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2017-iEvoBio / organization

Logistical details, Suggestions for discussion topics, Agenda
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Software Bazaar: PhyloNet-HMM #15

Open kevinjliu opened 7 years ago

kevinjliu commented 7 years ago

Authors: Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh Source code: https://bioinfocs.rice.edu/software/phmm License: GNU GPLv3 Abstract: One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression, which is the integration of genetic material from one species into the genome of an individual in another species. The evolution of several groups of eukaryotic species has involved hybridization, and cases of adaptation through introgression have been already established. In this work, we report on PhyloNet-HMM—a new comparative genomic framework for detecting introgression in genomes. PhyloNet-HMM combines phylogenetic networks with hidden Markov models (HMMs) to simultaneously capture the (potentially reticulate) evolutionary history of the genomes and dependencies within genomes. A novel aspect of our work is that it also accounts for incomplete lineage sorting and dependence across loci. Application of our model to variation data from chromosome 7 in the mouse (Mus musculus domesticus) genome detected a recently reported adaptive introgression event involving the rodent poison resistance gene Vkorc1, in addition to other newly detected introgressed genomic regions. Based on our analysis, it is estimated that about 9% of all sites within chromosome 7 are of introgressive origin (these cover about 13 Mbp of chromosome 7, and over 300 genes). Further, our model detected no introgression in a negative control data set. We also found that our model accurately detected introgression and other evolutionary processes from synthetic data sets simulated under the coalescent model with recombination, isolation, and migration. Our work provides a powerful framework for systematic analysis of introgression while simultaneously accounting for dependence across sites, point mutations, recombination, and ancestral polymorphism.

k8hertweck commented 7 years ago

Thank you for your submission to the Software Bazaar! We've included you on the list of presenters for June 24, 6-8 pm (same time and place as first Evolution poster session). There will be tables, power sources, and signs available. Please let us know if you have any questions!

kevinjliu commented 7 years ago

Hi Kate,

Unfortunately, I'm scheduled to present a poster during the first poster session. I'll have to withdraw my entry to the Software Bazaar. Can you please remove me from the list of presenters? Thanks.

On Wed, Jun 14, 2017 at 11:31 AM, Kate Hertweck notifications@github.com wrote:

Thank you for your submission to the Software Bazaar! We've included you on the list of presenters for June 24, 6-8 pm (same time and place as first Evolution poster session). There will be tables, power sources, and signs available. Please let us know if you have any questions!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/2017-iEvoBio/organization/issues/15#issuecomment-308468879, or mute the thread https://github.com/notifications/unsubscribe-auth/AbxnngzGX6I0FGQqIx4GxA0npK_0CURcks5sD_zRgaJpZM4NtEPT .

k8hertweck commented 7 years ago

Sorry to hear of this conflict (but often unavoidable as far as these large meetings go!). We would be happy to include a sign at the Bazaar directing folks to your poster (assuming it's related to the software in question?). Additionally, there has been some interest in organizing folks for a Bazaar during a later poster session. Would this be of interest to you?

kevinjliu commented 7 years ago

Sure, that would be great. Yes, my poster is related to the software demo that I was planning to give.

Yes, I would be interested in participating in a later Software Bazaar. Let me know what you all decide.

Thanks!

On Mon, Jun 19, 2017 at 12:17 PM, Kate Hertweck notifications@github.com wrote:

Sorry to hear of this conflict (but often unavoidable as far as these large meetings go!). We would be happy to include a sign at the Bazaar directing folks to your poster (assuming it's related to the software in question?). Additionally, there has been some interest in organizing folks for a Bazaar during a later poster session https://github.com/2017-iEvoBio/organization/issues/12#issuecomment-308475581. Would this be of interest to you?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/2017-iEvoBio/organization/issues/15#issuecomment-309490524, or mute the thread https://github.com/notifications/unsubscribe-auth/AbxnntwBGBOV7Lra7CXRt-br79DUuK5sks5sFp8bgaJpZM4NtEPT .

k8hertweck commented 7 years ago

Awesome, what is your poster number? @daisieh, can we get an addendum to this sign that includes the poster number?

kevinjliu commented 7 years ago

My poster is # P88. Thanks!

On Tue, Jun 20, 2017 at 10:08 PM, Kate Hertweck notifications@github.com wrote:

Awesome, what is your poster number? @daisieh https://github.com/daisieh, can we get an addendum to this sign that includes the poster number?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/2017-iEvoBio/organization/issues/15#issuecomment-309942201, or mute the thread https://github.com/notifications/unsubscribe-auth/AbxnnhawC6XxTs4jh18DYrIFgbEAjOifks5sGHswgaJpZM4NtEPT .