We meet other Wednesday 4:30-5:30PM (03/11/2020) Journal club is meeting via Zoom until further notice.
Current topic: Please volunteer to present any paper related to genomics!
Past topics: Graph genomes; Long read sequencing; Repetitive DNA and transposable elements; Data Structures; Epigenetics
| Date | Presenter | Location | Paper |
|---|---|---|---|
| February 12 | Nae-Chyun Chen | Malone 338 | https://www.biorxiv.org/content/10.1101/2019.12.20.884924v1 |
| February 26 | Bohan Ni | Malone 338 | https://www.nature.com/articles/s41564-019-0656-6 |
| March 11 | Sam Kovaka | Zoom | https://doi.org/10.1016/j.molcel.2012.10.016 |
| March 25 | Mike Alonge | Zoom | https://www.biorxiv.org/content/10.1101/790279v1 |
| April 8 | Daniel Baker | Zoom | https://www.biorxiv.org/content/10.1101/852889v1 |
| April 22 | Samantha Zarate | Zoom | https://www.biorxiv.org/content/10.1101/2020.03.14.992248v1 |
| May 6 | Hirak Sarkar (Guest Speaker) | Zoom | https://www.biorxiv.org/content/10.1101/2020.04.07.029967v1 |
| May 20 | Zoom |
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
Hirak Sarkar, Avi Srivastava, Hector Corrada Bravo, Michael I Love, Rob Patro
doi: https://doi.org/10.1101/2020.04.07.029967 bioRxiv (2020)
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Sergey Nurk, Brian P. Walenz, Arang Rhie, Mitchell R. Vollger, Glennis A. Logsdon, Robert Grothe, Karen H. Miga, Evan E. Eichler, Adam M. Phillippy, Sergey Koren
doi: https://doi.org/10.1101/2020.03.14.992248 bioRxiv (2020)
Diversified RACE Sampling on Data Streams Applied to Metagenomic Sequence Analysis
Benjamin Coleman, Benito Geordie, Li Chou, R. A. Leo Elworth, Todd J. Treangen, Anshumali Shrivastava
doi: https://doi.org/10.1101/852889 bioRxiv (2019)
Massive haplotypes underlie ecotypic differentiation in sunflowers
Marco Todesco et al.
doi: https://doi.org/10.1101/790279 bioRxiv (2019)
Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates
Gregory Hannum et al.
doi: https://doi.org/10.1016/j.molcel.2012.10.016 Molecular Cell (2013)
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing
Karel Brinda et al.
doi: https://doi.org/10.1038/s41564-019-0656-6 Nature Microbiology (2020)
Distance Indexing and Seed Clustering in Sequence Graphs
Xian Chang et al.
doi: https://doi.org/10.1101/2019.12.20.884924 bioRxiv (2019)
Efficient chromosome-scale haplotype-resolved assembly of human genomes
Shilpa Garg et al.
doi: https://doi.org/10.1101/810341 bioRxiv (2019)
Technical artifact drives apparent deviation from Hardy-Weinberg equilibrium at CCR5-∆32 and other variants in gnomAD
Konrad J. Karczewski, Laura D. Gauthier, Mark J. Daly
doi: https://doi.org/10.1101/784157 bioRxiv (2019)
Telomere-to-telomere assembly of a complete human X chromosome
Karen H. Miga et al.
doi: https://doi.org/10.1101/735928 bioRxiv (2019)
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
Allegra A. Petti et al.
doi: https://doi.org/10.1038/s41467-019-11591-1 Nature Communications (2019)
The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight.
Francine E. Garrett-Bakelman et al.
doi: 10.1126/science.aau8650 Science (2019)
"Fast and accurate long-read assembly with wtdbg2." Jue Ruan and Heng Li. doi: https://doi.org/10.1101/530972 bioRxiv (2019)
"Assembly of Long Error-Prone Reads Using Repeat Graphs." Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel. A. Pevzner. doi: https://doi.org/10.1101/247148 bioRxiv (2018)
BagMinHash - Minwise Hashing Algorithm for Weighted Sets.
Otmar Ertl
doi: https://doi.org/10.1145/3219819.3220089 arXiv (2018)
Locality sensitive hashing for the edit distance.
Guillaume Marcais, Dan DeBlasio, Prashant Pandey, Carl Kingsford
doi: https://doi.org/10.1101/534446 bioRxiv (2019)
Nanopore native RNA sequencing of a human poly(A) transcriptome.
Rachael E. Workman et al.
doi: https://doi.org/10.1101/459529 bioRxiv (2018)
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro
doi: https://doi.org/10.1101/464222 bioRxiv (2018)
Using long-read sequencing to detect imprinted DNA methylation
Scott Gigante et al.
doi: https://doi.org/10.1101/445924 bioRxiv (2018)
The MUMmer Saga
"Alignment of Whole Genomes." A.L. Delcher, S. Kasif, R.D. Fleischmann, J. Peterson, O. White, and S.L. Salzberg, Nucleic Acids Research, 27:11 (1999), 2369-2376.
Engineering Quantitative Trait Variation for Crop Improvement by Genome Editing
Rodríguez-Leal et al.
https://doi.org/10.1016/j.cell.2017.08.030
SpliceVec: Distributed feature representations for splice junction prediction
Aparajita Dutta, Tushar Dubey, Kusum Kumari Singh, Ashish Ananda
doi: 10.1016/j.compbiolchem.2018.03.009 Computational Biology and Chemistry (2018)
Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription
Igor Vilfan et al.
doi: 10.1186/1477-3155-11-8 J Nanobiotechnology (2013)
The Key Role of Epigenetics in Human Disease Prevention and Mitigation
Andrew P. Feinberg
doi: 10.1056/NEJMra1402513 New England Journal of Medicine (2018)
Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation
John Beaulaurier et al.
doi: 10.1038/nbt.4037 Nature Biotechnology (2018)
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
Meilina Ong-Abdullah et al.
doi: 10.1038/nature15365 Nature (2015)
Mantis: A Fast, Small, and Exact Large-Scale Sequence Search Index
Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro
doi: 10.1101/217372 bioRxiv (2017)
A General-Purpose Counting Filter: Making Every Bit Count
Prashant Pandey, Michael A. Bender, Rob Johnson, Rob Patro
doi: 10.1145/3035918.3035963 SIGMOD Proceedings (2017)
Landscape of Somatic Retrotransposition in Human Cancers
Eunjung Lee et al.
doi: 10.1126/science.1222077 Science (2012)
The B73 Maize Genome: Complexity, Diversity, and Dynamics
Patrick S. Schnable et al.
doi: 10.1126/science.1178534 Science (2009)
Improved maize reference genome with single-molecule technologies
Yinping Jiao et al.
doi: 10.1038/nature22971 Nature (2017)
Linear Assembly of a Human Y Centromere using Nanopore Long Reads
Miten Jain, Hugh E. Olsen, Daniel J. Turner, David Stoddart, Kira V. Bulazel, Benedict Paten, David Haussler, Huntington Willard, Mark Akeson, Karen H. Miga
doi: 10.1101/170373 bioRxiv (2017)
Coming of age: ten years of next-generation sequencing technologies
Sara Goodwin, John D. McPherson, W. Richard McCombie
doi:10.1038/nrg.2016.49 Nature Reviews Genetics (2016)
Minimap2: fast pairwise alignment for long DNA sequences
Heng Li
arXiv:1708.01492 arXiv (2017)
Nonhybrid, finished microbial genome assemblies from long-read smrt sequencing data
Chen-Shan Chin, David H Alexander, Patrick Marks, Aaron A Klammer, James Drake, Cheryl Heiner, Alicia Clum, Alex Copeland, John Huddleston, Evan E Eichler, Stephen W Turner, Jonas Korlach
DOI http://doi.org/10.1038/nmeth.2474 Nature Meethods (2013)
Direct determination of diploid genome sequences
Neil I Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M Church, David B Jaffe
DOI http://doi.org/10.1101/gr.214874.116 Genome Research (2017)
BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal
Marcus Stoiber, James Brown
Paper http://www.biorxiv.org/content/biorxiv/early/2017/05/01/133058.full.pdf BioRxiv (2017)
A complete bacterial genome assembled de novo using only nanopore sequencing data
Nicholas J Loman, Joshua Quick, Jared T Simpson
DOI http://doi.org/10.1038/nmeth.3444 Nature Methods (2015)
De Novo Repeat Classification and Fragment Assembly
Paul A. Pevzner, Haixu Tang, Glenn Tesler
DOI http://doi.org/10.1101/gr.2395204 Genome Research (2004)
Succinct Colored De Bruijn Graphs
Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul Morley, Keith Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher
DOI https://doi.org/10.1093/bioinformatics/btx067 Bioinformatics (2017)
Super helpful blog post: http://alexbowe.com/succinct-debruijn-graphs/
A new strategy to reduce allelic bias in RNA-Seq readmapping
Ravi Vijaya Satya, Nela Zavaljevski, Jaques Reifman
DOI https://doi.org/10.1093/nar/gks425 Nucleic Acids Research (2012)
WASP: allele-specific software for robust molecular quantitative trait locus discovery.
Bryce van de Geijn, Graham McVicker, Yoav Gilad, Jonathan K. Pritchard
DOI https://doi.org/10.1038/nmeth.3582 Nature Methods (2015)
AlleleSeq: analysis of allele‐specific expression and binding in a network framework
Joel Rozowsky, Alexej Abyzov, Jing Wang, Pedro Alves, Debasish Raha, Arif Harmanci, Jing Leng, Robert Bjornson, Yong Kong, Naoki Kitabayashi, Nitin Bhardwaj, Mark Rubin, Michael Snyder, Mark Gerstein
DOI https://doi.org/10.1038/msb.2011.54 Molecular Systems Biology (2011)