Church Lab & Lipper Center Meeting Schedule

NOTICE:     Mon/Thu meetings are restricted to lab members, current rotation students, and collaborators with consent of the speaker. Guest lectures & Journal meetings are open to the scientific community. All meetings and topics are subject to change up to the last minute so check this page.

Monday & Thursday Meetings at 12:30 to 1:45 PM in Alpert Building room 561, adjacent to the Genetics Department library (*** indicates other times or locations.)

DATE      SPEAKER     Title (please update your titles)
Apr 29 Mon    Jason Stewart (Guest speaker) "Expression databases and standards"
May 09 Thu    Feng Gao (Guest Speaker, U. Mich.)" Analysis of DNA Regulation  "
May 13 Mon    Jun Zhu   RNA-protein interactions, alternative splicing, and crosslinking.
May 16 Thu    Dat H Nguygen (Guest speaker) Biological Antifreezes: A New Hypothesis for the Mechanism of Function
May 30 Thu    Megan Jewett(DARPA Team - Meet with Church Lab)
Jun 06 Thu    Adnan Derti    "Alternative Splicing"
Jun 13 Thu    Doug Selinger   Degrading the messenger
Jun 17 Mon    Sasha Wait     "Quantum Teleportation and Artificial Souls".
Jun 20 Thu*** Brett Chevalier (Guest Speaker) Time:2:15-3:15   Engineering new endonucleases
Jun 24 Mon    Vasudeo Badarinaryana  "Automating stem cell culture & proteomics-
Jul 01 Mon    Kyriacos Leptos  Massively Parallel masses
Jul 08 Mon    Yonatan Grad  MicroRNAs & enhancers
Jul 11 Thu    Matthew Wright Genomes-To-Life
Jul 15 Mon    Aimee Dudley   Yeast cell cycle and the absolute abundance of RNA.
Jul 18 Thu    Jake Jaffe   Mycoplasmology meeting report and discussion
Jul 22 Mon    Dan Janse  Making proteins vanish and appear quickly
Jul 25 Thu    Rob Mitra    Cis-ness in DNA & RNA
Jul 29 Mon    Daniel Segre   Optimal fluxes, replication, and spatial configuration of microbes
Aug 05 Mon    Ji Qui (Guest speaker)
Aug 08 Thu    Patrik D'haeseleer   Networks and data reliability. Aimee & Dennis meeting reports.
Aug 12 Mon    Gary Gao"Pattern Discovery in Biological Sequences."(guest speaker)
Aug 19 Mon    Jay Shendure   SNPs, HEP & antisense.
Aug 22 Thu    Wayne Rindone "BioSPICE"
Aug 26 Mon    Xiaoxia Lin (Guest Speaker) "Mathematical modeling and optimization: from chemical processes to biological systems." Matt ISMB meeting report.
Aug 29 Thu    Tzachi Pilpel   Combine and conquer
Sep 05 Thu   Jingdong Tian   In vitro translatomics
Sep 09 Mon    Zhou Zhu   Connecting motifs with transcription factors
Sep 12 Thu   Allegra Petti   Signaling cross-talk
Sep 16 Mon   no meeting
Sep 19 Thu    Dennis Vitkup   functional genetic polymorphisms
Sep 23 Mon    Jason Warner (Guest Speaker) "Role of N-linked Oligosaccharide Flexibility in Mannose Phosphorylation of Lysosomal Enzyme Cathepsin L"
Sep 30 Mon   John Aach The mixed tissue issue -OR- modeling replication
Oct 07 Mon   Sung Choe   Mammalian transcription control
Oct 17 Thu   Jake Jaffe   The gliding proteome(s)
Oct 21 Mon   Nathan Walsh   Non-random words of wisdom
Oct 24 Thu   Nikos Reppas   homologous recombin(autom)ation
Oct 28 Mon   Vasudeo Badarinaryana   From stem to steuron
Oct 31 Thu   Jun Zhu ALternative splice-styles
Nov 07 Thu   Xiaoman Li (Guest Speaker)"Some statistical issues in shotgun sequence assembly".
Nov 14 Thu   David Gifford & Rick Young (Guest speakers from MIT)"Reconstruction of regulatory networks"
Nov 18 Mon   Doug Selinger    SBC
Nov 21 Thu   David Schoenfield (Guest speaker from MGH) "Multiple Organ Failure (MOF) RNA-array analyses."
Nov 25 Mon   Adnan Derti mammalian genome splicing
Dec 02 Mon   Peter Kharchenko   Deep consequences of surface residues
Dec 05 Thu   Kyriacos Leptos   quantitative mass spec.
Dec 09 Mon   Yonatan Grad    microRNA microcosms
Dec 16 Mon   Aimee Dudley   The optimal organelle's time has come
Dec 19 Thu   Daniel Segre, Allegra Petti, Matthew Wright, Tzachi Pilpel, George Church - Meeting Reviews
Jan 09 Thu  Computational & Systems Biology CSBi Symposium MIT-E51
Jan 13 Mon   Wayne Rindone  "BioSPICE/OAA/SBML"
Jan 16 Thu   Patrik D'haeseleer  Working the net
Feb 03 Mon   Matthew Wright  Folding the genome map
Feb 05 Wed***Jay Shendure "The Polonator" (Please note this is on Wednesday)
Feb 06 Thu   Martin Steffen
Feb 10 Mon   No lab meeting -- DOE GtL meeting in DC
Feb 13 Thu   Dept. Seminar: Laura Rusche.
Feb 20 Thu   Anders Bergkvist   Extending the codon code
Feb 24 Mon   Daniel Janse   Large Scale Phenotypic Screen Using the Yeast Deletion Library Set
Feb 27 Thu   Kang Shen, UCSF (Dept. seminar)
Mar 03 Mon   Monica P. Colaiacovo, Stanford (Dept. seminar)
Mar 06 Thu   No Lab Meeting
Mar 10 Mon   No Lab Meeting
Mar 13 Thu   Jingdong Tian  Can ribosomes make ribosomes?
Mar 17 Mon   No lab meeting (Dept. Seminar)
Mar 20 Thu***DARPA Review Mtg in place of lab meeting(Earlier time 10:00 am - 1200pm)
Mar 24 Mon   Allegra Petti  Operons and functional intersections
Mar 27 Thu   Gaddy Getz (Guest speaker) "Analysis of Gene Expression Data"
Mar 31 Mon   No Lab Meeting
Apr 03 Thu   No Lab Meeting
Apr 07 Mon   Trey Ideker (Guest Speaker)"Digesting large molecular interaction networks into manageable pieces"
Apr 10 Thu   Liran Carmel (Guest Speaker) "Classification and Visualization of Multivariate Data - Electronic Nose at Work"
Apr 14 Mon   Galit Shenhar (Guest Speaker) "Design principles of protein networks in living mammalian cells."
Apr 17 Thu   Manchun Lu (Guest Speaker)" The Surface Invasive Cleavage Assay for High-throughput Single Nucleotide Polymorphism (SNP) Analysis"
Apr 21 Mon   Nikos Reppas  Vectorology
Apr 24 Thu   Jun Zhu  So many spliceforms
Apr 28 Mon   Dennis Vitkup  Base Pairs gone bad
May 01 Thu***(noon) Rick Kelley, Baylor College of Medicine(Department of Molecular and Cell Biology ) HMS Genetics Dept. Seminar on Drosophila dosage compensation
May 05 Mon   Vasudeo Badarinaryana  Stem cell proteomics
May 08 Thu   Adnan Derti  The accomsplices
May 12 Mon   Zhou Zhu  Cell Cycler
May 15 Thu   Peter Kharchenko  Proteinterfaces
May 19 Mon   No Lab Meeting (Computational Biology Symposium)
May 22 Thu   No Lab Meeting (Genetics Retreat)
May 26 Mon   No Lab Meeting (Memorial day)
May 29 Thu   Daniel Segre   ReFlux
Jun 02 Mon   Wayne Rindone  BioSpicy
Jun 05 Thu   John Aach  1D to 4D HRCA & polony PDE models
Jun 09 Mon   Elizabeth Weitzke (Guest Speaker)"A Genomic, Proteomic and Metabolic Kinetic Approach to Cell Modeling"
Jun 12 Thu   Charles Gao (Guest Speaker-ProteomTech)"PTR, not PCR, an Automated Refolding System for Making Human Recombinant Proteins from E-coli Inclusion Bodies."
Jun 16 Mon   Kun Zhang (Guest Speaker)"Detecting subtle changes of DNA copy number with QPCR assay: statistics, optimization and an application to tumor suppressor gene mapping"
Jun 19 Thu  John Wagner (Guest speaker) Virtual Cell project and SBML
Jun 23 Mon   Yonatan Grad  Micromotifs
Jun 26 Thu   No Lab Meeting
Jun 30 Mon   No Lab meeting
Jul 03 Thu   No lab meeting
Jul 07 Mon   Matthew Wright  Folding the genome map
Jul 10 Thu   No lab meeting (talk on biofilms and pseudomonas at noon at the Forsyth Institute).
Jul 14 Mon   Phillipe Marc  Comparative functional genomics
Jul 17 Thu   Jeffrey Chang (Guest speaker)"Automatic Extraction and Application of Knowledge from Biological Text"
Jul 21 Mon   George Church
Jul 24 Thu   Sung Choe
Jul 28 Mon   Sasha Wait
Jul 31 Thu   Aimee Dudley  Nuclear and unclear
Aug 04 Mon   Nathan Walsh
Aug 07 Thu   Jake Jaffe
Aug 11 Mon   Jingdon Tian & nbsp; Synthetic genes, genomes, & ribosomes
Aug 14 Thu   Gary Gao
Aug 18 Mon   Kyriacos Leptos  Massamatics
Aug 21 Thu   Dat Nguyen   Non-linear optimization algorithms
Aug 25 Mon   Xiaoxia Lin
Aug 28 Thu   Adnan Derti
Sep 01 Mon   Labor Day
Sep 04 Thu   Allegra Petti
Sep 08 Mon   Dennis Vitkup
Sep 11 Thu   Doug Selinger
Sep 15 Mon   Steve Munroe
Sep 18 Thu   No Lab Meeting
Sep 22 Mon   Peter Kharchenko
Sep 25 Thu   Dan Janse Making proteins unstable on demand
 
 


 If anyone needs to reschedule (or change title), please check with Cindy as far in advance as possible. If you are going to discuss articles, please give copies of one or two key articles a week in advance to Cindy or place copies in the journal area of WAB5 or HIM4. Reports about major scientific meetings will be given on either the Monday or Thursday closest to the return of the participants. Please make sure that our schedule reflects this.
Genetics Dept. Seminars Wed at noon in WAB 563
(except as noted ***)
Church lab lecture tour

Jan 25-30, 2001 World Economic Forum 2001 in Davos (George Church)

Feb 22, 2001 Showcase meeting: Where do we go from HUGO? at The Pierre in NYC (George Church)

Mar 13, 2001. Experiencing the Frontiers of Biomedical Technology HST Symposium, Boston, MA (George Church)

Apr 21-24, 2001 Recomb 2001 in Montreal (George Church)

May 8, 2001 CGR lecture in Cambridge, MA (George Church)

May 24, 2001 Mass. Biotech Council Science Symposium session "MINING THE GENOME", 2:45-4:30pm at the Westin Copley Place, Boston. (George Church)

June 22, 2001 DIMACS Workshop on Integration of Diverse Biological Data (Tzachi Pilpel)

Jun 13-14, 2001 Armenise Symposium: Cancer Biology & Post-Genomics Grand Hotel Borromee, Lago Maggiore in Italy (George Church)

Jul 21-25, 2001 ISMB 2001 in Copenhagen, Denmark (Tzachi Pilpel)

Aug 23-26, 2001 Santa Cruz Human Genome Workshop at UCSC (George Church).

Sep 12, 2001 New England Bioinformatics Group (NEBiG) and Abbott Bioresearch Center: Microarray Data Analysis Toward Understanding Autoimmunity. Worcester, MA (George Church)

Sep 13-15, 2001 PNL, SDSC, and Sun: Computational Challenges In The Post-Genomic Age-II. Durham, NC. (George Church)

Nov 27-Dec 1, 2001 DARPA BioCOMP meeting Monterey, CA (George Church)

Dec 1, 2001 E.coli resources meeting, Chicago, IL (Doug Selinger)

Dec 17, 2001 Biomedical Informatics Grand Rounds Mon 11 AM Children's Hospital, Boston (George Church)

Jan 27-31, 2002   DOE Genome Meeting, Santa Fe, NM (Rob Mitra & Wayne Rindone)

Jan 31, 2002  Whitehead Institute Functional Genomics Seminar Series (George Church)

Feb 12, 2002 MIT Mathematics Dept: "The challenge of integrating informational, spatial, temporal, and optimal models: toward synthetic biology.

Feb 14, 2002    BWH Clinical Pathology Conference Series: "Relating Genetic differences to Gene Expression and Cell Proliferation: Technologies and Models." (George Church)

Feb 26, 2002    Harvard Inst. Medicine Genomics Center 1st floor Conference at Noon: "Genome-wide measures and system models for protein interactions and cell proliferation." (George Church)

Feb 27, 2002    HMS Cannon Room 4:00 to 6:00 PM BBS minisymposium on Functional Genomics & Informatics (George Church, Martha Bulyk, Fritz Roth, Marc Vidal)

Mar 18-19, 2002 Gaithersburg, MD DOE Genomes to Life Mathematics Workshop (Matthew Wright)

Mar 23, 2002 E. coli Model Cell Consortium (Emc^2) meeting (Doug Selinger).

Apr 1, 2002   BU Bioinformatics Dept, "Genome systems models and measures connecting genotype with phenotype." (George Church)

May 1, 2002  at 10:50 AM Boston CHI Macro Results Through MicroArrays Keynote Presentation: "Array Quantitation for Modeling Mutations Affecting RNA, Protein Interactions, and Proliferation" (George Church)

May 22-24, 2002  Washington DC DARPA IPTO Bio-Computation PI Meeting (George Church)

Jun 4, 2002 Archemix at 11:00 AM "Polonies" (George Church).

Jun 11, 2002 Yale at 4:00 PM "Systems models and measures connecting genotype to phenotype" (George Church).

Jun 19, 2002 Harvard CGR at 3 PM. "From proteomics to a highly interconnected model of replication and selection." (George Church)

Jun 24-28, 2002 MIT 20.01s Bioinformatics: Principles, methods and applications. (George Church).

July 7-12, 2002 Vienna 14th International Organization for Mycoplasmology (IOM) Congress (Jake Jaffe)

July 23, 2002 Sequencing and resequencing the biome. Pooks Hill Bethesda Marriott (George Church)

July 26, 2002 Fri at 9:00 AM Humboldt Univ. & Boston Univ. Bioinformatics workshop in Boston. Keynote: "Biosystems Measures and Models of Reproductive Fitness" (George Church)

July 28-Aug2 GRC Genomics & Structural/Evolutionary Bioinformatics Mount Holyoke (Dennis Vitkup)

July 30-Aug 4 Yeast meeting 2002 Madison, WI (Aimee Dudley)

Aug3-6 ISMB02 & SIGSIM02 Edmonton (Matt Wright)

Sept 4, 2002 Serono (George Church).

Sept 13, 2002 DNA Microarrays in Biology and Medicine Lausanne, Switzerland (Doug Selinger)

Oct 2, 2002 Genome Sequencing and Analysis Conf. (GSAC) Boston (George Church)

Nov. 8, 2002   University of Massachusetts Boston, Genome "Systems models: Genotype to Phenotype" (George Church).

Dec 9-11, 2002 DARPA NSF San Diego, CA (Daniel Segre)

Dec 13-15, 2002 ICSB-3 Karolinska Institutet, Stockholm, Sweden (George Church).

Feb 7, 2003   Univ. of Texas Biomedical Sciences 7th Mini-Symposium, Houston. Keynote (George Church).

Feb 10-12, 2003 First DOE Genomes to Life Workshop, Arlington, VA, (George Church)

Mar 30 - Apr2, 2003 New Horizons in Genomics (DOE), Santa Fe, NM (George Church).

Apr 11-12, 2003 The Future of Human Nature, Boston (George Church).

May 13-16, 2003 DARPA/NSF BioComp meeting, Ft. Lauderdale, FL (Wayne Rindone)

May 17-18, 2003 Recomb 2003 DNA Sequencing Technologies and Computation, Stanford, CA (Jay Shendure).

May 18-22, 2003. American Society for Microbiology (ASM) Colloquium 215 on Systems Microbiology. Washington DC convention center.   4D and Optimality Models of Replicative Fitness (George Church)

Sep 16-19, 2003.Third Virtual Conference on Genomics and Bioinformatics, Access Grid locations (George Church)

Nov 13, 2003.Systeomics 2003 Boston. Keynote: Integrating Methods & Models to "Program" Replicating Systems (George Church)

*****************************************************************************
Friday D/J Seminars at Noon in WAB 563
Feb  15/02    Jake Jaffe
Mar  08/02    Aimee Dudley
Apr  05/02    Kyriacos Leptos
Apr  26/02    Yonaton Grad
May  03/02    Daniel Segre
May  31/02   Martin Steffen


Church Lab Journal Club

        **************  NOTE TIME AND ROOM CHANGE  MUdd 3rd floor Tues noon ************

The purpose of the Church Lab journal club is to explore various topics related to functional genomics and computational biology.  Suggested formats for presentations include analyses of relevant journal articles (current or historical), tutorials (software packages, web sites, statistical algorithms), brain-storming sessions on how to apply new techniques within the lab, etc.

Wednesday biological modeling journal discussions in Mudd 3rd floor conference room.    Journal articles should be distributed 1 week in advance.  Attendance is open to all.

DATE SPEAKER FOOD TOPIC
January 14, 00 Saeed                  Priya            Introduction to Clustering
January 28, 00 John                   Aimee            Single Nucleotide Polymorphisms
February 11, 00 Barak                  Felix            Modeling Baterial Chemotaxis
February 25, 00 Tzachi                 Paula            BLAST Theory
March 10, 00 Paula                  Tzachi           AlignACE
March 24, 00 Aimee                  Allegra          Evolution of the yeast Mitochondrial genome
April 7, 00 Abby’s Thesis Defense
April 21, 00          --------------------------
May 5, 00  Priya                  Nick             FRAP/FLIP analysis
May 26, 00 Adnan/Itai            Dan             Gene fusions in S. cerevisiae
June 9, 00 Doug                   Rob              Artificial life
June 23, 00 Jeremy                 Vasu             Genetic toggle switches
July 7, 00            --------------------------
July 21, 00 Tzachi                 Jeremy           Matlab tutorial - I
July 28, 00 Tzachi                 Priya            Matlab tutorial - II
Sept 22, 00  Nick                   Aimee            Flux Ratio Analysis
Oct 20, 00 Post-doc candidate for the Roth lab
Nov 3, 00 Cheng Li         Barak       Model based analysis of oligonucleotide DNA arrays
Nov 17, 00 Atul Butte          Novel bioinformatics techniques in functional genomics
Dec 1, 00 Jadwiga Bienkowska             A bayesian approach to protein fold recognition
Jan 12, 01 Fri Rob Mitra                                 Proteomics
Jan 26, 01 Fri WAB 4th floor conf. room   Patrik         Robustness SFI , Philip Ball.
Feb 9, 01 Fri Room C212 Savageau's genetic regulation papers
Feb 20, 01 Tue 11:30 Mudd 304A Overview of modeling methods: Stochastic, Bayesian,...
Mar 9, 01 Fri 2:00  Room C212 Nik Metabolic Control Analysis
Mar 20, 01 Tue 11:30   Mudd 304A Metabolic (& small world) Networks
Apr 3, 01 Tue 11:30 Mudd 304A Modularity : Wagner, G.P. and L. Altenberg 1996. Complex adaptations and the evolution of evolvability. Evolution 50:967-976 Arnone MI, Davidson EH 1997. The hardwiring of development: organization and function of genomic regulatory systems. Development 1997 May;124(10):1851-64
Apr 17, 01 Tue 11:30   Mudd 304A Peter K Petri Nets
May 1, 01 Tue 11:30   Mudd 304A Stochastics II
May 15, 01 Tue 11:30   Mudd 304A Differential Equation models
May 29, 01 Tue 11:30  Mudd 304A Integrated RNA & proteomics Ideker et al.
Jun 12, 01 Tue 11:30   NE43-518 Alexander Hartemink Networks & Expression
Jun 26, 01 Tue 11:30   Mudd 304A Allegra Petti: Emergent properties of networks of biological signaling pathways. Science 283: 381 (1999). Bhalla, et al.
10-Jul-2001 Tue 11:30   Mudd 304A Tzachi Pilpel: Regulatory element detection using correlation with expression. Nature Genet. 27, 167-171 (2001). Bussemaker, et al.
24-Jul-2001 Tue 11:30 Mudd 304A Peter & Patrik: Stochastic differential equations (&geometric Brownian Motion) (1) Tomas Bjork(2) Jan Nygaard Nielsen(3)Peter Laurence
21-Aug-2001 Tue 11:30 Mudd 304A Peter : complex networks by the Barabasi group

29-Jan-2002 Tue 11:30 Mudd 304A Patrik : Reka Albert and Barabasi's review on "Statistical mechanics of complex networks" Chapter VI (small-world networks) and VII (the scale-free model)

5-Feb-2002 Tue 11:30 Mudd 304A Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants Hin Yan Tong et al, Science Dec 14 2001: 2364-2368.

5-Mar-2002 Tue 11:30 AM Mudd 304A Whole-istic Biology Lisa Chong and L. Bryan Ray Science Mar 1 2002: 1661. Systems Biology: A Brief Overview Hiroaki Kitano Reverse Engineering of Biological Complexity Marie E. Csete and John C. Doyle

20-Mar-2002 Wed 10:00 AM Mudd 2nd floor conference (note new time!) A Genomic Regulatory Network for Development (Davidson et al Science 2002 ; more detailed background: Genomic Cis-Regulatory Logic (Science 1998) , Yuh et al Development

3-Apr-2002 Wed 10:00 AM Mudd 2nd floor conf: same topic as last time plus: Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control. Yuh et al (2001) Development 128 (5): 617

30-Apr-2002 Wed 10:00 AM Mudd 2nd floor conf (202): A preprint from Reka Alberts (see Patrik) and The segment polarity network is a robust developmental module. von Dassow, G. et al. Nature 406, 188-192 (2000)

15-May-2002 Wed 10:00 AM Mudd 2nd floor conf (202):
John : Topological & causal structure of the yeast transcriptional regulatory network N. Guelzim, S Bottani, P Bourgine & F Kepes. Nat. Gen 31:60-63.
Daniel : Network motifs in the transcriptional regulation network of Escherichia coli SS Shen-Orr, R Milo, S Mangan, U Alon. Nat Gen 31:64-68.
Debra : The identification of functional modules from the genomic association of genes Berend Snel, Peer Bork, and Martijn A. Huynen PNAS 99(9):5890-5895
Patrik : Reverse engineering gene networks using singular value decomposition and robust regression M. K. Stephen Yeung, Jesper Tegnr, and James J. Collins. PNAS 99:6163-6168

21-Jan-2003, Tue 10-11:30 am in the Folin Wu room (next to Canon conference room). Markus W. Covert and Bernhard Palsson Transcriptional Regulation in Constraints-based Metabolic Models of E. coli J. Biol. Chem. 2002 277:28058-28064

8-Jul-2003 Tue noon. Mudd 3rd floor conference.
Pfeiffer T, Schuster S, Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways. Science. 2001 Apr 20;292(5516):504-7. Erratum Science 2001 Aug 24;293(5534):1436. Supporting info.
Pfeiffer T, Bonhoeffer S. An evolutionary scenario for the transition to undifferentiated multicellularity. Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1095-8 . Supporting Info

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Old labmeeting lists: Nov98-Apr99 , Jul99-Dec99 , Dec99-Aug00 , Jul00-Dec00, Nov00-May01, Apr01-Oct01 , Apr01-Dec02 , May02-Feb03 .

A list of Genome related Meetings

Last update: 22-Apr-2003 by GMC.