Overview
This Radcliffe Exploratory Seminar will held at the Radcliffe
Institute for Advanced Study on June 5-6, 2017.
The focus of this exploratory seminar is three scientific areas
where advances in computational methods could lead to dramatic opportunities for scientific discovery: phylogenomics, proteomics, and metagenomics. We pose the following two questions for each topic:
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What are the most substantial and important biological questions you would like to answer, for which new methods are needed (i.e., where current methods are either inappropriate, or have insufficient accuracy or scalability)? What are the requirements for these methods?
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What new algorithmic design paradigms might be able to make advances on answering these biological questions?
Thus, the focus of this exploratory seminar is to identify opportunities for substantial breakthroughs, by encouraging us to explicitly imagine a world where methods are no longer a limiting factor,
and to identify limitations of existing methods and properties of datasets that make current methods insufficient, or possibly inappropriate. The discussion will also include how to model the computational problems appropriately, so that new methods could be developed with improved accuracy. Finally, where appropriate, new methods will be discussed, that provide an advance on the current standard protocols, and that substantially advance the state of the art.
Agenda
Please see
this PDF for the
final
schedule, including location of meals.
(However, the schedule for talks is not provided, and will
be determined later.)
Attendees
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Vineet Bafna, UCSD
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Bonnie Berger, MIT
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Nick Grishin, HHMI and UT Southwestern
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Cara Magnabosco, Simons Center
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Siavash Mirarab, UCSD
-
Jian Peng, UIUC
-
Mihai Pop,
University of Maryland
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Sriram Sankararaman, UCLA
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Ramunas Stepenauskas, Bigelow Lab
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Tandy Warnow, UIUC (organizer)
Talks
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Vineet Bafna will talk about "Detecting ecDNA elements with sequence data"
during the challenges session, and
about "Detecting favored mutations in selective sweeps" during the
solutions session.
(PPTX)
-
Bonnie Berger will talk about compressive metagenomics
and binning with OPAL.
(PDF)
-
Nick Grishin will talk about (1) difficulties with phylogenies from genomic short reads: rooting and
missing regions, and
(2) problems with alignment of distant sequences.
-
Cara Magnabosco will talk about the challenges associated with interpretable feature selection in metagenomic data.
(PDF)
-
Siavash
Mirarab will talk about multi-locus species tree estimation in the
presence of gene tree discordance due to incomplete lineage
sorting.
-
Jian Peng will talk about protein structure prediction
and multiple sequence alignment
during the challenges session.
-
Mihai Pop will talk about "Naming the unknown bugs in microbiomes" for
the challenge session, and
"Metagenomics analysis at the strain level resolution" for the
solution session.
-
Sriram Sankararaman will speak about
challenges in modeling admixture using modern and ancient genomes.
- Ramunas Stepenauskas will talk about microbial single cell genomics
(PDF)
-
Tandy Warnow will speak about challenges in multiple sequence
alignment during the challenges session, and about
ensembles of HMMs during the solutions session.
(PDF)
Suggested Reading
- "Single-cell genomics reveals hundreds of
coexisting subpopulations in Wild Prochlorococcus",
Nadav Kashtan et al., Science 344, 416 (2014)
(PDF)
-
"Insights into the phylogeny and coding
potential of microbial dark matter",
Christian Rinke et al., Nature 499, 431 (2013)
(PDF)
-
"Potential for Chemolithoautotrophy
Among Ubiquitous Bacteria Lineages
in the Dark Ocean,"
Brandon Swan et al., Science 333, (2011)
(PDF)
-
"A new view of the tree of life."
Laura A. Hug et al.,
Nature Microbiology, 1 (2016): 16048.
(HTML)
-
"On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria."
Rochelle M. Soo et al.
Science, 355.6332 (2017): 1436-1440.
(HTML)
-
"Integrative modeling of gene and genome evolution roots the archaeal tree of life."
Tom A. Williams et al.,
Proceedings of the National Academy of Sciences, (2017): 201618463.
(HTML)
-
"Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity" by
Kristen M. Turner et al., Nature 543, 122-125, 2017.
(HTML)
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"Metagenomic binning through low density hashing."
Yunan Luo et al.,
bioRxiv
doi: https://doi.org/10.1101/133116.
(HTML).
-
(HTML), news article
about the paper by Locey and Lennon, PNAS 2016
(the "trillions" of microbial species).
See also (PDF) for the PNAS paper by Locey and Lennon.
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"Entropy-scaling search of massive biological data".
Y. William Yu, Noah M. Daniels, David C. Danko and Bonnie Berger
Cell Systems, (2015) 2:130-140
(HTML).
-
"Compressive mapping for next-generation sequencing."
Deniz Yorukoglu, Yun William Yu, Jian Peng, and Bonnie Berger.
Nature Biotechnology (2016) 34, 374-376.
(HTML)
-
"Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data".
Joseph Pickrell and Jonathan Pritchard, PLOS Genetics 2012
(HTML)
-
"Ancient Admixture in Human History".
Nick Patterson et al. Genetics 2012
(HTML)