Dr. Michael Eisen

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Dr. Michael Eisen Michael Eisen majored in math as an undergraduate at Harvard, and used the department’s utter lack of interest in what students did outside of math class to pursue his true loves of ecology and evolutionary biology. He did his PhD in biophysics with Don Wiley, trying to unite his quantitative side with his interest in biology by using X-ray crystallography to study the evolution of influenza virus proteins. After a stint as the play-by-play voice of the Columbia Mules Professional Baseball Club, he joined the labs of Pat Brown and David Botstein at the dawn of the era of functional genomics. He played multiple roles in the development of DNA microarrays as a tool for studying biology, his biggest contribution being a 1998 paper showing how clustering methods can reveal underlying biological structure in genomic data. He began his independent career at Lawrence Berkeley National Lab, before moving to the Department of Molecular and Cell Biology at UC Berkeley where he is now a Professor and HHMI Investigator. In addition to the main focus of his lab – using experimental, computational and evolutionary methods to study spatial patterns of gene regulation in the early Drosophila embryo – he has a longstanding interest in the varied microorganisms that have evolved to manipulate animal behavior, the subject of his talk today. Outside of the lab, he has been a fervent and occasionally strident advocate for opening up the system of scholarly publishing, founding, along with Brown and Harold Varmus, the Public Library of Science (PLOS). More recently he has dabbled in politics and serves as an advisor to Impossible Foods, a company Brown started to create plant-based meats to end the planetary scourge of animal farming. .

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It Is NOT Junk a Blog About Genomes, DNA, Evolution, Open Science, Baseball and Other Important Things
it is NOT junk a blog about genomes, DNA, evolution, open science, baseball and other important things The Past, Present and Future of Scholarly Publishing By MIC H A EL EISEN | Published: MA RC H 2 8 , 2 0 1 3 Search To search, type and hit enter I gave a talk last night at the Commonwealth Club in San Francisco about science publishing and PLoS. There will be an audio link soon, but, for the first time in my life, Michael Eisen I actually gave the talk (largely) from prepared remarks, so I thought I’d post it here. I'm a biologist at UC An audio recording of the talk with Q&A is available here. Berkeley and an Investigator of the —— Howard Hughes Medical Institute. I work primarily On January 6, 2011, 24 year old hacker and activist Aaron Swartz was arrested by on flies, and my research encompases police at the Massachusetts Institute of Technology for downloading several million evolution, development, genetics, articles from an online archive of research journals called JSTOR. genomics, chemical ecology and behavior. I am a strong proponent of After Swartz committed suicide earlier this year in the face of legal troubles arising open science, and a co-founder of the from this incident, questions were raised about why MIT, whose access to JSTOR he Public Library of Science. And most exploited, chose to pursue charges, and what motivated the US Department of Justice importantly, I am a Red Sox fan. (More to demand jail time for his transgression. about me here).
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Gene Co-Expression Network Mining Using Graph Sparsification
Gene Co-expression Network Mining Using Graph Sparsification THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Jinchao Di Graduate Program in Electrical and Computer Engineering The Ohio State University 2013 Master’s Examination Committee: Dr. Kun Huang, Advisor Dr. Raghu Machiraju Dr. Yuejie Chi ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! Copyright by Jinchao Di 2013 ! ! Abstract Identifying and analyzing gene modules is important since it can help understand gene function globally and reveal the underlying molecular mechanism. In this thesis, we propose a method combining local graph sparsification and a gene similarity measurement method TOM. This method can detect gene modules from a weighted gene co-expression network more e↵ectively since we set a local threshold which can detect clusters with di↵erent densities. In our algorithm, we only retain one edge for each gene, which can generate more balanced gene clusters. To estimate the e↵ectiveness of our algorithm we use DAVID to functionally evaluate the gene list for each module we detect and compare our results with some well known algorithms. The result of our algorithm shows better biological relevance than the compared methods and the number of the meaningful biological clusters is much larger than other methods, implying we discover some previously missed gene clusters. Moreover, we carry out a robustness test by adding Gaussian noise with di↵erent variance to the expression data. We find that our algorithm is robust to noise. We also find that some hub genes considered as important genes could be artifacts.
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Trevor John Hastie 1040 Campus Drive Stanford, CA 94305 Home Phone&FAX: (650) 326-0854
Trevor John Hastie 1040 Campus Drive Stanford, CA 94305 Home Phone&FAX: (650) 326-0854 Department of Statistics Born: June 27, 1953, South Africa Sequoia Hall Married, two children Stanford University U. S. citizen, S.A. citizen Stanford, CA 94305 E-Mail: [email protected] (650) 725-2231 Fax: 650/725-8977 Updated: June 22, 2021 Present Position 2013{ John A. Overdeck Professor of Mathematical Sciences, Stanford University. 2006{2009 Chair, Department of Statistics, Stanford University. 2005{2006 Associate Chair, Department of Statistics, Stanford University. 1999{ Professor, Statistics and Biostatistics Departments, Stanford University. Founder and co-director of Statistics department industrial aﬃliates program. 1994{1998 Associate Professor (tenured), Statistics and Biostatistics Departments, Stan- ford University. Research interests include nonparametric regression models, computer in- tensive data analysis techniques, statistical computing and graphics, and statistical consulting. Currently working on adaptive modeling and predic- tion procedures, signal and image modeling, and problems in bioinformatics with many more variables than observations. Education 1984 Stanford University, Stanford, California { Ph.D, Department of Statis- tics (Werner Stuetzle, advisor) 1979 University of Cape Town, Cape Town, South Africa { First Class Masters Degree in Statistics (June Juritz, advisor). 1976 Rhodes University, Grahamstown, South Africa { Bachelor of Science Honors Degree in Statistics. 1975 Rhodes University, Grahamstown, South Africa { Bachelor of Science Degree (cum laude) in Statistics, Computer Science and Mathematics. Awards and Honors 2020 \Statistician of the year" award, Chicago chapter ASA. 2020 Breiman award (senior) 2019 Recipient of the Sigillum Magnum, University of Bologna, Italy. 2019 Elected to The Royal Netherlands Academy of Arts and Science. 2019 Wald lecturer, JSM Denver.
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Ddawson2012.Pdf (700.6Kb)
Open Science and Crowd Science: Selected Sites and Resources Diane (DeDe) Dawson Natural Sciences Liaison Librarian University of Saskatchewan Saskatoon, Saskatchewan, Canada [email protected] Table of Contents Introduction Open Science Crowd Science Methods and Scope Open Science – Definitions and Principles Open Science – Open Lab Notebooks of Individuals and Lab Groups Open Science – Blogs Crowd Science – Projects for Individuals or Small Teams Crowd Science – Volunteer Distributed Computing Projects The Main Software Organizations Selected Projects Further Sources for Projects Selected Examples of Collaborative Science Sites for Specialists Main Software & Online Tools for Open Science Open Science Conferences and Community Conferences Further Reading/Viewing Videos Reports and White Papers Open e-Books Selected Essays, Articles, and Interviews References Introduction “To take full advantage of modern tools for the production of knowledge, we need to create an open scientific culture where as much information as possible is moved out of people’s heads and laboratories, and onto the network” (Nielsen 2011, p.183). New Internet technologies are radically enhancing the speed and ease of scholarly communications, and are providing opportunities for conducting and sharing research in new ways. This webliography explores the emerging “open science” and “crowd science” movements which are making use of these new opportunities to increase collaboration and openness in scientific research. The collaboration of many researchers on a project can enhance the rate of data-collection and analysis, and ignite new ideas. In addition, since there are more eyes to spot any inaccuracies or errors, collaborative research is likely to produce better quality results. Openness early in the research process alerts others to the work resulting in less duplication of efforts.
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Converting Scholarly Journals to Open Access: a Review of Approaches and Experiences David J
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In Memoriam: PNAS Editor-in-Chief Nicholas R. Cozzarelli (1938–2006) hen Nicholas R. Cozzarelli possessed a sharp, analytical memory, became Editor-in-Chief of which perhaps explains why he initially the Proceedings of the Na- chose to study pre-law at Princeton. tional Academy of Sciences However, after some undergraduate Wof the United States of America (PNAS) research, he began falling in love with in 1995, he inherited a journal that in science, and he graduated magna cum many ways had remained unchanged laude in 1960 with a bachelor’s degree since its inception in 1914. Yet in just in biology. Afterward, he attended Yale over a decade, he had—through a com- University School of Medicine (New bination of visionary leadership and Haven, CT) but soon realized that, de- sheer force of will—transformed PNAS spite his talents, he did not want to be a and raised it to a higher level. That physician. After a year, he transferred to transformation can be seen throughout Harvard Medical School (Boston, MA) the journal, from cover to last page. to embark on a journey of research, Since 1995, PNAS has experienced a which began with his graduate studies in marked rise in the number of submis- the laboratory of E. C. C. Lin, examin- sions and published papers, an improve- ing the genes and pathways regulating ment in the quality and variety of Escherichia coli glycerol metabolism. published material, and the introduction After receiving his Ph.D. from Har- of an innovative hybrid open access vard in 1966, Cozzarelli moved to Stan- model.
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IN BRIEF Accounted For
RESEARCH HIGHLIGHTS content or isochore location are IN BRIEF accounted for. The dovetailing of the authors’ experimental and bioinformatic data EVOLUTION provides extremely strong circumstan- tial evidence that L1 insertions Noise minimization in eukaryotic gene expression. decrease gene expression in vivo. Fraser, H. B. et al. PloS Biol. 27 Apr 2004 (doi:10.1371/journal.pbio.0020137) Moreover, this new work tallies with previous findings that gene expression Until now, the functional and evolutionary significance of stochastic is suppressed when full-length L1 (‘noisy’) fluctuations in the rates of protein production was a mys- sequences are inserted into introns. tery.Michael Eisen and colleagues have developed a model of sto- The authors also raise the intrigu- chastic gene expression in yeast to test their hypothesis that genes ing possibility that the mammalian that encode subunits of multiprotein complexes or that cause lethal- genome might have co-opted tran- ity when deleted would be sensitive to such variation. Their estimates scriptional suppression of L1 (which of the noise in protein production for most yeast genes confirm this probably first evolved to prevent hypothesis and indicate that natural selection minimizes noise in excessive mutagenic retrotransposi- gene expression. tion) as a mechanism for fine-tuning the relative levels of expression of dif- CANCER GENETICS ferent genes. If this model is correct, perhaps L1 is better viewed as more Impact of the KU80 pathway on NHEJ-induced of a genomic classroom assistant than genome rearrangements on mammalian cells. Han and colleagues followed up a problematic pupil? Guirouilh-Barbat, J. et al. Mol. Cell 14, 611–623 (2004) their experiments with a neat bit of Nick Campbell bioinformatics.
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NEHA SPENTA WADIA [email protected] • (+1) 413 695 5367
NEHA SPENTA WADIA [email protected] • (+1) 413 695 5367 EDUCATION University of California, Berkeley, Berkeley, CA, USA August 2015 - present Biophysics Graduate Group Redwood Center for Theoretical Neuroscience • PhD in Biophysics, advised by Professor Michael DeWeese. Expected May 2021 I work on problems in statistical physics and machine learning with the aim of developing new theoretical frameworks within which to understand network-level computations in brains. University of Waterloo and Perimeter Institute for Theoretical Physics, Waterloo, ON, Canada Perimeter Scholars International • Master of Science in Physics. June 2014 • Masters Research Essay: “Adventures in Two Dimensional Heisenberg Spin Systems in the Context of Solid State NMR”, advised by Professor David G. Cory (available at http://perimeterinstitute.ca/psi_essays/2014/Neha_Wadia.pdf). • Awards: Honorary Emmy Noether Scholarship. • Class valedictorian. Amherst College, Amherst, MA, USA • Bachelor of Arts in Physics, Magna Cum Laude. May 2013 • Cumulative GPA: 3.80/4.0, Physics GPA: 3.68/4.0. • Senior Honors Thesis: “Measurements of Branching Ratios for the B(0)-X(v) Transition in Thallium Fluoride to Determine its Potential for Laser Cooling”, advised by Professor Larry Hunter (available at https://www.amherst.edu/system/files/Wadia.pdf). • Awards: Forris Jewett Moore Graduate Fellowship. August 2013 – May 2014 • Student member of the Amherst College chapter of Sigma Xi, Scientific Honors Society. RESEARCH EXPERIENCE University of California, Berkeley, Berkeley, CA, USA • Rotation Student September 2015 – November 2015 I spent ten weeks as a rotation student in the laboratory of Professor Michael Eisen, who studies the function of enhancers in the genome and the interactions between pathogenic microbes and their animal hosts within the relevant ecological contexts.
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A Future Vision for PLOS Computational Biology
Editorial A Future Vision for PLOS Computational Biology Ruth Nussinov1,2* 1 Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America, 2 Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel With much trepidation I accepted the relevance. As Editor-in-Chief I will do my PLOS Computational Biology is broad; it great honor and responsibility of becom- best to have PLOS Computational Biology addresses diverse biological problems. We ing Editor-in-Chief of PLOS Computational continue these traditions. look forward to further expanding its Biology. I am fully aware of how hard it will Computational biology is often per- scope through the inclusion of outstanding be to step into the shoes of Philip Bourne, ceived as a single field; this however is methods and resource papers, opening up the Editor-in-Chief of the journal for the not the case. Like experimental biology, significant new research directions while last seven years, since it was founded by computational biology is enormously retaining and enhancing the strong scien- him, Steven Brenner, and Michael Eisen. broad; the only distinction from experi- tific merit of PLOS Computational Biology We are all deeply appreciative and mental biology is the means. This has publications. We further plan on improv- thankful to Phil for his unique role; and disadvantages and advantages: the main ing the pace of submissions processing. we are grateful that he will be continuing disadvantage is that conclusions based on PLOS Computational Biology is recognized by his association with the journal in the computations are often treated by biolo- the community as the premier journal in future in the role of Founding Editor-in- gists as less conclusive than those based on computational biology.
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Gene Expression in Early Drosophila Embryos Is Highly Conserved Despite Extensive Divergence of Transcription Factor Binding
Gene expression in early Drosophila embryos is highly conserved despite extensive divergence of transcription factor binding. Mathilde Paris1, Tommy Kaplan1,2, Xiao Yong Li1,3, Jacqueline E. Villalta2, Susan E. Lott1,4, Michael B. Eisen1,2 1 Department of Molecular and Cell Biology, University of California BerKeley, BerKeley, California, United States of America, 2 School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel, 3 Howard Hughes Medical Institute, University of California BerKeley, BerKeley, California, United States of America, 4 Department of Evolution and Ecology, University of California, Davis, California, United States of America. Corresponding authors: MP and MBE ABSTRACT To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertooK a systematic study of transcription factor binding and gene expression in the blastoderm embryos of four species that sample much of the diversity in the 60 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, as measured by mRNA-seq to the genome-wide binding of four transcription factors involved in early development, as measured by ChIP-seq (Bicoid, Giant, Hunchback and Krüppel). Surprisingly, we found that mRNA levels are much better conserved than individual binding events. We looKed at binding characteristics that may explain such evolutionary disparity. As expected, we found that binding divergence increases with phylogenetic distance. Interestingly, binding events in non-coding regions that were bound strongly by single factors, or bound by multiple factors, were more liKely to be conserved. As this class of sites are most liKely to be involved in gene regulation, the divergence of other bound regions may simply reflect their lack of function.
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The Rise and Fall of a Community-Driven Model of Scientific Communication Joachim Schöpfel
Open access - the rise and fall of a community-driven model of scientific communication Joachim Schöpfel To cite this version: Joachim Schöpfel. Open access - the rise and fall of a community-driven model of scientific communi- cation. Learned Publishing, Association of Learned and Professional Society Publishers, 2015, 28 (4), pp.321-325. 10.1087/20150413. hal-01282744 HAL Id: hal-01282744 https://hal.archives-ouvertes.fr/hal-01282744 Submitted on 13 Jun 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License Open Access – The Rise and Fall of a Community-Driven Model of Scientific Communication Opinion Paper Joachim Schöpfel GERiiCO laboratory, University of Lille 3 [email protected] Key points • In 25 years, open access, i.e. free and unrestricted access to scientific information, has become a significant part of scientific communication. However, its success story should not conceal a fundamental change of its nature. • Open access started, together with the Web, at the grassroots, as a bottom-up, community-driven model of open journals and repositories. Today the key driving forces are no longer community-driven needs and objectives but commercial, institutional and political interests.
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Michael Eisen's Angry, Hypocrisy Drenched Assault on Informed
Michael Eisen's Angry, Hypocrisy Drenched Assault on Informed Consent using Massive Fallacious Reasoning while Ironically Brandishing the Banner of "Science" (c) Copyright 2012 David Dilworth (Eisen may have set a New World Record by committing Six Logical Fallacies with a Single Sentence.) The Genetically modified (GMO) food conflict surfaced in California where Food Safety proponents have put GMO food labeling on the November 2012 ballot so consumers can make an informed choice. GMO manufacturing corporations including Monsanto oppose labeling. Though I'd written a letter to a British researcher about iti the GMO campaign hadn't really caught my attention until I ran across an article, or more accurately found an article that ran over me and rational discourse. Entitled "The anti-GMO campaign's dangerous war on science"ii it is written by a genetic researcher in California named Michael Eisen claiming to support Open Science. The article caught my attention because I've been helping work for good science for a few decades, I'm aware of real attacks on science philosophy and credibility and I am a bit familiar with environmental impacts iii - so sounds good right ? Wow, was I ever in for a disturbing surprise. With deeply profound irony an "infuriated" Eisen claims he's fighting to defend science ("My vested interest here is science, and what I write here, I write to defend it"). Instead his article assaults and batters science reasoning and logic so relentlessly I had to set it aside for a few days to recover from my shocked dismay. "Well I'm angry, making sense gets in the way." "Coupling" British TV seriesiv If I'd found so much as one valid electronic breath defending science methodology, reasoning or logic in the article I wouldn't have written this.
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