Fall 2018

Lab meetings are held 2-3 pm in 712 BioSci. Anyone is welcomed to join!

Dec 14 Chen

Dec 7 Rebekah

OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences

https://www.biorxiv.org/content/early/2018/11/08/466201 

Nov 30 Chapter 7 and 8 of Harmon book Sep 14 Chapter 6 of Harmon book https://lukejharmon.github.io/pcm/chapters/ 

Oct 26 to Nov 16 No lab meeting due to people traveling

Oct 22 Delphine and Diego

A maximum pseudo-likelihood approach for phylogenetic networks

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-16-S10-S10

Oct 19 Lab trip to Taylor Falls

Oct 12 Ya

Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics https://academic.oup.com/mbe/article/31/11/3081/2925722 

Oct 5 Delphine introducing her work on C2 physiology and goal for her visit

Sep 28 Chen project update

Sep 21 No lab meeting. Diego and Ya in Mexico

Sep 14 Chapter 6 of Harmon book https://lukejharmon.github.io/pcm/chapter6_beyondbm/ 

Sep 7 Chapter 5 of Harmon book https://lukejharmon.github.io/pcm/chapter5_mvbm/

Difference between correlation vs. regression

Previous semesters

Summer 2018

Aug 31 No lab meeting. Happy labor day!

Aug 24 Rebekah Fulbright proposal

Aug 22 Diego ABBA-BABA test

Detection and Polarization of Introgression in a Five-Taxon Phylogeny

https://academic.oup.com/sysbio/article/64/4/651/1650669 

Great discussion on the promise and limitations of using ABBA-BABA test for detecting introgression.

Aug 17 Diego hybridization

Phylogenomics uncovers early hybridization and adaptive loci shaping the radiation of Lake Tanganyika cichlid fishes https://www.nature.com/articles/s41467-018-05479-9

Aug 10 Chen

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae https://www.sciencedirect.com/science/article/pii/S1674205218301898

Aug 3 (Ya away)

Jul 27 No lab meeting since folks are just back from Botany

Jul 20 Botany practice talk

Jun 8–Jul 13 No lab meeting due to people traveling

May 30 SSB practise talk: Chen and Diego

May 25 Chain of Lakes Lab Trip

May 18 Chen benchmark paper figure review

May 11 Chapter 4 of Harmon’s Comparative methods book https://lukejharmon.github.io/pcm/chapter4_fitbm/

And the 1985 PIC paper: Felsenstein, J. 1985. Phylogenies and the comparative method. Am. Nat. 125:1–15.

We went through the math but couldn’t figure out the branch extension bit form either the Harmon book or the 1985 PIC paper

Spring 2018

2018-4-20 Chapter 3 of Harmon’s comparative methods book

https://lukejharmon.github.io/pcm/chapters/ 

2018-4-13 Diego

Chapter 1 and 2 from Luke’s book https://lukejharmon.github.io/pcm/chapter1_introduction/ 

We loved the book. Flipping lizards makes a lot of sense!

2018-4-6 Chen

A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm. https://www.ncbi.nlm.nih.gov/pubmed/28011783

Doesn’t seem that helpful..

2018-3-30 Rebekah

Stochastic Mapping of Morphological Characters

http://www.nielsenlab.org/wp-content/uploads/2011/07/Huelsenbeck-J.-P.-Syst.-Biol.-2003.pdf 

2018-3-23 No lab meeting (Ya faculty meeting)

2018-3-16 Spring break

2018-3-9 Rebekah project methods in niche analysis

Combining Historical Biogeography with Niche Modeling in the Caprifolium Clade of Lonicera (Caprifoliaceae, Dipsacales) https://academic.oup.com/sysbio/article/59/3/322/1703086

2018-3-2 Ya Co-expression network + phylogenomics in non-model species

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism http://onlinelibrary.wiley.com/doi/10.1002/ajb2.1017/full 

2018-2-14 Rebekah lead a discussion of Ch 2 in the book

Carnivorous Plants: Physiology, ecology, and evolution

2018-2-7 Chen share ideas on his DGE benchmark project

Fall 2017

2017-11-12 Diego

IsoSel: Protein Isoform Selector for phylogenetic reconstructions

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0174250

2017-11-10 Chen

Read mapping softwares

Problem with low % uniquely mapped in polyploids?

2017-11-8 Diego & Chen

Papers on synteny-informed homology inference. Essentially one method but these papers cite previous paper for calculating scores:

GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm

(the benchmark paper)

https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0684-2 

Quantitative synteny scoring improves homology inference and partitioning of gene families

(the paper introducing modified algorithm)

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-S15-S12

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

(The original algorithm paper)

http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000063&type=printable 

2017-11-3 Chen

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

http://www.nature.com/nbt/journal/v33/n3/full/nbt.3122.html 

https://ccb.jhu.edu/software/stringtie/ 

2017-11-1 Diego

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses https://www.nature.com/articles/s41598-017-13236-z

2017-10-25 Ya

A critical comparison of technologies for a plant genome sequencing project

https://www.biorxiv.org/content/early/2017/10/11/201830?rss=1 

2017-9-26 Chen

WGCNA: an R package for weighted correlation network analysis

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559

2017-9-25 Rebekah

Gene ontology

Annotated genes and non-annotated genomes: cross-species use of Gene Ontology in ecology and evolution research

Primmer et al. 2013 Molecular Ecology

http://onlinelibrary.wiley.com/doi/10.1111/mec.12309/full 

Summer 2017

2017-8 Chen

OrthoFinder, OrthoMCL, vs. other orthology inference methods

2017-5-10 Chen

Wisecaver et al. 2017 Plant Cell

A Global Co-expression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants

http://www.plantcell.org/content/early/2017/04/13/tpc.17.00009.abstract 

Lab meeting ideas:

How to organize/backup data and code: Jpyter, Git, markdown file

Everyone share their own tips

Everyone share a paper they read

Small useful linux tools

awk

screen

Papers for the future (feel free to add/delete)

OrthoFinder2

https://www.biorxiv.org/content/biorxiv/early/2018/11/08/466201.full.pdf

Amalgamated cross-species transcriptomes indicate organ-specific 2 preadaptation for functional shifts in gene expression

https://www.biorxiv.org/content/biorxiv/early/2018/09/05/409888.full.pdf 

https://academic.oup.com/mbe/article/35/9/2296/5050468

Accurate Detection of Convergent Amino-Acid Evolution with PCOC

C4 etc as examples

Do plants have a segregated germline?

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2005439 

Metabolite evolution

Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway.

Moghe GD, et al. Elife. 2017.

Molecular dating

http://www.biorxiv.org/content/biorxiv/early/2017/09/01/113720.full.pdf?%3Fcollection=

Brown 2017 SysBio

Steve Kelly 1KP C4

Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis

Steven Kelly, Sarah Covshoff, Samart Wanchana, Vivek Thakur, Paul Quick, Yu Wang, Martha Ludwig, Richard Bruskiewich, Alisdair Fernie, Rowan Sage, Zhijian Tian, Zixian Yan, Jun Wang, Yong Zhang, Xin-Guang Zhu, Gane Ka-Shu Wong, Julian Hibberd

doi: https://doi.org/10.1101/163097 

http://www.biorxiv.org/content/early/2017/07/13/163097 

Stenz 2015 SysBio

Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh

https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syv039

Weber 2016

Macroevolution of perfume signalling in orchid bees

http://onlinelibrary.wiley.com/doi/10.1111/ele.12667/full 

Fundamentals and Recent Developments in Approximate Bayesian Computation

http://sysbio.oxfordjournals.org/content/early/2016/09/07/sysbio.syw077.full.pdf?papetoc 

Folk paper on ancestral niche reconstruction

http://www.biorxiv.org/content/biorxiv/early/2017/04/20/129189.full.pdf