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Bits of DNA | Reviews and commentary on computational biology by Lior PachterReviews and commentary on computational biology by Lior Pachter
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Reviews and commentary on computational biology by Lior Pachter
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The Needleman-Wunsch algorithm | Bits of DNA
https://liorpachter.wordpress.com/2013/09/21/the-needleman-wunsch-algorithm
Reviews and commentary on computational biology by Lior Pachter. September 21, 2013 in education. I recently completed a term as director of our Center for Computational Biology. And one of the things I am proud of having accomplished is helping Brian McClendon, program administrator for the Center, launch a new Ph.D. program in computational biology at UC Berkeley. 8221; by Temple Smith. Advances in Applied Mathematics 2. 8220;, Needleman and Wunsch, Journal of Molecular Biology 48. The Needleman-Wunsch...
How to average genome-wide data | Bits of DNA
https://liorpachter.wordpress.com/2015/07/13/how-to-average-genome-wide-data
Reviews and commentary on computational biology by Lior Pachter. How to average genome-wide data. July 13, 2015 in papers. Tags: civil rights act. For a complementary perspective see the article by journalist Ingi Freyr Vilhjálmsson. Two months later, in a sharply worded rebuttal, the company argued that the reported discrepancies in prices between Samherji hf. and the market were flawed. Specifically, they argued, the Central Bank had incorrectly averaged numbers. Resulting in a Simpson’s paradox. My fo...
Nicholas Wade’s troublesome inheritance | Bits of DNA
https://liorpachter.wordpress.com/2014/06/04/nicholas-wades-troublesome-inheritance
Reviews and commentary on computational biology by Lior Pachter. Nicholas Wade’s troublesome inheritance. June 4, 2014 in guest post. Tags: A Troublesome Inheritance. There has recently been something of an uproar over the new book. By Nicholas Wade, with much of the criticism centering on Wade’s claim that race is a meaningful biological category. This subject is one with which I. 10 A simple pair of digits that conferred on me numerous rights and privileges denied to the majority of the population.
The two-body opportunity | Bits of DNA
https://liorpachter.wordpress.com/2014/10/10/the-two-body-opportunity
Reviews and commentary on computational biology by Lior Pachter. October 10, 2014 in expository. This year half of the Nobel prize in Physiology or Medicine was awarded to May-Britt Moser and Edvard Moser, who happen to be both a personal and professional couple. Interestingly, they are not the first but rather the. And even if one presumes that it is, the term is an oxymoron because in physics the problem is solved whereas in academia it is used in a way that implies it is. Assigns to each string a valu...
The perfect human is Puerto Rican | Bits of DNA
https://liorpachter.wordpress.com/2014/12/02/the-perfect-human-is-puerto-rican
Reviews and commentary on computational biology by Lior Pachter. The perfect human is Puerto Rican. December 2, 2014 in expository. Recent news of James Watson’s auction of his Nobel Prize medal. Has unearthed a very unpleasant memory for me. In March 2004 I attended an invitation only genomics meeting at the famed Banbury Center. The Center only added to the allure. I felt that I had received an invitation to the genomics equivalent of Skull and Bones. And he made a point to disparage Rosalind Franklin ...
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The Grand Locus
http://blog.thegrandlocus.com/tag/gumbel
Life for statistical sciences. June babies and bioinformatics. Filed under extreme value fallacy. 8226; 06 April 2014 •. In July 1982, paleontologist Steven Jay Gould. Was diagnosed with cancer. Facing a median prognosis of only 8 months survival, he used his knowledge of statistics to prepare for the future. As he explains in The Median Isn’t the Message. If half of the patients died of this rare case of mesothelioma. If not the median. Then what is the message? June babies and anorexia.
Once upon a BLAST | The Grand Locus
http://blog.thegrandlocus.com/2014/06/once-upon-a-blast
Life for statistical sciences. Once upon a BLAST. Filed under series: focus on. 8226; 30 June 2014 •. Point well taken. But this unspoken academic pact has sealed what I call the. In simple words, the curse is that by putting all the emphasis on the results, researchers become blind to the research. Because they never discuss it. How to carry out good research? How to discover things? These are the questions that nobody raises (well, almost. Where did I leave off? Is the director of the NCBI. Dynamic] al...
RNA-seq Analysis
http://nextgenseek.com/category/rna-seq-analysis
Making Sense of Next-Gen Sequencing Data. You are here: Home. Archives for RNA-seq Analysis. Kallisto paper summary: Near-optimal RNA-seq quantification. May 31, 2015. Middot; 1 Comment. Middot; Tagged With: kallisto. Bayesian Approach to Single-Cell RNA-Seq Differential Expression Analysis. June 12, 2014. Middot; 1 Comment. Middot; Tagged With: DE in Single-Cell RNA-seq. July 25, 2013. Middot; Leave a Comment. Recently just started playing with TopHat, after a while back, for doing gene expression quant...
Next Generation Technologist - Page 2 of 15 - Next Generation Sequencing, Marketing, and the Genomic Revolution
http://www.yuzuki.org/page/2
Next Generation Sequencing, Marketing, and the Genomic Revolution. Next Generation Sequencing, Marketing, and the Genomic Revolution. Fundamentals of Next Generation Sequencing. One door opens, and another door closes. Highlights from the American Association for Cancer Research Meeting, Philadelphia 2015 #AACR15. Complete human diplotypes & Google X Life Sciences podcast. Theral Timpson produces a weekly podcast at Mendelspod.com, and in his latest edition he interviews me about Google X Life Scienc...
freakonometrics.hypotheses.org
STT6705V | Freakonometrics
http://freakonometrics.hypotheses.org/category/courses/stt6705v
Is it that stupid to make extremely long term forecast when studying mortality? I received recently a comment by FCA ( here. Who raised an important question, about forecast in dynamic mortality models. (S)he mentioned that from his(her) point of view, the econometric models I considered were “good to predict for the next, say, 3 or 4 years. Not for the next 50 years…”. Which was the message I tried to stress last year in a conference about retirement in France ( here. For sketches of the R code,. A[i] B...
Debora S. Marks Lab
https://marks.hms.harvard.edu/people.html
Marks Lab Members and Collaborators. Debora S. Marks. Rohan defended his PhD on the evolution of laboratory and natural populations of Escherichia coli at Michigan State University in 2016. His main interest is molecular evolution. Rohan is especially interested in whether coevolution at the molecular scale is sufficient (or not) in driving the evolution of complex cellular lifeforms. Postdoc (joint with Chris Sander). Postdoc (joint with Chris Sander). Charlotta is a Bioinformatics PhD student from the ...
freakonometrics.hypotheses.org
ensae | Freakonometrics
http://freakonometrics.hypotheses.org/category/courses/ensae
La vie d’un sinistre…. Pour illustrer un peu le cours d’actuariat de l’assurance dommage, un petit exemple de ce que peut être une base de sinistres (je serais ravi d’en avoir que je puisse partager avec les étudiants, dans le cours). Regardons par exemple un sinistre,. On a les dates des opérations, avec des paiements et/ou des réestimations de la charge dossier/dossier. Pour visualiser la vie de ce sinistre, on peut utiliser. Correspondant à l’année de survenance 2007,. ENSAE, Devoir 3. Pour le troisiè...
Longest runs and DNA alignments | The Grand Locus
http://blog.thegrandlocus.com/2014/12/longest-runs-and-dna-alignments
Life for statistical sciences. Longest runs and DNA alignments. Filed under sequence alignment. 8226; 31 December 2014 •. It also holds for PacBio and Oxford Nanopore by the way). The problem of sequence alignment. Gets a lot of attention from bioinformaticians (the list of alignment software. Counts more than 200 entries). Yet, the statistical aspect of the problem is often neglected. In the post Once upon a BLAST. David Lipman explained that the breakthrough of BLAST. Longest runs of 1s. P(X 0 leq x) a...
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Petit journal Martiniquais . 08/06/2006 at 2:37 AM. 19/10/2008 at 12:31 AM. Subscribe to my blog! POT DE DEPART 15 JUIN 2008 TARTANE. Alors Pierrot ça fait du bien de s'asseoir un peu non? Tu danseras plus tard. Don't forget that insults, racism, etc. are forbidden by Skyrock's 'General Terms of Use' and that you can be identified by your IP address (66.160.134.11) if someone makes a complaint. Please enter the sequence of characters in the field below. Posted on Sunday, 19 October 2008 at 12:25 AM.
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Bits of DNA | Reviews and commentary on computational biology by Lior Pachter
Reviews and commentary on computational biology by Lior Pachter. In biology n does not go to infinity. August 14, 2015 in reviews. Strong exponential time hypothesis. I recently read a “. Column in the Boston Globe titled “ For 40 years, computer scientists looked for a solution that doesn’t exist. 8221; that caused me to facepalm so violently I now have pain in my right knee. The article is about the recent arXiv posting:. Strong Exponential Time Hypothesis. This type of “lower bound” reduct...While the...
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