Posts Tagged ‘#genomics’

My notes from 2015 CSHL Conference on THE EVOLUTION OF SEQUENCING TECHNOLOGY

July 21, 2015

Tweets:
https://storify.com/markgerstein/favorite-tweets-from-evolseq-i0biohist15

TAG
https://linkstream2.gerstein.info/tag/i0biohist15/

http://meetings.cshl.edu/meetings.aspx?meet=biohist&year=15

CSHL Genentech Center Conferences
on the History of Molecular Biology and Biotechnology
THE EVOLUTION OF SEQUENCING TECHNOLOGY:
A HALF-CENTURY OF PROGRESS

July 16 – 19, 2015

SCHEDULE BELOW

Cold Spring Harbor Laboratory Genentech Center Conferences on the History of Molecular Biology and Biotechnology

THE EVOLUTION OF SEQUENCING TECHNOLOGY: A HALF-CENTURY OF PROGRESS July 16 – 19, 2015

Grace Auditorium

Thursday, July 16
7:00 pm – Session I—Early Days

Friday, July 17
9:00 am – Session II – Capturing Sequences/Survey
2:00 pm – Session III – Access to Sequence—From Past to the

Future
4:30 pm – Poster Session – Wine & Cheese Reception

7:00 pm – Session IV – Scaling to Genomes Saturday, July 18

9:00 am – Session V – Sequences to Genomes
1:45 pm – Session VI – All Roads Lead to DNA: Beyond Genomes 5:00 pm – Panel Discussion – Steps and mis-steps during the

development of sequencing technologies 6:00 pm – Cocktails and Banquet

Sunday, July 19
9:00 am – Session VII – Human Variation & Disease 12:00 Noon – Lunch and Departures

Mealtimes at Blackford Hall are as follows:

Breakfast 7:30 am-9:00 am Lunch 11:30 am-1:30 pm Dinner 5:30 pm-7:00 pm Bar is open from 5:00 pm until late

Cover Art: Fred Sanger at the LMB

Thursday, 7:00 pm: Session I – Early Days moderated by Bob Waterston

James Watson, Cold Spring Harbor Laboratory “Early Days with DNA” George Brownlee, University of Oxford, UK
“The early days of RNA sequencing at the LMB” Gillian Air, University of Oklahoma
“Integration of protein & DNA sequencing for PhiX174” Clyde Hutchison, J. Craig Venter Institute “Sequencing of PhiX174”

COFFEE BREAK
Wally Gilbert, Harvard University
“Origin of DNA Sequencing”
Tom Maniatis, Columbia University Medical Center

“The transition from RNA to DNA sequencing in the Sanger lab: The DNA sequence of the phage lambda operator/promoter regions””

Joachim Messing, Waksman Institute, Rutgers University “Development of M13 cloning systems for sequencing”

Friday 9:00 am: Session II—Capturing Sequences moderated by Mila Pollock

Lee Hood, Institute of Systems Biology “Automation of Sanger Sequencing” Lloyd Smith, University of Wisconsin, Madison “Fluorescence-based automated DNA Sequencing” Norman Dovichi, University of Notre Dame “Development of capillary electrophoresis” Mostafa Ronaghi, Illumina, Inc.
“Development of pyrosequencing”

COFFEE BREAK

Session II—Capturing Sequences moderated by Miguel Garcia-Sancho (continued) Shankar Balasubramanian, University of Cambridge, UK
“Early development of Solexa technology-key insights & technical breakthroughs” Jonas Korlach, Pacific Biosciences

“Technical innovations of SMRT Sequencing and applications of long-read sequencing”

Hagan Bayley, University of Oxford, UK “Nanopore Sequencing”

Friday, 2:00 pm: Session III—Access to Sequence from the past to the future moderated by Miguel Garcia-Sancho

David Lipman, NCBL/NLM National Institutes of Health “Origins of GenBank” Graham Cameron, Founder, Ex-Director EMBL
“DNA database prehistory”

Jim Ostell, NCBL/ National Center for Biotechnology Information “Databases for the future”
Miguel Garcia-Sancho, University of Edinburgh
“Sequencing & computing technologies: a Historical Convergence” Mila Pollock, Cold Spring Harbor Laboratory

“Genome legacy (preserving the history)”
4:30 pm: Wine & Cheese Reception on Davenport Lawn

Friday, 7:00 pm: Session IV – Scaling to Genomes moderated by Mark Adams

Jean Weissenbach, Genoscope—CNRG, France “Genoscope early efforts at automation” Stanley Tabor, Harvard Medical School
“How enzymology enabled advances in DNA sequencing”

Session IV – Scaling to Genomes (continued)
Melvin Simon, CalTech
“Large insert cloning”
William Efcavitch, Molecular Assemblies, Inc. “Technology development in scaling up Sanger sequencing” COFFEE BREAK

Jane Rogers, The Genome Analysis Centre UK
“Scaling up Sanger sequencing in the genome era”
Richard Myers, HudsonAlpha Institute for Biotechnology
“A personal perspective on DNA sequencing from 1978 to 2015” Yoshuiyuki Sakaki, University of Tokyo, Japan

“From the proposal of automated DNA sequencing to the completion of the Human Genome: Japanese contribution to Human Genome sequencing”

Saturday, 9:00 am: Session V – Sequences to Genomes moderated by Richard Roberts

J. Craig Venter, J. Craig Venter Institute
“Whole genome shotgun sequencing”
Hamilton Smith, J. Craig Venter Institute “Haemophilus influenzae and the value of completeness” Philip Green, University of Washington

“Sequence quality & assembly”

COFFEE BREAK

James Kent, University of California, Santa Cruz “Integrating the Sequence & Map into a genome” Gene Meyers, Max Planck Institute, Germany “Shotgun assembly strategies”

Suzanna Lewis, Lawrence Berkeley National Laboratory “Making sense of genomes with visualization and collaboration”

Saturday, 1:45 pm: Session VI – All Roads Lead to DNA: Beyond Genomes moderated by Jane Rogers

Mark Adams, J Craig Venter Institute “Sequencing ESTs for gene discovery” Barbara Wold, CalTech
“Developments & Applications of RNA-seq” Jack Gilbert, University of Chicago “Metagenomic Sequencing”

COFFEE BREAK

Piero Carninci, RIKEN, Japan
“cDNA Sequencing for genome analysis & biological interpretation” Jay Shendure, University of Washington
“Novel applications of DNA sequencing
Victor Ling, BC Cancer Agency, Canada
“Fractionation & sequences of large pyrimidine oligonucleotides—1970-71”

BREAK

Saturday, 5:00 pm: Panel Discussion—Steps and mis-steps during the development of sequencing technologies

Richard McCombie Cold Spring Harbor Laboratory Richard Roberts, New England BioLabs
Cheryl Heiner, Pacific Biosciences

Saturday, 6:00 pm: Cocktails and Banquet in Blackford Hall

(Cocktails location TBA)

Sunday, 9:00 am: Session VII – Human Variation and Disease moderated by Barbara Wold

Robert Waterston, University of Washington
“C. elegans: How complete can we get?” Huanming Yang, Beijing Genomics Institute, China “China: a latecomer to the global sequencing effort” Debbie Nickerson, University of Washington “Sequencing in human genetics”

COFFEE BREAK

Mark Gerstein, Yale University “ENCODE”
David Bentley, Illumina, Inc., UK “Genomes for Medicine”

Jim Lupski, Baylor College of Medicine “Applications of sequencing in clinical genetics”

12:00 Noon: Lunch and Departures

Organizers:

Mark Adams, J. Craig Venter Institute Nigel Brown, University of Edinburgh, UK

Mila Pollock, Cold Spring Harbor Laboratory Robert Waterston, University of Washington

Special Thanks to our Major Supporter

Machine learning applications in genetics and genomics : Nature Reviews Genetics : Nature Publishing Group

May 30, 2015

#Machinelearning applications in…genomics
http://www.nature.com/nrg/journal/v16/n6/full/nrg3920.html Nice overview of key distinctions betw generative & discriminative models

In their review, “Machine learning in genetics and genomics”, Libbrecht and Noble overview important aspects of application of machine learning to genomic data. The review presents illustrative classical genomics problems where machine learning techniques have proven useful and describes the differences between supervised, semi-supervised and unsupervised learning as well as generative and discriminative models. The authors discuss considerations that should be made when selecting the right machine learning approach depending on the biological problem and data at hand, provide general practical guidelines and suggest possible solutions to common challenges.

Comparative genomics reveals insights into avian genome evolution and adaptation

May 16, 2015

Comparative #genomics reveals insights into avian…#evolution http://www.sciencemag.org/content/346/6215/1311 Less repeats & dups in birds; woodpecker, an exception

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang1,2,*,†,
Cai Li1,3,*,
….
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†

My notes from 2015 CSHL Conference on The Biology of Genomes

May 10, 2015

http://meetings.cshl.edu/meetings/2015/genome15.shtml
https://storify.com/markgerstein/favorite-tweets-from-bog15-i0bog15 https://linkstream2.gerstein.info/tag/i0bog15/

The evolutionary history of lethal metastatic prostate cancer : Nature : Nature Publishing Group

May 2, 2015

The evolutionary history of…metastatic prostate #cancer http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14347.html Unexpected: polyclonal "seeding" w/ much met-to-met spread

Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage

May 2, 2015

Transmissible Dog #Cancer #Genome Reveals…History of…Cell Lineage http://www.sciencemag.org/content/343/6169/437.abstract 1.9M somatic mutations from origin ~11K yrs ago

Summarizing 4 conferences last week: AACR ’15, ISEV ’15, BioIT ’15 & ICEBEM 2015

April 28, 2015

AACR 2015
http://www.aacr.org/Meetings/Pages/MeetingDetail.aspx?EventItemID=25#.VT8JXa1Viko https://linkstream2.gerstein.info/tag/i0pcawg15/

ISEV/ERCC Education Day – ISEV – International Society for
Extracellular Vesicles
http://www.isevmeeting.org/isevercc-education-day.html
https://linkstream2.gerstein.info/tag/i0isev/

2015 Bio-IT World Conference & Expo
http://www.bio-itworldexpo.com/
https://linkstream2.gerstein.info/tag/i0bioit15/
http://lectures.gersteinlab.org/summary/Progressive-summarization-large-scale-data-interpret-cancer–20150423-i0bioIT15/

8th International Conference on Ethics in Biology, Engineering & Medicine (ICEBEM 2015)
http://www.downstate.edu/orthopaedics/bioethics/
http://lectures.gersteinlab.org/summary/Soc-n-Tech-Soln-to-Privacy-in-Personal-Genomics–20150424-i0icebem15/

Tweets for all of them
https://storify.com/markgerstein/favorite-tweets-from-bioit-15-aacr-15-and-isev-15-16

“The Race” to Clone BRCA1

April 25, 2015

The Race to Clone #BRCA1 http://www.sciencemag.org/content/343/6178/1462.abstract
Lessons on #LOF mutations, synthetic lethality, silly gene names & the 2-hit hypothesis

synthetic lethality (PARP inhibitors), gene names (RING fingers)

10x

April 23, 2015

http://www.ncbi.nlm.nih.gov/pubmed/25477383

also
http://www.ncbi.nlm.nih.gov/pubmed/25477383
Nucleic Acids Res. 2015 Feb 27;43(4):e23. doi: 10.1093/nar/gku1252. Epub 2014 Dec 3.
Allele-specific copy number profiling by next-generation DNA sequencing. Chen H1, Bell JM2, Zavala NA2, Ji HP2, Zhang NR3.

perhaps related?

Health: Make precision medicine work for cancer care

April 20, 2015

Make #precisionmedicine work for cancer http://www.nature.com/news/health-make-precision-medicine-work-for-cancer-care-1.17301 @MarkARubin1: >90% of…patients carry a mutation that may be drug-responsive

QT:{{"
“Hugely complicated genomic reports are rarely available in electronic form and are seldom tied to basic information about the patient. Whole-genome sequencing on tumour samples from nearly 14,000 people by the International Cancer Genome Consortium (ICGC), for instance, has revealed nearly 13 million mutations across the genome.


Since 2013, working with a team of computational biologists from Weill Cornell and the Centre for Integrative Biology at the University of Trento in Italy, my colleagues and I have conducted a pilot programme to determine the feasibility of tying genomic to clinical data in real time. So far, we have created easy-to-read reports for 250 people with cancer.

We have discovered that more than

"more than 90% of our patients carry a mutation that may be responsive to a known drug — although less than 10% of the patients may be eligible for a clinical trial either for logistical reasons or because there is insufficient evidence to warrant trying a non-approved drug.”
"}}