15th RECOMB Comparative Genomics Satellite Workshop

List of Accepted Papers -The workshop proceedings are now available online at Springer: https://link.springer.com/book/10.1007/978-3-319-67979-2

• The similarity distribution of paralogous gene pairs created by recurrent alternation of polyploidization and fractionation
  Yue Zhang and David Sankoff
• A tractable variant of the Single Cut or Join distance with duplicated genes
  Aniket Mane, Pedro Feijao and Cedric Chauve.
• Generation and Comparative Genomics of Synthetic Dengue Viruses
  Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Shimshi Atar, Tahel Altman, Justin Julander and Tamir Tuller
• ASTRAL-III: increased scalability and impacts of contracting low support branches
  Chao Zhang, Erfan Sayyari and Siavash Mirarab
• Algorithms for Computing the Family-Free Genomic Similarity under DCJ
  Diego P. Rubert, Gabriel L. Medeiros, Edna A. Hoshino, Marilia Braga, Jens Stoye and Fábio V. Martinez
• New Algorithms for Genomic Duplication Problem
  Jarosław Paszek and Pawel Gorecki
• TreeShrink: efficient detection of outlier tree leaves
  Uyen Mai and Siavash Mirarab.
• Rearrangement Scenarios Guided by Chromatin Structure
  Sylvain Pulicani, Pijus Simonaitis, Eric Rivals and Krister Swenson
• A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems under DCJ
  Pavel Avdeyev, Nikita Alexeev, Yongwu Rong and Max Alekseyev.
• Orientation of Ordered Scaffolds
  Sergey Aganezov and Max Alekseyev
• Finding Teams in Graphs and its Application to Spatial Gene Cluster Discovery
  Tizian Schulz, Jens Stoye and Daniel Doerr
• Inferring Local Genealogies on Closely Related Genomes
  Ryan Elworth and Luay Nakhleh
• Enhancing Searches for Optimal Trees using SIESTA
  Pranjal Vachaspati and Tandy Warnow.
• On the Rank-Distance Median of 3 Permutations
  Leonid Chindelevitch and Joao Meidanis
• Statistical Consistency of Coalescent-based Species Tree Methods under Models of Missing Data
  Michael Nute and Jed Chou.
• Fast Heuristics for Resolving Weakly Supported Branches using Duplication, Transfers, and Losses
  Han Lai, Maureen Stolzer and Dannie Durand

List of Posters

1. Ramil Nurtdinov, Alexandre Esteban, Sebastian Ullrich, Amaya Abad, Carme Arnan, Maria Sanz, Dmitri Pervouchine, Cecilia Klein, Beatrice Borsari, Marina Ruiz, Alessandra Breschi, Silvia Perez, Rory Johnson, Thomas Graf and Roderic Guigo
   The comparative transcriptomics analysis of CEBPa induced immune cell transdifferentiation in human and mouse
2. Marina Marcet-Houben and Toni Gabaldón
   Evolution of gene order in fungi
3. Joaquim Aguirre-Plans, Emre Guney, Jordi Mestres and Baldo Oliva
   Prediction of drug combinations using drug target and protein-protein interaction information
4. Milana Frenkel-Morgenstern, Alessandro Gorohovski, Somnath Tagore, Vaishnovi Sekar, Miguel Vazquez and Alfonso Valencia
   Chimeric Protein-Protein Interaction Networks Reveal Alterations in Cancer-Specific Phenotypes
5. Ron Zeira and Ron Shamir
   Sorting cancer genomes using double-cut-and-joins, duplications and deletions
6. Claudia Fontsere, David A. Hughes, Jessica Hernandez Rodriguez, Peter Frandsen, Pascaline Le Goura, Nelly Menard, Hans R. Siegismund, Arcadi Navarro, Chritina Hvilsom, and Tomas Marques-Bonet
   Impact of ebolavirus on Gorilla gorilla gorilla diversity
7. Alberto Meseguer, Oriol Fornes, Juan I. Fuxman Bass and Baldo Oliva
   Predicting the impact of mutations on transcription factor binding
8. Wasiu Akanni
   Genome-wide ortholog assessment in Ensembl
9. Carla Bello and Fyodor Kondrashov
   Evolution of human-specific lncRNAs through exon duplication
10. Raquel Garcia-Perez, Gloria Mas Marti, Meritxell Riera, Antoine Blancher, Marc Marti-Renom, Luciano di Croce, Jose Luis Gomez-Skarmeta, David Juan and Tomas Marques-Bonet
    Recent evolution of the epigenetic regulatory landscape in human and other primates
11. Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi Meudt and Luay Nakhleh
    Bayesian Inference of Phylogenetic Networks from Bi-allelic Genetic Markers
12. Panagiotis Agioutantis and Vassiliki Lila Koumandou
    Bioenergetic Diversity of the Human Gut Microbiome
13. Vassiliki Lila Koumandou and Sophia Kossida
    Evolution of b-type cytochromes in prokaryotes
14. Sergio Castillo-Lara and Josep F Abril
    A human-planarian interologs network to annotate planarian transcriptomes: PlanNET
15. Chunfang Zheng, Yuji Jeong, Madisyn Turcotte and David Sankoff
    Resolution effects in ancestral genomes reconstruction
16. Olivier Poirion, Kumardeep Chaudhary, Sijia Huang and Lana Garmire
    DeepProg: Multi-omics integration to predict cancer survival subtypes
17. Mark Forteza, Cedric Chauve and Aniket Mane
    Improving gene clustering into gene families
18. Sílvia Pérez-Lluch, Alessandra Breschi, Cecilia Coimbra Klein, Marina Ruiz-Romero, Emilio Palumbo, Amaya Abad, Carme Arnan and Roderic Guigo
    Natural Antisense Transcription along development and evolution
19. Lukas Kuderna
    A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0)
20. Pedro Feijao, Jennifer Gardy, William Hsiao, Cedric Chauve and Leonid Chindelevitch
    MentaLiST: A better, faster tool for MLST typing of bacterial pathogens from WGS data
21. Nikita Alexeev, Pavel Avdeyev and Max Alekseyev
    Genome Halving Problems and Embedded Graphs
22. Sylvain Pulicani, Pijus Simonaitis, Eric Rivals and Krister Swenson
    Rearrangement Scenarios Guided by Chromatin Structure