| 8:00 - 9:00 | Registration in the Calit2 Lobby (Direction) |
| 9:15 - 11:05 | Keynote and Proceedings Talks in CSE 1242 (Computer Science and Engineering; next to Calit2) |
| 11:05 - 11:25 | Refreshment Break in Calit2 Lobby |
| 11:25 - 12:15 | Proceedings Talks in CSE 1242 |
| 12:15 - 1:45 | Lunch Break (lunch on your own) Price Center Food Court or Restaurants at Sixth College |
| 1:45 - 3:35 | Keynote and Proceedings Talks in CSE 1242 |
| 3:35 - 4:00 | Refreshment Break in Calit2 Lobby |
| 4:00 - 4:50 | Proceedings Talks in CSE 1242 |
| 5:00 - 6:30 | Poster Session in Calit2 Lobby |
| 8:00 - 9:00 | Registration |
|---|---|
| 9:00 - 9:15 | Welcome and Instructions |
| 9:15 - 10:15 | Keynote Talk The secret life of cheese: Microbial interactions and evolution in a "simple" microbiome, Rachel Dutton (chair: Siavash Mirarab) |
| Session 1: Evolution (chair: Lingling Jin) | |
| 10:15 - 10:40 | On the comparison of bacteriophage populations, Anne Bergeron, Marie-Jean Meurs, Romy Valiquette and Krister Swenson |
| 10:40 - 11:05 | Syntenic dimensions of genomic evolution, Zhe Yu and David Sankoff |
| 11:05 - 11:25 | Refreshment Break |
| Session 2: Phylogenetics (chair: Krister Swenson) | |
| 11:25 - 11:50 | Fast and accurate branch support calculation for distance-based phylogenetic placements, Navid Bin Hasan, Avijit Biswas, Metin Balaban, Siavash Mirarab and Md. Shamsuzzoha Bayzid |
| 11:50 - 12:15 | The Sackin Index of Simplex Networks, Louxin Zhang |
| 12:15 - 1:45 | Lunch Break |
| 1:45 - 2:45 | Keynote Talk Evolutionary Dynamics of the Human Gut Microbiome, Nandita Garud (chair: Siavash Mirarab) |
| Session 3: Phylogenetics (chair: Manuel Lafond) | |
| 2:45 - 3:10 | Phylogenetic Placement Problem: A Hyperbolic Embedding Approach, Yueyu Jiang, Puoya Tabaghi and Siavash Mirarab |
| 3:10 - 3:35 | Phylogenetic Network Dissimilarity Measures That Take Branch Lengths Into Account, Berk Yakici, Huw Ogilvie and Luay Nakhleh |
| 3:35 - 4:00 | Refreshment Break |
| Session 4: Genomic Sequencing (chair: Anne Bergeron) | |
| 4:00 - 4:25 | Benchmarking penalized regression methods in machine learning for single cell RNA sequencing data, Bhavithry Sen Puliparambil, Jabed Tomal and Yan Yan |
| 4:25 - 4:50 | Deciphering the tissue-specific regulatory role of intronless genes across cancers, Aviña-Padilla Katia, José Antonio Ramirez-Rafael, Gabriel Emilio Herrera Oropez, Guillermo Romero, Octavio Zambada-Moreno, Ishaan Gupta and Maribel Hernandez Rosales |
| 5:00 - 6:30 | Poster Session I |
| 8:00 - 9:00 | Registration |
|---|---|
| 9:15 - 10:15 | Keynote Talk Dosage sensitivity in evolution and disease, Aoife McLysaght (chair: David Sankoff) |
| Session 5: Homology and Reconciliation (chair: Mukul Bansal) | |
| 10:15 - 10:40 | The Complexity of Finding Common Partitions of Genomes with Predefined Block Sizes, Manuel Lafond, Adiesha Liyanage, Binhai Zhu and Peng Zou |
| 10:40 - 11:05 | Reconciliation with Segmental Duplication, Transfer, Loss and Gain, Yoann Anselmetti, Mattéo Delabre and Nadia El-Mabrouk |
| 11:05 - 11:25 | Refreshment Break |
| Session 6: Homology and Reconciliation (chair: Maribel Hernandez Rosales) | |
| 11:25 - 11:50 | Quantifying Hierarchical Conflicts in Homology Statements, Krister Swenson, Afif Elghraoui, Faramarz Valafar, Siavash Mirarab and Mathias Weller |
| 11:50 - 12:15 | Partial Gene Transfer and its Impact on Gene Tree Reconstruction, Sumaira Zaman and Mukul S. Bansal |
| 12:15 - 1:45 | Lunch Break |
| Session 7: Metagenomics & Genome Rearrangments (chair: Qiyun Zhu) | |
| 1:45 - 2:10 | Using computational synthetic biology tools to modulate gene expression within a microbiome, Liyam Chitayat Levi, Ido Rippin, Moran Ben Tulila, Rotem Galron and Tamir Tuller |
| 2:10 - 2:35 | Metagenomics Binning of Long Reads Using Read-Overlap Graphs, Anuradha Wickramarachchi and Yu Lin |
| 2:35 - 3:00 | A Mixed Integer Linear Programming Algorithm for Plasmid Binning, Aniket Mane, Mahsa Faizrahnemoon and Cedric Chauve |
| 3:00 - 3:25 | Sorting by k-Cuts on Signed Permutations, Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Geraldine Jean, Guillaume Fertin, Ulisses Dias and Zanoni Dias |
| 3:35 - 4:00 | Refreshment Break |
| Session 8: Genome Rearrangements (chair: Yan Yan) | |
| 4:00 - 4:25 | A New Approach for the Reversal Distance with Indels and Moves in Intergenic Regions, Klairton Lima Brito, Andre Rodrigues Oliveira, Alexsandro Oliveira Alexandrino, Ulisses Dias and Zanoni Dias |
| 4:25 - 4:50 | Chromothripsis rearrangements are informed by 3D genome organization, Alexey Zabelkin, Natalia Petukhova, Vitaly Dravgelis, Sergey Aganezov and Nikita Alexeev |
| 4:50 - 5:00 | Closing Remarks |
| 5:00 - 6:30 | Poster Session II |