Recomb Comparative Genomics

Four Days of Inspiration!

- October 2014, New York - Cold Spring Harbor

The twelfth RECOMB-CG satellite workshop brings together leading researchers in the mathematical, computational and life sciences to discuss cutting edge research in comparative genomics, with an emphasis on computational approaches and novel experimental results. The program includes both invited speakers and contributed talks.


We invite high-quality original full papers on topics related to comparative genomics. The submitted papers must have not been published or under the consideration for publication in any other journal or conference with formal proceedings. Papers are 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,
  • - evolution and phylogeny,
  • - genomic variation,
  • - comparative epigenomics,
  • - genome evolution,
  • - paleogenomics,
  • - cancer evolutionary genomics.
Any other research topics not listed here and relevant to comparative genomics will also be considered.

The Meeting

The 12th edition of Recomb-CG will be held at Cold Spring Harbor Laboratory (CSHL) in Cold Spring Harbor, in the immediate vicinity of New York City, USA.

Papers & Posters

All accepted papers will have to be presented by one on the authors at the conference. Accepted papers will be invited to be published in the journal BMC Genomics, following the journals publication policy. BMC will charge publication fees independently from the conference registration. Download Call for Papers (click here).
We also welcome poster submissions. Download Call for Posters (click here).

Key Dates

Papers Submission Deadline

Submissions must be received in electronic form by 11:59 pm (GMT-4).

Papers Acceptance Notification

Papers Final version due

The final version of the papers must be sent in electronic form

Poster submission deadline

Submissions must be received in electronic form by 11:59 pm (GMT-4)

Conference Starts



Submission closed

Submissions must be received in electronic form by 11:59pm (GMT-4), Sep 12th, 2014.

Posters abstract submissions should follow the format below (download example):
  • Title of the poster, in Times New Roman size 14
  • Authors and affiliations list, in Times New Roman size 12
  • Abstract text should be limited to 2500 characters, in Times New Roman size 12

Poster sessions are held in Bush Auditorium and Grace Lobby/Tent. Posters should fit within 1.22m x 1.22m (4 ft X 4 ft). Supplies for hanging posters are provided. Note that the poster areas are equipped with wireless internet access so you can demo software and web sites if you bring a laptop equipped with wireless modem. Laptops may be available from the Laboratory for a small rental/set-up charge.

Papers should be submitted via the EasyChair system

Submission closed

Submissions must be received in electronic form by 11:59pm (GMT-4), June 27th July 3rd, 2014.

We invite submissions up to 16 pages in the BMC Genomics submission format, with double-spaced lines. Additional material can be made available for the reviewers as an appendix. BMC guidelines: http://www.biomedcentral.com/bmcgenomics/authors/instructions/researcharticle
And the formats are :

Accepted Papers

View Proceedings at BMC Genomics BMC_Genomics
  • 1  - Caroline Anne Larlee, Chunfang Zheng and David Sankoff. Near-medians that avoid the corners; a combinatorial probability approach
  • 2  - Daniel Doerr, Jens Stoye, Sebastian Böcker and Katharina Jahn. Identifying Gene Clusters by Discovering Common Intervals in Indeterminate Strings
  • 3  - Arash Jamshidpey, Aryo Jamshidpey and David Sankoff. Sets of medians in the non-geodesic pseudometric space of unsigned genomes with breakpoints
  • 4  - Caleb Weinreb, Layla Oesper and Ben Raphael. k-breaks and open adjacencies: a measure for simultaneous rearrangements in cancer genomes
  • 5  - Billel Benzaid and Nadia El-Mabrouk. Gene order alignment on trees with multiOrthoAlign
  • 6  - Yu Lin, Sergey Nurk and Pavel Pevzner. What is the difference between the breakpoint graph and the de Bruijn graph?
  • 7  - Md. Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow. Disk Covering Methods Improve Phylogenomic Analyses
  • 8  - Chunfang Zheng, Alex Kononenko, Jim Leebens-Mack, Eric Lyons and David Sankoff. Gene families as soft cliques with backbones: Amborella contrasted with other flowering plants
  • 9  - Maureen Stolzer, Dannie Durand and Larry Wasserman. Accuracy of birth-death and gain models for inferring evolutionary events
  • 10 - Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova and Gabriella Trucco. Explaining Evolution via Constrained Persistent Perfect Phylogeny
  • 11 - Theo Zimmerman, Siavash Mirarab and Tandy Warnow. BBCA: Improving the scalability of *BEAST using random binning
  • 12 - Manuel Lafond and Nadia El-Mabrouk. Orthology and Paralogy Constraints: Satisfiability and Consistency
  • 13 - Alexandra Dana and Tamir Tuller. Properties and Determinants of Codons Decoding Time Distributions
  • 14 - Alexander Lobkovsky, Yuri Wolf and Eugene Koonin. Estimation of prokaryotic supergenome size and composition from gene frequency distributions
  • 15 - Veli Mäkinen and Daniel Valenzuela. Recombination-aware alignment of diploid individuals
  • 16 - Cécile Pereira, Alain Denise and Olivier Lespinet. A Meta-approach for improving the prediction and the functional annotation of ortholog groups
  • 17 - Hossein Khiabanian, Zachary Carpenter, Jeffrey Kugelman, Joseph Chan, Vladimir Trifonov, Elyse Nagle, Travis Warren, Patrick Iversen, Sina Bavari, Gustavo Palacios and Raul Rabadan. Viral diversity and clonal evolution from unphased genomic data
  • 18 - Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian Sig Jensen, Chris Mason, Susanne Barth and Laxmi Parida. Comparative Exomics of Phalaris cultivars under salt stress
  • 19 - Eric C.H. Chen and David Sankoff. Gene expression and fractionation resistance
  • 20 - Ketil Malde. Estimating the information value of polymorphic sites using pooled sequences

Accepted Posters

Download Abstracts Best Student Poster
sponsored by IBM Research
  • 1  - Ogun Adebali, Davi Ortega and Igor Zhulin. CDvisto: a Comprehensive Domain Visualization Tool
  • 2  - Charlotte Darby, Maureen Stolzer and Dannie Durand. What’s in a name? An expanded classification of xenologs
  • 3  - Minli Xu, Jeffrey Lawrence and Dannie Durand. Comparative genomics sheds light on the evolution and function of the Highly Iterative Palindrome -1 motif in Cyanobacteria
  • 4  - Manuel Lafond, Emmanuel Noutahi, Jonathan Séguin, Magali Semeria, Nadia El-Mabrouk, Laurent Gueguen and Eric Tannier. Gene Tree Correction with TreeSolver
  • 5  - Anna Paola Carrieri and Laxmi Parida. SimRA: Rapid & Accurate Simulation of Populations based on Random-Graph Models of ARG
  • 6  -  Francesco Abate, Sakellarios Zairis, Elisa Ficarra, Andrea Acquaviva, Chris Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami and Raul Rabadan. Pegasus: annotation and prediction of oncogenic gene fusion events as a supervised learning task
  • 7  - Daniel Doerr, Jens Stoye and Katharina Jahn. Discovering common intervals in multiple indeterminate strings
  • 8  - Guillaume Holley, Roland Wittler and Jens Stoye. Bloom Filter Trie - a data structure for pan-genome storage
  • 9  - Manfred Klaas, Paul Cormican, Thibauld Michel and Susanne Barth. Genotyping by sequencing of a collection of Miscanthus spp. accessions
  • 10 - Han Lai and Dannie Durand. How much are you willing to pay? Selecting costs for reconciliation with duplication and transfers
  • 11 - Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson and Tandy Warnow. ASTRAL: fast and accurate species tree estimation from gene trees
  • 12 - Siavash Mirarab, Nam-Phuong Nguyen and Tandy Warnow. PASTA: ultra-large multiple sequence alignment
  • 13 - Alexandra Dana and Tamir Tuller. The effect of tRNA levels on decoding times of mRNA codons
  • 14 - Ghada Badr and Arwa Alturki. CompPSA: A Component-Based Pairwise RNA Secondary Structure Alignment Algorithm
  • 15 - Robert Aboukhalil, Joan Alexander, Jude Kendall, Michael Wigler and Gurinder Atwal. Single-cell sequencing: How many is many enough?
  • 16 - Cedric Chauve, Yann Ponty and João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
  • 17 - Sapna Sharma and Klaus F. X. Mayer. Genome and sequence characteristics indicate frequent introgressive hybridization events in monocots and dicots
  • 18 - Nina Luhmann, Cedric Chauve, Jens Stoye and Roland Wittler. Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework
  • 19 - Ghada Badr and Haifa Alaqel. Genome Rearrangement for RNA Secondary Structure Using a Component-Based Representation: An Initial Framework
  • 20 - Di Huang and Ivan Ovcharenko. Identifying risk-associated regulatory SNPs in ChIP-seq enhancers
  • 21 - Kevin Emmett and Raul Rabadan. Characterizing Horizontal Gene Transfer in Microbial Evolution using Topological Data Analysis
  • 22 - Mehmet Gunduz, Esra Gunduz, Omer Faruk Hatipoglu, Gokhan Nas, Elif Nihan Cetin, Bunyamin Isik and Ramazan Yigitoglu. Role of p33ING1b in Head and Neck Cancer
  • 23 - Pedro Feijao, Fábio V Martinez, Marília Braga and Jens Stoye. The Family-Free Double Cut and Join and its application to ortholog detection
  • 24 - Corey Hudson and Kelly Williams. LearnedPhyloblocks: Novel Genomic Islands through Phylogenetic Profiling
  • 25 - Philip Davidson, Luisa Hiller, Michael T. Laub and Dannie Durand. Tracking the Evolution of a Signal Transduction Pathway Architecture with Comparative Genomics
  • 26 - Krister Swenson and Mathieu Blanchette. Linking Genome Rearrangements and Chromatin Conformation
  • 27 - Filippo Utro, Deniz Yorukoglu, David Kuhn, Saugata Basu and Laxmi Parida. Topological Data Analysis to detect population admixture in recombining chromosomes
  • 28 - Yee Him Cheung, Nevenka Dimitrova and Wim Verhaegh. Achieving Cross-Platform Compatibility of Gene Expression Data
  • 29 - Filippo Utro, Daniel E. Platt and Laxmi Parida. K-mer Analysis of Ebola sequences differentiates outbreaks

Keynote Speakers


Organizing Committee & Program Chairs

  • Laxmi Parida

    IBM Research

  • Bud Mishra

    New York University

  • Gurinder Singh Atwal

    Cold Spring Harbor Laboratory

Web, Publication and Poster Chairs

  • Filippo Utro

    IBM Research

  • Niina Haiminen

    IBM Research

Program Committee

  • Gabriela Alexe

    Harvard Medical School, USA

  • Anne Bergeron

    Universite du Quebec a Montreal, Canada

  • Gyan Bhanot

    Rutgers, USA

  • Cedric Chauve

    Simon Fraser University, Canada

  • Miklos Csuros

    Universitè de Montreal, Canada

  • Nevenka Dimitrova

    Philips Research, USA

  • Nadia El-Mabrouk

    University of Montreal, Canada

  • Katharina Jahn

    Bielefeld University, Germany

  • Asif Javed

    GIS A-STAR, Singapore

  • Stefano Lonardi

    UC Riverside, USA

  • Ion Mandoiu

    University of Connecticut, USA

  • Macha Nikolski

    University Bordeaux, France

  • Aida Ouangraoua

    INRIA, France

  • Megan Owen

    Lehman College, USA

  • Itsik Pèer

    Columbia University, USA

  • Teresa Przytycka


  • Raul Rabadan

    Columbia University, USA

  • Marie-France Sagot

    INRIA, France

  • Jens Stoye

    Bielefeld University, Germany

  • Krister Swenson

    Institut de Biologie Computationnelle, France

  • Eric Tannier

    INRIA, France

  • Yufeng Wu

    University of Connecticut, USA

  • Sophia Yancopoulos

    Feinstein Institute for Medical Research, USA

  • Chunfang Zheng

    University of Ottawa, Canada


Sunday at-a-glance


Wine and Cheese Reception

Invited Talk

Joseph Nadeau

Monday at-a-glance


Invited Talk

Adam Siepel

Tea Break

Contributed Talks

Genome Rearrangment - I


Contributed Talks

Genomics/Exomics - I

Tea Break (& Poster set-up)

Contributed Talks

Phylogeny/Phylogenomics - I


Invited Talk

Doreen Ware

Tuesday at-a-glance


Contributed Talks

Phylogeny/Phylogenomics - II

Tea Break

Contributed Talks

Genome Rearrangement - II


Contributed Talks

Genomics/Exomics - II

Tea Break

Poster Session

Invited Talk

Jaume Bertranpetit

Cocktail Hour

Gala Dinner

Wednesday at-a-glance


Invited Talk

Ajay Royyuru

Tea Break

Contributed Talks

Evolution models and Implications

Closing Remarks


Poster take-down


Conference Will Be Held At

Cold Spring Harbor Laboratory

One Bungtown Road, Cold Spring Harbor, NY 11724

The Cold Spring Harbor Laboratory (CSHL) is a private, non-profit institution with research programs focusing on cancer, neurobiology, plant genetics, genomics and bioinformatics (more information at http://www.cshl.edu/).

Meeting information

Please see detailed additional meeting information regarding RECOMB-CG meeting at CSHL (click here).

Venue Map

Please see detailed location information at the CSHL campus map (click here).


If you have questions about logistic/travel regarding Recomb-CG 2014, please contact Katharine Bradley kbradley -at- cshl.edu

Getting Here

By Train

Take the Long Island Railroad (LIRR) to Syosset train station (Port Jefferson line). There is a shuttle service available from Syosset train station to CSHL on weekdays (see this pdf for the schedule:http://meetings.cshl.edu/shuttle.pdf. You can also take a taxi for the few miles trip from the train station to CSHL.
For LIRR schedules and fares see http://lirr42.mta.info/
Note "peak" train fares are in effect during morning and afternoon rush hours (other times "off peak" fares). It is advisable to purchase a ticket at the station before boarding the train.

By Car

Please see detailed directions at the CSHL website: http://www.cshl.edu/About-Us/Directions/

Travel Notes

CSHL is located 35 miles (55 kilometers) northeast from midtown Manhattan. Travel time from Manhattan is approximately 1.5 hours by public transport (including last 2 miles by taxi), or 1 hour by car (up to 2 hours with traffic). The closest airports are LaGuardia and JFK in New York and Newark in New Jersey.


Sponsorship plays a major role in the success of our event.

Main Sponsors


  • October 21

    RECOMB-CG Photos

    News Image

    The photos are now available (click here).

  • July 28

    Accepted Papers

    News Image

    The list of accepted papers is now available (click here).

  • July 28

    Call for Posters

    News Image

    We welcome poster submissions. Submissions must be received in electronic form by 11:59pm (GMT-4), September 12th, 2014. Download Call for Posters (click here).

  • April 05

    Registration Open

    News Image

    Now it is possible to register to attend Recomb-CG 2014 via this form (click here)

  • April 01

    Call For Papers

    News Image

    We welcome paper submissions and accepted articles will be published in the open access international online journal BMC Genomics. BMC will charge publication fees independently from the conference registration. All accepted papers will have to be presented by one of the authors at the conference. We also welcome poster submissions. Submissions must be received in electronic form by 11:59pm (GMT-4), June 27th, 2014. Download Call for Papers (click here).

  • February 07

    Conference Location at Cold Spring Harbor Laboratory - New York

    News Image

    The twelfth RECOMB-CG satellite workshop will be held at Cold Spring Harbor Laboratory (in the immediate vicinity of New York City, USA) 19 - 22 October 2014


Contact info

If you have questions or comments regarding Recomb-CG 2014.

Email: parida -at- us.ibm.com

Logistic/travel questions

If you have questions about logistic/travel regarding Recomb-CG 2014, please contact Katharine Bradley kbradley -at- cshl.edu