WHAT's NEW SINCE OUR LAST NEWSLETTER? the Power of One!
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Computational Methods Addressing Genetic Variation In
COMPUTATIONAL METHODS ADDRESSING GENETIC VARIATION IN NEXT-GENERATION SEQUENCING DATA by Charlotte A. Darby A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland June 2020 © 2020 Charlotte A. Darby All rights reserved Abstract Computational genomics involves the development and application of computational meth- ods for whole-genome-scale datasets to gain biological insight into the composition and func- tion of genomes, including how genetic variation mediates molecular phenotypes and disease. New biotechnologies such as next-generation sequencing generate genomic data on a massive scale and have transformed the field thanks to simultaneous advances in the analysis toolkit. In this thesis, I present three computational methods that use next-generation sequencing data, each of which addresses the genetic variations within and between human individuals in a different way. First, Samovar is a software tool for performing single-sample mosaic single-nucleotide variant calling on whole genome sequencing linked read data. Using haplotype assembly of heterozygous germline variants, uniquely made possible by linked reads, Samovar identifies variations in different cells that make up a bulk sequencing sample. We apply it to 13cancer samples in collaboration with researchers at Nationwide Childrens Hospital. Second, scHLAcount is a software pipeline that computes allele-specific molecule counts for the HLA genes from single-cell gene expression data. We use a personalized reference genome based on the individual’s genotypes to reveal allele-specific and cell type-specific gene expression patterns. Even given technology-specific biases of single-cell gene expression data, we can resolve allele-specific expression for these genes since the alleles are often quite different between the two haplotypes of an individual. -
Big Data, Moocs, and ... (PDF)
HHMI Constellation Studios for Science Education November 13-15, 2015 | HHMI Headquarters | Chevy Chase, MD Big Data, MOOCs, and Quantitative Education for Biologists Co-Chairs Pavel Pevzner, University of California- San Diego Sarah Elgin, Washington University Studio Objectives Discuss existing challenges in bioinformatics education with experts in computational biology and quantitative biology education, Evaluate best practices in teaching quantitative and computational biology, and Collaborate with scientist educators to develop instructional modules to support a biology curriculum that includes quantitative approaches. Friday | November 13 4:00 pm Arrival Registration Desk 5:30 – 6:00 pm Reception Great Hall 6:00 – 7:00 pm Dinner Dining Room 7:00 – 7:15 pm Welcome K202 David Asai, HHMI Cynthia Bauerle, HHMI Pavel Pevzner, University of California-San Diego Sarah Elgin, Washington University Alex Hartemink, Duke University 7:15 – 8:00 pm How to Maximize Interaction and Feedback During the Studio K202 Cynthia Bauerle and Sarah Simmons, HHMI 8:00 – 9:00 pm Keynote Presentation K202 "Computing + Biology = Discovery" Speakers: Ran Libeskind-Hadas, Harvey Mudd College Eliot Bush, Harvey Mudd College 9:00 – 11:00 pm Social The Pilot Saturday | November 14 7:30 – 8:15 am Breakfast Dining Room 8:30 – 10:00 am Lecture session 1 K202 Moderator: Pavel Pevzner 834a-854a “How is body fat regulated?” Laurie Heyer, Davidson College 856a-916a “How can we find mutations that cause cancer?” Ben Raphael, Brown University “How does a tumor evolve over time?” 918a-938a Russell Schwartz, Carnegie Mellon University “How fast do ribosomes move?” 940a-1000a Carl Kingsford, Carnegie Mellon University 10:05 – 10:55 am Breakout working groups Rooms: S221, (coffee available in each room) N238, N241, N140 1. -
Psychic’ Sally Morgan Scuffles with Toward a Cognitive Psychology U.K
Science & Skepticism | Randi’s Escape Part II | Martin Gardner | Monster Catfish? | Trent UFO Photos the Magazine for Science and Reason Vol. 39 No. 1 | January/February 2015 Why the Supernatural? Why Conspiracy Ideas? Modern Geocentrism: Pseudoscience in Astronomy Flaw and Order: Criminal Profiling Sylvia Browne’s Art and Science FBI File More Witch Hunt Murders INTRODUCTORY PRICE U.S. and Canada $4.95 Published by the Committee for Skeptical Inquiry C I Ronald A. Lindsay, President and CEO Massimo Polidoro, Research Fellow Bar ry Karr, Ex ec u tive Di rect or Benjamin Radford, Research Fellow Joe Nickell, Senior Research Fellow Richard Wiseman, Research Fellow www.csicop.org James E. Al cock*, psy chol o gist, York Univ., Tor on to David H. Gorski, cancer surgeon and re searcher at Astronomy and director of the Hopkins Mar cia An gell, MD, former ed i tor-in-chief, Barbara Ann Kar manos Cancer Institute and chief Observatory, Williams College New Eng land Jour nal of Med i cine of breast surgery section, Wayne State University John Pau los, math e ma ti cian, Tem ple Univ. School of Medicine. Kimball Atwood IV, MD, physician; author; Clifford A. Pickover, scientist, au thor, editor, Newton, MA Wendy M. Grossman, writer; founder and first editor, IBM T.J. Watson Re search Center. Steph en Bar rett, MD, psy chi a trist; au thor; con sum er The Skeptic magazine (UK) Massimo Pigliucci, professor of philosophy, ad vo cate, Al len town, PA Sus an Haack, Coop er Sen ior Schol ar in Arts and City Univ. -
Cloud Computing and the DNA Data Race Michael Schatz
Cloud Computing and the DNA Data Race Michael Schatz April 14, 2011 Data-Intensive Analysis, Analytics, and Informatics Outline 1. Genome Assembly by Analogy 2. DNA Sequencing and Genomics 3. Large Scale Sequence Analysis 1. Mapping & Genotyping 2. Genome Assembly Shredded Book Reconstruction • Dickens accidentally shreds the first printing of A Tale of Two Cities – Text printed on 5 long spools It was theIt was best the of besttimes, of times, it was it wasthe worstthe worst of of times, times, it it was was the the ageage of of wisdom, wisdom, it itwas was the agethe ofage foolishness, of foolishness, … … It was theIt was best the bestof times, of times, it was it was the the worst of times, it was the theage ageof wisdom, of wisdom, it was it thewas age the of foolishness,age of foolishness, … It was theIt was best the bestof times, of times, it was it wasthe the worst worst of times,of times, it it was the age of wisdom, it wasit was the the age age of offoolishness, foolishness, … … It was It thewas best the ofbest times, of times, it wasit was the the worst worst of times,of times, itit waswas thethe ageage ofof wisdom,wisdom, it wasit was the the age age of foolishness,of foolishness, … … It wasIt thewas best the bestof times, of times, it wasit was the the worst worst of of times, it was the age of ofwisdom, wisdom, it wasit was the the age ofage foolishness, of foolishness, … … • How can he reconstruct the text? – 5 copies x 138, 656 words / 5 words per fragment = 138k fragments – The short fragments from every copy are mixed -
BENG181/CSE 181/BIMM 181 Molecular Sequence Analysis Instructor: Pavel Pevzner
COURSE ANNOUNCEMENT FOR WINTER 2021 BENG181/CSE 181/BIMM 181 Molecular Sequence Analysis https://sites.google.com/site/ucsdcse181 Instructor: Pavel Pevzner ● phone: (858) 822-4365 ● e.mail: [email protected] ● web site: bioalgorithms.ucsd.edu Teaching Assistants: ● Andrey Bzikadze ([email protected]) ● Hsuan-lin (Charlene) Her ([email protected]) Time: 6:30-7:50 Mon/Wed, Place: online (seminar Friday 4:00-4:50 online) Zoom link for the class: https://ucsd.zoom.us/j/99782745100 Zoom link for the seminar: https://ucsd.zoom.us/j/96805484881 Office hours: PP: (Th 3-5 online), TAs (online Tue 1-2 PM and 4-5 PM or by appointment online) PP zoom link: https://ucsd.zoom.us/j/96986851791 Andrey Bzikadze zoom link: https://ucsd.zoom.us/j/94881347266 Hsuan-lin (Charlene) Her zoom link: https://ucsd.zoom.us/j/95134947264 Prerequisites: The course assumes some prior background in biology, some algorithmic culture (CSE 101 course on algorithms as a prerequisite), and some programming skills. Flipped online class. Starting in 2014, the Innovative Learning Technology Initiative (ILTI) at University of California encourages professors to transform their classes into online offerings available across various UC campuses. Dr. Pevzner is funded by the ILTI and NIH to develop new online approaches to bioinformatics education at UCSD. Since 2014, well before the COVID-19 pandemic, all lectures in this class are available online rather than presented in the classroom. Multi-university class. This class closely follows the textbook Bioinformatics Algorithms: an Active Learning Approach that has now been adopted by 140+ instructors from 40+ countries. -
Steven L. Salzberg
Steven L. Salzberg McKusick-Nathans Institute of Genetic Medicine Johns Hopkins School of Medicine, MRB 459, 733 North Broadway, Baltimore, MD 20742 Phone: 410-614-6112 Email: [email protected] Education Ph.D. Computer Science 1989, Harvard University, Cambridge, MA M.Phil. 1984, M.S. 1982, Computer Science, Yale University, New Haven, CT B.A. cum laude English 1980, Yale University Research Areas: Genomics, bioinformatics, gene finding, genome assembly, sequence analysis. Academic and Professional Experience 2011-present Professor, Department of Medicine and the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University. Joint appointments as Professor in the Department of Biostatistics, Bloomberg School of Public Health, and in the Department of Computer Science, Whiting School of Engineering. 2012-present Director, Center for Computational Biology, Johns Hopkins University. 2005-2011 Director, Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies 2005-2011 Horvitz Professor, Department of Computer Science, University of Maryland. (On leave of absence 2011-2012.) 1997-2005 Senior Director of Bioinformatics (2000-2005), Director of Bioinformatics (1998-2000), and Investigator (1997-2005), The Institute for Genomic Research (TIGR). 1999-2006 Research Professor, Departments of Computer Science and Biology, Johns Hopkins University 1989-1999 Associate Professor (1996-1999), Assistant Professor (1989-1996), Department of Computer Science, Johns Hopkins University. On leave 1997-99. 1988-1989 Associate in Research, Graduate School of Business Administration, Harvard University. Consultant to Ford Motor Co. of Europe and to N.V. Bekaert (Kortrijk, Belgium). 1985-1987 Research Scientist and Senior Knowledge Engineer, Applied Expert Systems, Inc., Cambridge, MA. Designed expert systems for financial services companies. -
The Use of Complementary and Alternative Medicine
Consultation report The use and promotion of complementary and alternative medicine: making decisions about charitable status Introduction The Commission ran a public consultation on this subject between 13 March and 19 May 2017, as part of our review of how we decide whether organisations that use or promote complementary and alternative medicine (CAM) therapies are charities. Our review is not about whether complementary and alternative therapies and medicines are ‘good’ or ‘bad’, but about what level of evidence the Commission should require when making assessments about an organisation’s charitable status. We would like to thank everyone who took the time to take part. This report sets out a summary of the responses received. The consultation We received over 670 written responses, far in excess of the number usually received for a Commission consultation. We also held two discussion events at our London office for organisations with a particular perspective on the issues under consideration. The majority of responses received were from individuals apparently writing in a personal capacity, but we also received over 100 submissions from people representing, or connected with, organisations with an interest in the consultation. The names of those organisations are set out in the annex to this report. The responses varied widely in length, detail and content. Given the welcome and exceptionally high level of engagement with the consultation, it has taken longer than initially anticipated to analyse the responses. However, we are grateful for the high level of engagement; the responses have helped further our understanding the breadth and complexity of the CAM sector. -
SKEPTICAL INQUIRER Vol
SKEPTICAL INQUIRER Vol. 1818,, No . 2No. 2 ^^ Winter 1994 Winter / 1994/$6.2$6.255 Paul Kurtz William Grey THE NEW THE PROBLEM SKEPTICISM OF 'PSI' Cancer Scares i*5"***-"" —-^ 44 "74 47CT8 3575" 5 THE SKEPTICAL INQUIRER is the official journal of the Committee for the Scientific Investigation of Claims of the Paranormal, an international organization. Editor Kendrick Frazier. Editorial Board James E. Alcock, Barry Beyerstein, Susan J. Blackmore, Martin Gardner, Ray Hyman, Philip J. Klass, Paul Kurtz, Joe Nickell, Lee Nisbet, Bela Scheiber. Consulting Editors Robert A. Baker, William Sims Bainbridge, John R. Cole, Kenneth L. Feder, C. E. M. Hansel, E. C. Krupp, David F. Marks, Andrew Neher, James E. Oberg, Robert Sheaffer, Steven N. Shore. Managing Editor Doris Hawley Doyle. Contributing Editor Lys Ann Shore. Business Manager Mary Rose Hays. Assistant Business Manager Sandra Lesniak. Chief Data Officer Richard Seymour. Computer Assistant Michael Cione. Production Paul E. Loynes. Asst. Managing Editor Cynthia Matheis. Art Linda Hays. Audio Technician Vance Vigrass. Librarian Jonathan Jiras. Staff Alfreda Pidgeon, Ranjit Sandhu, Sharon Sikora, Elizabeth Begley (Albuquerque). Cartoonist Rob Pudim. The Committee for the Scientific Investigation of Claims of the Paranormal Paul Kurtz, Chairman; professor emeritus of philosophy, State University of New York at Buffalo. Barry Karr, Executive Director and Public Relations Director. Lee Nisbet, Special Projects Director. Fellows of the Committee James E. Alcock,* psychologist, York Univ., Toronto; Robert A. Baker, psychologist, Univ. of Kentucky; Stephen Barrett, M.D., psychiatrist, "author, consumer advocate, Allentown, Pa. Barry Beyerstein,* biopsychologist, Simon Fraser Univ., Vancouver, B.C., Canada; Irving Biederman, psychologist, Univ. -
Nhs Liverpool Clinical Commissioning Group Governing Body Tuesday 14Th June 2016 at 1Pm Boardroom, the Department, Lewis’S Building Renshaw Street L1 2Sa
` NHS LIVERPOOL CLINICAL COMMISSIONING GROUP GOVERNING BODY TUESDAY 14TH JUNE 2016 AT 1PM BOARDROOM, THE DEPARTMENT, LEWIS’S BUILDING RENSHAW STREET L1 2SA Part 1: Introductions and Apologies 1.1 Declarations of Interest All 1.2 Minutes and action points from the meeting Attached on 10th May & 26th May 2016 All 1.3 Matters Arising All Part 2: Updates 2.1 Feedback from Committees: Report no: GB 39-16 Primary Care Commissioning Committee – Dave Antrobus 17th May 2016 Finance Procurement & Contracting Committee Dr Nadim Fazlani - 24th May 2016 Healthy Liverpool Programme Board – Tom Jackson 25th May 2016 Committees in Common – 1st June 2016 Katherine Sheerin Quality Safety & Outcomes Committee – Dave Antrobus 7th June 2016 2.2 Chief Officer’s Update Verbal Katherine Sheerin 2.3 NHS England Update Verbal Phil Wadeson 2.4 Public Health Update Verbal Dr Sandra Davies 2.5 Update from Health & Wellbeing Board Verbal nd 2 June 2016 Katherine Sheerin Page 1 of 2 Part 3: Performance 3.1 CCG Corporate Performance Report Report no: GB 40-16 Stephen Hendry Part 4: Strategy and Commissioning 4.1 Life Expectancy and Mortality Trends in Liverpool Report no: GB 41-16 Dr Sandra Davies 4.2 NHS Liverpool CCG – Financial Strategy 2016/2021Report no: GB 42-16 Tom Jackson 4.3 Review of Homeopathy Services Report no: GB 43-16 Ian Davies Part 5: Governance 5.1 Liverpool Community Health Capsticks Report Report no: GB 44-16 - an overview Katherine Sheerin 5.2 Complaints, Subject Access Requests, Report no: GB 45-16 Freedom of Information Requests and Ian Davies MP Enquiries 2015-2016 6. -
THE BIG CHALLENGES of BIG DATA As They Grapple with Increasingly Large Data Sets, Biologists and Computer Scientists Uncork New Bottlenecks
TECHNOLOGY FEATURE THE BIG CHALLENGES OF BIG DATA As they grapple with increasingly large data sets, biologists and computer scientists uncork new bottlenecks. EMBL–EBI Extremely powerful computers are needed to help biologists to handle big-data traffic jams. BY VIVIEN MARX and how the genetic make-up of different can- year, particle-collision events in CERN’s Large cers influences how cancer patients fare2. The Hadron Collider generate around 15 petabytes iologists are joining the big-data club. European Bioinformatics Institute (EBI) in of data — the equivalent of about 4 million With the advent of high-throughput Hinxton, UK, part of the European Molecular high-definition feature-length films. But the genomics, life scientists are starting to Biology Laboratory and one of the world’s larg- EBI and institutes like it face similar data- Bgrapple with massive data sets, encountering est biology-data repositories, currently stores wrangling challenges to those at CERN, says challenges with handling, processing and mov- 20 petabytes (1 petabyte is 1015 bytes) of data Ewan Birney, associate director of the EBI. He ing information that were once the domain of and back-ups about genes, proteins and small and his colleagues now regularly meet with astronomers and high-energy physicists1. molecules. Genomic data account for 2 peta- organizations such as CERN and the European With every passing year, they turn more bytes of that, a number that more than doubles Space Agency (ESA) in Paris to swap lessons often to big data to probe everything from every year3 (see ‘Data explosion’). about data storage, analysis and sharing. -
UNIVERSITY of CALIFORNIA RIVERSIDE RNA-Seq
UNIVERSITY OF CALIFORNIA RIVERSIDE RNA-Seq Based Transcriptome Assembly: Sparsity, Bias Correction and Multiple Sample Comparison A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Computer Science by Wei Li September 2012 Dissertation Committee: Dr. Tao Jiang , Chairperson Dr. Stefano Lonardi Dr. Marek Chrobak Dr. Thomas Girke Copyright by Wei Li 2012 The Dissertation of Wei Li is approved: Committee Chairperson University of California, Riverside Acknowledgments The completion of this dissertation would have been impossible without help from many people. First and foremost, I would like to thank my advisor, Dr. Tao Jiang, for his guidance and supervision during the four years of my Ph.D. He offered invaluable advice and support on almost every aspect of my study and research in UCR. He gave me the freedom in choosing a research problem I’m interested in, helped me do research and write high quality papers, Not only a great academic advisor, he is also a sincere and true friend of mine. I am always feeling appreciated and fortunate to be one of his students. Many thanks to all committee members of my dissertation: Dr. Stefano Lonardi, Dr. Marek Chrobak, and Dr. Thomas Girke. I will be greatly appreciated by the advice they offered on the dissertation. I would also like to thank Jianxing Feng, Prof. James Borneman and Paul Ruegger for their collaboration in publishing several papers. Thanks to the support from Vivien Chan, Jianjun Yu and other bioinformatics group members during my internship in the Novartis Institutes for Biomedical Research. -
MICHAEL HEAP Bsc, Msc, Phd, Afbpss
THE SKEPTICAL INTELLIGENCER The Quarterly Magazine of ASKE THE ASSOCIATION FOR SKEPTICAL ENQUIRY Vol 23, 2020, Number 4 (Winter) Incorporating the Skeptical Adversaria: the ASKE Newsletter ________________________________________________________________________ Edited by Michael Heap To access a Word or pdf copy of this issue, please contact the Editor at [email protected]. If you are an ASKE member in the UK and would like a paper copy, again email the Editor. CONTENTS Regular features and announcements From the ASKE Chair 2 Language on the Fringe 5 Logic and Intuition 3 Of Interest 16 The European Scene 4 Upcoming Events 18 Medicine on the Fringe 4 About ASKE 19 Contributed articles Skepticism, Racism, Science, Semantics and More: Recent Controversies Mark Newbrook 7 Book reviews and commentaries Shaping Psychology: Perspectives on Legacy, Controversy and the Future of the Field reviewed by Michael Heap 13 Seriously Curious: The Economist Explains: the Facts and Figures that Turn your World Upside Down reviewed by Ray Ward 15 Skeptical Intelligencer, Winter 2020 FROM THE ASKE CHAIR Michael Heap The ASKE website have been established in countries evidence-based perspective. (Can I Constrained by my (slowly improving) across the world (notes 2 & 3). have my cheque now Mr Murdoch?) IT skills, I have now refurbished the The need is to ensure that the public On 28.11.20, the Times colour ASKE website at http://www.aske- in general are mindful that there is a lot magazine included an article on Lyric skeptics.org.uk/. This is still a work in of blatantly false and ultimately quite Jain, ‘the 25-year-old from progress and there is material to be dangerous information ‘out there’, Staffordshire taking on the world of added and replaced (and will be much of it only serving the interests and fake news and conspiracy theories’.