Paper Reading Group

Dept. of Computer Science and Engineering, University of Connecticut. PI: Yufeng Wu

This contains the list of topics/papers we have read in our paper reading group.


Spring 2017

Date
Paper
Presenter
2/21/2017
Introduction to neural network. Chapter 6 of Duda, et al' book. Y. Wu
2/14/2017
Research presentation on multispecies coalescents.
Y. Wu
1/24/2017
A paper on deep learning in population genetics.
J. Pei
1/17/2017
Linear separation algorithms and proof of convergence. Chapter 5 of Duda, et al' book.
Y. Wu

Fall 2016

Date
Paper
Presenter
12/1/2016
Research presentation: circular RNA
X. Li
11/15/2016
Research presentation: a computational problem in genetics
J. Pei
11/8/2016
Research presentation: recombination and genealogy inference
S. Mirzaei
11/1/2016
Research presentation: repeat finding
C. Chong
10/25/2016
A paper on the bandit problem: The non-stochastic multiarmed bandit problem
Y. Wu
10/18/2016
A paper on long reads assembly
C. Chu
10/11/2016
Reinforcement learning from Sutton's book
Y. Wu
10/4/2016
Reinforcement learning from Sutton's book Y. Wu
9/27/2016
Reinforcement learning from Sutton's book Y. Wu

Spring and summer 2016

Date
Paper
Presenter
8/16/2016
A paper on coalescent in species tree (monophyly)
J. Pei
7/25/2016
A paper from ISMB 2016 on repeat finding
C. Chu
7/18/2016
A paper on natural selection
J. Pei
7/4/2016
A paper on circular RNA
X. Li
6/6/2016
A paper on natural selection
J. Pei
5/16/2016
Repeatscount: A method for finding repeats from assembled genomes (paper).
C. Chu
4/26/2016
Kraken: ultrafast metagenomic sequence classification using exact alignments.

An algorithm to estimate effective population size (seems to be an interesting problem):
http://www.genetics.org/content/200/1/285

C. Chu

J. Pei
4/19/2016
A paper on population ancestral coefficient estimate.
J. Pei
4/12/2016
Presentation practice.
A paper on circular RNA.
S. Mirzaei
X. Li
4/05/2016
Presentation practice
S. Mirzaei
3/29/2016
Papers on long reads error correction (paper 1, paper 2).
X. Li
3/22/2016
A paper on population size estimate.
J. Pei
3/8/2016
A paper on alignment-free sequence comparison
C. Chu
3/1/2016
The DALIGNER paper.
X. Li

Fall 2015


Date
Paper
Presenter
10/26/2015
Gradient methods (from book: Nonlinear Programming)
Y. Wu

10/19/2015
A paper on genome assembly using BWT.
C. Chu
10/12/2015
On eigenvalue of Google pagerank matrix :
http://nlp.stanford.edu/pubs/secondeigenvalue.pdf
J. Pei
10/5/2015
A paper on 1000 Genomes Project: link

The TreeMix paper.

C. Chu

S. Mirzaei


Spring and Summer 2015

Date
Paper
Presenter
7/6/2015
A paper on tandem repeat finding:
http://bioinformatics.oxfordjournals.org/content/30/24/3491.short

A paper on species tree inference: http://www.ncbi.nlm.nih.gov/pubmed/26072508
C. Chu


S. Mirzaei
6/29/2015
A paper on long reads sequence assembly: http://www.nature.com/nbt/journal/v33/n6/full/nbt.3238.html#supplementary-information

A paper on species tree inference: http://bioinformatics.oxfordjournals.org/content/30/17/i541.full
C. Chu

S. Mirzaei
6/22/2015
A paper on HMM training: http://www.cs.columbia.edu/~djhsu/papers/hmm.pdf

Misassembly detection:
http://bioinformatics.oxfordjournals.org/content/31/12/i80.abstract
J. Pei

X. Li
6/15/2015
A paper on spectral method: http://www.ncbi.nlm.nih.gov/pubmed/8854662

A paper on repeat analysis (Dfam): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531169/
Y Wu

C. Chong
5/17/2015
A paper on species delimitation: http://www.genetics.org/content/194/1/245.short

Some topics on constrained optimization
J. Pei

Y. Wu
5/12/15
Treangen, Todd J., and Steven L. Salzberg. "Repetitive DNA and next-generation sequencing: computational challenges and solutions." Nature Reviews Genetics 13.1 (2012): 36-46.
Kerzendorfer, Claudia, Tomasz Konopka, and Sebastian MB Nijman. "A thesaurus of genetic variation for interrogation of repetitive genomic regions."Nucleic acids research (2015): gkv178

Logistic regression and application in association mapping: Genome-wide association analysis by lasso penalized logistic regression
C. Chu



Y. Wu
4/27/15
Holtgrewe, Manuel, Leon Kuchenbecker, and Knut Reinert. "Methods for the detection and assembly of novel sequence in high-throughput sequencing data." Bioinformatics (2015): btv051.

PILER: identification and classification of genomic repeats
C. Chu

Y. Wu
4/6/15
A paper on population admixture: Link

Caspi, Anat, and Lior Pachter. "Identification of transposable elements using multiple alignments of related genomes." Genome research 16.2 (2006): 260-270.  and
Liu, George E., et al. "Comparative analysis of Alu repeats in primate genomes." Genome research
J. Pei

C. Chu
3/27/15
Deorowicz, Sebastian, et al. "KMC 2: Fast and resource-frugal k-mer counting."Bioinformatics (2015): btv022.
MSPKmerCounter: A fast and memory efficient approach for k-mer counting

Analysis of nanopore data using hidden Markov models
Link: http://bioinformatics.oxfordjournals.org/content/early/2015/02/27/bioinformatics.btv046.abstract
C. Chu


X. Li
3/9/15
Toward almost closed genomes with GapFiller

The MSMC paper
X. Li

S. Mirzaei
2/16/15
On species delimitation: paper
J. Pei
2/9/15
A paper on ancient DNA: paper
C. Chu
1/19/15
A paper on finding repeats in genomes: paper.
C. Chu

Fall 2014

Date
Paper
Presenter
11/24/14
Human reference genome and single molecule sequencing: paper
C. Chu
11/17/14
Sequence assembly: paper
C. Chu
11/10/14
A paper on species delimitation:  paper

A paper on variation finding: paper
J. Pei

X. Li
10/20/14
A paper on genetics.

A paper on cell lineage mutations.
J. Pei

C. Chu
9/30/14
A paper on coalescent theory
J. Pei
9/10/14
A paper on recombination analysis.

A paper on sequence data analysis (repeat finding).
S. Mirzaei

C. Chu
8/23/14
A paper on population admixture inference.
J. Pei

Spring 2014
Date
Paper
Presenter
4/14/14
A paper on somatic mutation finding.
R. Jiang
4/7/14
A paper on tumor ploidy and purity: paper.
Y. Wu
3/24/14
A sequence reads mapping paper.
R. Jiang
3/17/14
A paper on coalescent HMM (a paper to appear in RECOMB 14).
J. Pei
3/10/14
A paper on hybridization and coalescent theory.
S. Mirzaei
3/3/14
Another paper on sequencing and population genetics: paper.
C. Chu
2/24/14
Sequencing and population genetics: paper
R. Jiang
2/17/14
A paper on diffusion theory in genetics: paper.
J. Pei
2/3/14
A paper on approximate string matching: paper. If time permits, will also read another related paper.
C. Chu
1/27/14
A paper on haplotype and BWT: paper
R. Jiang


Fall 2013
Date
Topics and links
Presenter
12/2/13
Papers on sequencing: paper1, paper2
C. Chu
11/25/13
Another population demographic history inference paper.
J. Pei
11/18/13
A population demography inference paper by Li and Durbin (2011): paper, supplementry info.
Y. Wu
11/11/13
Code walkthrough for sequence reads alignment
R. Jiang
11/4/13
Population demographic history inference: paper
J. Pei
10/28/13
Inference approach for population demographic history paper.
Y. Wu
10/21/13
No meeting.

10/14/13
A RNA-seq paper: STAR: ultrafast universial RNA-seq aligner

A reads mapping paper
C. Chu

R. Jiang
10/7/13
No meeting

9/30/13
Overview of models for Gene flow and Population Structure in Genetics: the Structure paper, a paper on isolation with migration model and its computation
Y. Wu
9/23/13
Approximate Bayesian Computation in population genetics (paper)

Build phylogenetic networks from triplets (Paper)
J. Pei

S. Mirzaei
9/16/13
RNA splicing junction finding: PASSion

Sequence read alignment: BWA-SW
C. Chu

R. Jiang
9/9/13
RNA seq reads mapping: TopHat2 (2013), GSNAP (2010)
Y. Wu
9/2/13
Holiday

8/26/13
DNA sequence reads error correction methods: the SHREC approach, the Reptile paper, another paper related to Reptile
Y. Wu
8/19/13
Topics on the boosting algorithm (chapter 10 of this book).

Cancer DNA analysis. Absolute quantification of somatic DNA alterations in human cancer
J. Pei

R. Jiang
8/12/13
Finding population short indels with sequencing data: The Dindel paper

Using boosting to identify selected sites: The 2011 paper
C. Chu

S. Mirzaei
8/5/13
Applications of machine learning in population genetics problems.
Learning Natural Selection from the Site Frequency Spectrum, by R. Ronen, et al., Genetics, 2013 (in press)
A Fast Estimate for the Population Recombination Rate Based on Regression, Genetics, 2013 (in press)
Y. Wu