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--- webinars [2021/10/25 16:56] – [Online journal club] Lars Arvestad
+++ webinars [2024/10/14 18:24] (current) – [Past webinars] Alexey Markin
@@ Line 1: / Line 1: @@
-===== Online journal club =====
+===== Online journal club (ISCB Academy webinars)=====
 ISCB and SMBE are collaborating to organize an online journal club (as part of the ISCBacademy series of webinars) on Evolution and Comparative Genomics.
@@ Line 11: / Line 11: @@
 ===== Next webinar =====
-**Speaker: Claudia Solis-Lemus**
+To be announced soon!
+===== Past webinars =====
+** April 25, 2024 **
+**Title: Reconstructing the horizontal movement of genes using Bayesian phylogenetic network inference**
+by **Nicola F. Müller** (University of California San Francisco).
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2024#133]]
+Read the article : [[https://www.nature.com/articles/s41467-022-31749-8]]
+Watch the webinar : [[https://www.youtube.com/watch?v=8HbYg6ki5cg]]
+--------------------
+** November 10, 2023 **
+**Title: Phylogenetic network estimation from site patterns using composite likelihood**
+by **Sungsik Kong** (University of Wisconsin-Madison).
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2023#124]]
+Read the article : [[https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syae054/7817714]]
+Watch the webinar : [[https://www.youtube.com/watch?v=OONdZfSLh0A]]
+--------------------
+** Tuesday  April 11, 2023 at 10:30AM EDT**
+**Title: Machine learning enables prediction of metabolic system evolution in bacteria**
+by **Naoki Konno** (University of Tokyo).
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2023#102]]
+Read the article : https://www.science.org/doi/full/10.1126/sciadv.adc9130
+Watch the webinar : https://www.youtube.com/watch?v=16aRqv15bOI
+--------------------
+** Tuesday November 1, 2022 at 10:30AM EDT**
+**Title: Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses**
+by **Mohammed El-Kebir** (University of illinois).
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2022#84]]
+Read the article : https://academic.oup.com/mbe/article/39/7/msac133/6608352
+Watch the webinar : https://www.youtube.com/watch?v=k8YwpMmv9lE
+--------------------
+** Wednesday April 12, 2022 at 10:30AM EDT**
+**Title: Combining evolution and proteomics to discover protein complexes conserved across plants**
+by **Claire McWhite** (University of Texas at Austin).
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2022#64]]
+Read the article : [[https://doi.org/10.1016/j.cell.2020.02.049]]
+Watch the webinar : https://www.youtube.com/watch?v=bJzCYAi1guA
+--------------------
+** Tuesday November 2, 2021 at 11:00AM EDT**
 **Title: Scalable Inference of Phylogentetic Networks**
-**November 2, 2021 at 11:00AM EDT**
+by **Claudia Solis-Lemus** (University of Wisconsin).
-Phylogenetic network inference plays an important role in the reconstruction of the tree of life, given the widespread gene flow among different organisms. However, there are many challenges in the inference of reticulate evolution such as network reconstruction and interpretation, and difficulties to summarize network uncertainty. In this talk, I will explain the current difficulties in network statistical inference and present a new scalable method based on pseudolikelihood theory. I will also present extensions of standard trait evolution tools to networks, such as phylogenetic regression or ANOVA, ancestral trait reconstruction, and Pagel's lambda test of phylogenetic signal. All the new tools are implemented in the open-source Julia package PhyloNetworks.
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2021#49]]
+Read the articles : [[https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896]]; [[https://arxiv.org/abs/2010.01758]]
-===== Past webinars =====
+Watch the webinar : https://www.youtube.com/watch?v=J9HjsJ9PaGI
-**Wednesday September 30, 2020 at 11:00AM EDT**:
+--------------------
+** Thursday January 28, 2021 at 11:00AM EDT**
+**Title: SaGePhy: A phylogenetic simulation framework for gene and subgene evolution**
+by **Soumya Kundu** (University of Connecticut).
+Read the summary : [[https://www.iscb.org/cms_addon/academy/history?year=2021#32]]
+Read the article : https://academic.oup.com/bioinformatics/article/35/18/3496/5305633
+Watch the webinar : https://www.youtube.com/watch?v=P8P_yDeInN4
+--------------------
+**Wednesday September 30, 2020 at 11:00AM EDT**
 **RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference**
@@ Line 28: / Line 121: @@
 by **Alexey Kozlov and Alexandros Stamatakis** (Heidelberg Institute for Theoretical Studies).
-Read the summary : https://www.iscb.org/iscbacademy-upcoming#kozlov
+Read the summary : https://www.iscb.org/cms_addon/academy/history?year=2020#24
 Read the article : https://academic.oup.com/bioinformatics/article/35/21/4453/5487384
-Registration : https://iscb.swoogo.com/iscbacademy-04-kozlov
+Watch the webinar : https://www.youtube.com/watch?v=nSLVcgPfUUo
+--------------------
-**Monday August 24, 2020**:
+**Monday August 24, 2020**
 **Unravelling the mystery of orphan genes to understand the origins of genetic novelty**
@@ Line 40: / Line 135: @@
 presented by **Nikos Vakirlis** (Alexander Fleming Biomedical Sciences Research Center).
-Read the summary : https://www.iscb.org/iscbacademy-archive#vakirlis
+Read the summary : https://www.iscb.org/cms_addon/academy/history?year=2020#22
 Read the articles : https://doi.org/10.7554/eLife.53500 ; https://doi.org/10.1038/s41467-020-14500-z
@@ Line 48: / Line 143: @@
 --------------------
-**Tuesday July 7, 2020**:
+**Tuesday July 7, 2020**
 **Genetic Basis Of De Novo Appearance Of Carotenoid Ornamentation In Bare-Parts Of Canaries**
@@ Line 54: / Line 149: @@
 presented by **Malgorzata Gazda** (Universidade do Porto).
-Read the summary : https://www.iscb.org/iscbacademy-archive#gazda
+Read the summary : https://www.iscb.org/cms_addon/academy/history?year=2020#18
 Read the article : https://doi.org/10.1093/molbev/msaa006
@@ Line 62: / Line 157: @@
 --------------------
-**Friday June 12, 2020**:
+**Friday June 12, 2020**
 **Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies**
@@ Line 68: / Line 163: @@
 presented by **Erfan Sayyari** (UCSD).
-Read the summary : https://www.iscb.org/iscbacademy-archive#sayyari
+Read the summary : https://www.iscb.org/cms_addon/academy/history?year=2020#14
 Read the article : https://doi.org/10.1093/molbev/msw079