gene Prediction in Bacterial GenomesLars Romoth, Lizzy Gerischer, Stefanie König, Mario Stanke
19Homeologous Non-Reciprocal Translocations (HNRT) Induce Selectable Genetic Variation in Brassica napusBirgit Samans, Boulos Chalhoub, Rod Snowdon
20New methods for the identification of syntenic blocks in multiple genome comparisonsDaniel Doerr, Bernard Moret
21Co-regulation of paralog genes in the three-dimensional chromatin architectureJonas Ibn-Salem, Miguel A. Andrade-Navarro
22Evolution of the chemotaxis signaling repertoire of plant pathogenic bacteriaJeremy D. Glasner, Nicole T. Perna
23Genome rearrangements and the dispersion of fragile regionsPriscila Biller, Laurent Gueguen, Carole Knibbe, Eric Tannier
24BFT-Comp – Alignment-free and reference-free compression of pan-genome sequencing readsGuillaume Holley, Faraz Hach
25Onctopus: A New Joint Model for Reconstructing the Clonal and Subclonal Composition of Cancer SamplesLinda K. Sundermann, Amit G. Deshwar, Jens Stoye, Quaid Morris, Gunnar Rätsch
26Mining the genomes of lichen-forming fungi for biosynthetic genesAnjuli Meiser, Francesco Dal Grande, Imke Schmitt
27Comparative analysis of differential DNA methylation with ADMIREJens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
28Understanding entomopathogenic bacterial lifestyles through genome sequencingNicholas J. Tobias, Hendrik Wolff, Helge B. Bode

Welcome reception

We will start the conference with our welcome reception in the beautiful guest house of the Goethe University located in the Frauenlobstrasse. Starting from 6 pm we will serve drinks together with some snacks and you will have the opportunity for on-site registration.


Guest House Goethe University Frauenlobstrasse

Frauenlobstr. 1

D-60487 Frankfurt am Main


Maria Reinhardt, P: +49 (0)69 798 13100,

Getting to the guest house:

Please follow the directives at the guest house web page.

or take a look at the online map.

Conference Dinner

Our conference dinner will take place in a beautiful Villa from the end of the 19th century located in the midst of Frankfurt’s Diplomats’ Quarter. Distributed over four open rooms including the fireside lounge we will be able to host a maximum of 75 people. So it is a good idea to be quick in making your reservation. Tickets will be available for 45 Euro including food, non-alcoholic drinks and a limited amount of wine and beer. If you have any further question please do not hesitate to contact us.



Guest House Goethe University Ditmarstrasse

Ditmarstr. 4

D-60487 Frankfurt am Main


Maria Reinhardt, P: +49 (0)69 798 13100,

Getting to the guest house:

Please follow the directives at the guest house web page.

or take a look at the online map.

Christophe Dessimoz, UCL Department of Genetics, Evolution & Environment, London, U.K.

CDHierarchical Orthologous Groups: a unifying and scalable framework for large-scale gene evolution

Sequencing data are rapidly piling up. Because many genes are highly conserved in sequence and function across different species—in some cases despite billions of years of intervening evolution—knowledge painstakingly gleaned through experiments can often be propagated across evolutionarily related genes. In theory, the more we know about the sequence universe, the easier elucidating these evolutionary relationships should get. Frustratingly however, the opposite seems true in practice: dealing with multiple species is conceptually and practically challenging, and as a result many evolutionary analyses remain stuck in a “two-species at a time” paradigm or only consider single-copy genes across multiple species. To overcome this impasse, I’ll introduce the concept of Hierarchical Orthologous Groups (HOGs)—nested groups of genes descending from a single ancestral gene within clades of interest. I’ll present an algorithm to accurately and efficiently infer HOGs. I will show how HOGs can be used to reconstruct ancestral genomes and to propagate functional knowledge from model species to non-model species.

Nicola Segata, Lab. of Computational Metagenomics, Centre for Integrative Biology (UNITN), University of Trento, Italy

nicolaStrain level microbial comparative genomics using shotgun metagenomics

Microbial comparative genomics is now routinely performed by sequencing the genome of target microorganisms cultivated in vitro. Advances in genome assembly and analysis approaches are providing very accurate tools for detecting genomic features (genes, SNPs, motifs, repeats) associated with the conditions of interest and with epidemiology patterns. This approach is however time consuming and generally applicable to only a fraction of human-associated microbes (typically pathogens) for which a known cultivation protocol is available. Shotgun metagenomics, on the other hand, provides an untargeted snapshot of the whole microbial diversity populating an environment, but accurate taxonomic profiling is still a challenging task. I will present here new methods we developed that are able to profile microbes from metagenomes with strain level resolution. This enables cultivation-free microbial population genomics and epidemiology studies using the several thousands of publicly available metagenomes. I will describe the novel computational framework for “meta-epidemiology” and discuss several results on human-associated commensals and opportunistic pathogens.

Annaliese S. Mason, Department of Plant Breeding, Justus Liebig University Giessen, Germany

Dr. Annaliese S. MasonInvestigating meiosis in allohexaploid Brassica

The Brassica genus contains many agriculturally significant crop species with interesting genomic relationships. Three diploid species (cabbage, turnip and black mustard; 2n = CC, AA and BB respectively) gave rise to allotetraploid species Indian mustard, Ethiopian mustard and oilseed rape (2n = AABB, BBCC and AACC). Although allohexaploid Brassica (2n = AABBCC) does not exist in nature, combining the three genomes may allow production of a new, vigorous hybrid crop species, as well as allowing investigation of polyploid speciation processes. Genome stability and meiotic behaviour were investigated in different allohexaploid Brassica populations using a high-throughput molecular genotyping approach. A, B and C-genome allele inheritance and meiotic interactions between the three genomes were quantified. Identification of the genetic and genomic factors underlying control of meiosis in Brassica will assist in production of a new, stable allohexaploid crop species.

RECOMB-CG in the past

2014: RECOMB-CG in New York – Cold Spring Harbor, US

2013: RECOMB-CG in Lyon – Villeurbanne, France

2012: RECOMB-CG in Niterói, Brazil

2011: RECOMB-CG in Galway, Ireland

2010: RECOMB-CG in Ottawa, Canada

2009: RECOMB-CG in Budapest, Hungary

2008: RECOMB-CG in Paris, France

2007: RECOMB-CG in San Diego, USA

2006: RECOMB-CG in Montréal, Canada

2005: RECOMB-CG in Dublin, Ireland

2004: RECOMB-CG in Bertinoro, Italy

2003: RECOMB-CG in Minneapolis, USA