NOTE: Mon/Thu meetings are restricted to lab members, rotation students, & collaborators with consent of the speaker. Guest lectures & Journal meetings are open to the scientific community. All meetings and topics are subject to change at the last minute so please check this page.
DATE
SPEAKER Title (please update your titles)
Jul 21 George Church Jul 24 Ed Fredkin Jul 28 Sung Choe Jul 31 Sasha Wait Aug 4 Aimee Dudley Aug 7 Steve Munroe Aug 11 Laura Stadman Aug 14 Jake Jaffe Aug 28 Jingdong Tian Sep 4 Gary Gao Sep 8 Kyriacos Leptos Sep 11 Adnan Derti Sep 15 Allegra Petti Sep 29 & Oct 2 move to 77 Ave Pasteur Oct 9 Peter Kharchenko Oct 16 Xiaoxia Lin Optimome & FBAome Oct 20 Dan Janse Oct 23 Dennis Vitkup Oct 30 Christian Hennig Genovoxx Nov 3 Nick Reppas Nov 6 Rhonda Harrison Nov 10 Nir Friedman Nov 13 Chris Varma Nov 24 Martin Steffen Dec 1 Dana Pe'er Dec 8 Jay Shendure Dec 11 Zhou Zhu & meeting reports: Xiaoxia, Sasha, Jill, Stan, Jingdong, Kun Dec 15 Mark DePristo prot folding Dec 18 Dan Segre Jan 5 Pingyu (Wong Lab) Bio.Net & image analysis Jan 12 Jun Zhu (1)lipofectamine polonies (2) bisulfite Jan 26 Pedro de Magalhaes Jan 29 Yonatan Grad enhancers Feb 2 Matt Wright Feb 9 Mike Jewett Stanford in vitro protein synth Feb 12 Joyce Macabea Feb 19 Sasha Wait Mar 1 No lab meeting DOE GTL in DCMar 08 Mon Christoph Dieterich & Stefan Roepcke (Guest speakers from Germany)
Apr 26 Mon
Partha Kanijilal Modeling using Orthogonal Transformation
Apr 29 Thu*** Bill
Agnew Neuro seminar on alternative
splicing; Goldenson 122
May 03 Mon Allegra Petti “Coordinating cell
functions”
May 06 Thu Andrey Gorin (ORNL) “Tandem MS”(Guest
Speaker)
May
10 Mon
Analysis
of Genomic Data Conference 77 Ave Pasteur
May 13 Thu *** Saeed
Tavazoie,
May
17 Mon
May 20 Thu Greg Porecca Personal Genome Sequences
May 27 Thu Esti Yager Lotem,
May
31 Mon Memorial Day
Jun
03 Thu No lab meeting (GMC in
Jun 07 Mon
German Cavelier, Genomic Information Systems Lab, Columbia Univ. "From
Computational Structural Biology to Computational Systems Biology"
Jun 10 Thu Synthetic Biology
meeting at MIT
Jun 14 Mon Kobi Benenson (Guest speaker) Molecular computer:'Smart
drug' in a test tube
Jun 17 Thu
Jun 21 Mon no meeting
Jun 24 Thu
Kyriacos Leptos MapQuant
Jun 28 Mon Dan Janse
Protein degrading drugs
Jul 1 Thu Jim Collins et al, Counters & Finite State
machines (NSF SynBio Summer challenge).
Jul 5 Mon no lab meeting
Jul 8 Thu
Jul 12 Mon Jan Korbel (Guest Speaker)
Jul 15 Thu Ben Williams Ploidy in istu
Jul 19 Mon
Jul
22 Thu
Kun Zhang How to do genome-wide
haplotyping in 10 days
Jul 26 Mon no lab
meeting.
Jul 29 Thu
Aug 02 Mon
Kavitha Venkatesan (Guest Speaker) "LSF/GRH transcription factor
family: A
Comparative Genomic Analysis of Evolution and Biological
Function"
Aug
05 Thu
Patrik D’haeseleer
Aug
09 Mon
Aug 12
Thu
Aug
19 Thu Dana Pe’er Lymphoid cell signaling; inferring causal
regulatory relations
Sep
09 Thu
Natasha Novikov Measures & models of in situ
chromosomal geometry in nuclei
Sep
13 Mon Daniel Segre
Optimal Regulation
Sep 16 Thu No lab
meeting (Roshashana)
Sep 20 Mon Xinshu (Grace) Xiao
(guest speaker) New System Identification Methods for Effective Probing of
Physiological and Biological Systems.
Sep 23 Thu Farren Isaacs (Guest Speaker) "Genetic
Modules: Autoregulatory Networks &
Riboregulators"
Sep 27 Mon Peter
Kharchencko The search for the universal
metabolite t6A
Sep 30 Thu*** Synthetic
Biology Meeting (Time is at
11:am)
Oct
14 Thu Even Forland (Guest
Speaker) Artificial Photosynthesis
Oct
18 Mon Chris Varma The
Pharmaceutical-Industrial Complex
Oct 21 Thu No Lab Meeting
Oct
25 Mon No lab meeting
Oct
28 Thu
No Lab Meeting
Nov
01 Mon
Nov
04 Thu
Matthew Wright 4D string theory of chromosomes
Nov
08 Mon
No Lab Meeting
Nov
11 Thu No Lab Meeting
Nov
15 Mon
Nov 16 Tue****Lab Meeting
with Chancellor Wrighton of WashU **(
Nov
18 Thu Sasha Wait Bio-quantum-computing
Nov
22 Mon Madeline Price
Methyl-epigenomics
Nov 25 Thu No
Lab Meeting
Nov
29 Mon Wayne Rindone,
Dec
02 Thu
Dec
06 Mon
Dat Nguyen Gene Expression Factorization
Dec
09 Thu
Jun Zhu Splicing Alternatives
Dec
13 Mon Allegra Petti SPIN
: Search for Pairwise INteractions
Dec 16 Thu No Lab Meeting
Dec
20 Mon
Kyriakos Leptos A day in the life of a
light harvester
Dec
23 Thu No Lab Meeting
Dec
27 Mon
No Lab Meeting
Dec
30 Thu
No Lab Meeting
Jan
03 Mon
No Lab Meeting
Jan
06 Thu
Jan 10 Mon Dana Pe’er Casual causality
Jan
13 Thu
Dan Janse
Jan
17 Mon
Jan
20 Thu
Wayne Rindone
Jan
24 Mon
Jan
27 Thu Zhou Zhu
Jan
31 Mon
Feb
03 Thu
Feb
07 Mon
Feb
10 Thu Kun Zhang
Feb
14 Mon
Peter Kharchenko
Feb
17 Thu
No Lab Meeting
Feb
21 Mon
No Lab Meeting
Feb
24 Thu
Feb
28 Mon
Madeline Price
Mar
03 Thu Chris Varma
Mar
07 Mon
Mar
10 Thu
Rhonda Harrison
Mar
14 Mon
Joseph Chou
Mar
17 Thu Matthew Wright
Mar
21 Mon Sasha
Wait
Mar
24 Thu
Mar
28 Mon
Mar
31 Thu
Mike Chou
Apr
04 Mon Abraham Rosenbaum
Apr
07 Thu
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 (
Feb 22, 2001 Showcase meeting:
Where do we go from HUGO? at The Pierre in NYC (
Mar 13, 2001. Experiencing
the Frontiers of Biomedical Technology HST Symposium, Boston, MA (
Apr 21-24, 2001 Recomb 2001 in Montreal (
May 8, 2001 CGR lecture in
Cambridge, MA (
May 24, 2001
Mass. Biotech Council Science Symposium session "MINING THE
GENOME", 2:45-4:30pm at the Westin Copley Place, Boston. (
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 (
Jul 21-25, 2001 ISMB 2001 in Copenhagen, Denmark (Tzachi Pilpel)
Aug 23-26, 2001
Santa Cruz Human Genome Workshop at UCSC (
Sep 12, 2001 New England Bioinformatics Group (NEBiG)
and Abbott Bioresearch Center: Microarray Data Analysis Toward Understanding
Autoimmunity. Worcester, MA (
Sep 13-15, 2001 PNL, SDSC, and Sun:
Computational Challenges In The Post-Genomic Age-II. Durham, NC. (
Nov 27-Dec 1,
2001 DARPA BioCOMP meeting Monterey, CA (
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 (
Jan 27-31, 2002 DOE Genome Meeting, Santa Fe, NM (Rob Mitra & Wayne Rindone)
Jan 31,
2002 Whitehead Institute Functional
Genomics Seminar Series (
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." (
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." (
Feb 27,
2002 HMS Cannon Room 4:00 to 6:00 PM
BBS minisymposium on Functional Genomics & Informatics (
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." (
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" (
May 22-24,
2002 Washington DC DARPA IPTO
Bio-Computation PI Meeting (
Jun 4, 2002
Archemix at 11:00 AM "Polonies" (
Jun 11, 2002
Yale at 4:00 PM "Systems models and measures connecting genotype to
phenotype" (
Jun 19, 2002 Harvard CGR at 3 PM.
"From proteomics to a highly interconnected model of replication and
selection." (
Jun 24-28, 2002 MIT
20.01s Bioinformatics: Principles, methods and applications. (
July 7-12, 2002
Vienna 14th International
Organization for Mycoplasmology (IOM) Congress (
July 23, 2002
Sequencing and resequencing the biome. Pooks Hill Bethesda Marriott (
July 26, 2002
Fri at 9:00 AM Humboldt Univ. & Boston Univ. Bioinformatics
workshop in Boston. Keynote: "Biosystems Measures and Models of
Reproductive Fitness" (
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 (
Sept 13, 2002 DNA Microarrays in Biology and Medicine Lausanne, Switzerland (Doug Selinger)
Oct 2, 2002 Genome Sequencing and
Analysis Conf. (GSAC) Boston (
Nov. 8,
2002 University of Massachusetts
Boston, Genome "Systems models: Genotype to Phenotype" (
Dec 9-11, 2002 DARPA NSF San Diego, CA (Daniel Segre)
Dec 13-15, 2002 ICSB-3 Karolinska
Institutet, Stockholm, Sweden (
Feb 7, 2003 Univ. of Texas Biomedical Sciences 7th Mini-Symposium,
Houston. Keynote (
Feb 10-12, 2003 First DOE Genomes to Life Workshop,
Arlington, VA, (
Mar 30 - Apr2,
2003 New Horizons in Genomics
(DOE), Santa Fe, NM (
Apr 11-12, 2003 The Future of Human
Nature, Boston (
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 (
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 (
Aug 26-28, 2003 Genomics and
Health: A Practical Guide to the Genomics Revolution Boston, MA (
Sep 16-19, 2003.Third
Virtual Conference on Genomics and Bioinformatics, Access Grid locations
(
Oct 22, 2003.
10:30 AM Novartis
Institutes for BioMedical Research Boston. Models and Measures of Single
Molecules in Human Physiology (
Feb 4, 2004. 9:30 AM. Bio-SPICE Design & Synthesis of useful replicating
biosystems. DARPA Meeting Adelphi, MD (
Feb 5, 2004. 4 PM. Measures,
models and synthesis of "optimal" replicating biosystems MIT
Biological Engineering Divis. (
Mar 1-2, 2004. DOE GtL
meeting. Marriott Wardman Park, Washington, DC (
Mar 3-4, 2004. MolTools meeting
Stockholm (
Mar 10,2004 TJU
CBAT, Phildelphia (
May 7,8, 2004. HMS Systems
Biology Retreat."Optimality in Synthetic Biosystems" (
May 10-11, 2004. International
Conference on Analysis of Genomic Data, The Conference Center at HMS, 77
Ave. Pasteur, Boston. Modeling time-series and perturbation analyses for RNA
and proteomics data streams. (
May 11, 2004 at 4-6 PM. CIMIT,
Boston. New Tools for Genome Engineering (
May 12, 2004 Broad
Inst. Seminars Computational Biology. Cambridge,MA (
May 14, 2004 ACLU Genomics Technology and Genetic Databases. Boston, MA (
May 20, 2004 Bauer Center, Cambridge, MA (
May 24, 2004 Dept.
of Genome Sciences, Univ. Washington, Seattle, WA (
Jun 2, 2004 Dept.
of Genetics. Washington Univ., St. Louis, MO (
Jun 10-12,2004 Synthetic Biology.
MIT, Cambridge MA (Geo.Church & Jingdong Tian)
Aug 17, 2004 ISB
Seminar (
Oct 1-3, 2004 SAGE2004
"Decoding the Omes" meeting, Boston Fairmont Copley Plaza Hotel. Keynote:
"New technologies and models for integrative systems biology." (
Oct 4, 2004 Berkeley
Synthetic Biology Dept. 100 Lewis Hall at 4 PM. (
Oct 6, 2004 U.
Wisconsin Omics Seminar Series. (
Oct 12-13, 2004 DARPA BioComp.
(
Oct 20-22, 2004 NHGRI CEGS
Annual meeting. (
Oct 22,2004 SACNAS meeting
"Personal Genomics and Synthetic Biology" (
Nov 9,2004 Univ. Texas Austin (
Nov 8, 2004 Amer.
Inst. of Chemical Engineers (AIChE) Symposium on "Bioinformatics and
Functional Genomics" , Austin TX, (
Dec 1, 2004 MGH-E Cancer
Center (
Apr 13, 2005 Duke University "Personal Genome/Transcriptome
Sequencing"(
May 4, 2005 CHI
Microarrays in Medicine Meeting, Boston WTC (
Jan 5-8, 2006 Genetics
Society of America, San Diego "The Genetics of Synthetics" (
*****************************************************************************
Friday
D/J Seminars at Noon in WAB 563
Feb 15/02
Mar 08/02
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
22-Jul-2003, Tue
Noon-2pm Mudd 3rd floor conference room. Westerhoff HV, Hellingwerf KJ, Van Dam
K. Thermodynamic
efficiency of microbial growth is low but optimal for maximal growth rate. Proc
Natl Acad Sci U S A. 1983 Jan;80(1):305-9
*************************
Old labmeeting
lists: Nov98-Apr99
, Jul99-Dec99
, Dec99-Aug00
, Jul00-Dec00,
Nov00-May01,
Apr01-Oct01
, Apr01-Dec02
, May02-Feb03
, May02-Aug03
.
A list of Genome related Meetings
Last update:
20-Oct-2003 by GMC.