NavigationBioinformatics for Cell Biologists (Spring -08)Course Information DBRM
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50 Recent Changes in ResearchSchool/CC1837_Y08S Web retrieved at 19:31 (GMT)
GroupOne
in ResearchSchool.CC1837_Y08S
This is the page for Group Smc1 (Christine, Charlotte and Giulia) Introduction SMC proteins represent a large family of ATPases that participate in many aspects ...
changed on 13 Jul 2009 - 12:00 by MartinDahlo
Splicing
in ResearchSchool.CC1837_Y08S
Splicing Practical In your quest to understand gene regulation instem cells you sequenced a cDNA library from mouse ES cells and found anapparent splice variant of ...
changed on 13 Jul 2009 - 12:00 by MartinDahlo
Schedule
in ResearchSchool.CC1837_Y08S
Day 1: 12 May 2008 09.00 09.45 (Room D224 at CMB, von Eulers v 3) Lecture: Introduction to the course, practical issues #8211; Matti Nikkola 09.45 10.15 Coffee ...
changed on 13 Jul 2009 - 12:00 by MartinDahlo
Practicals
in ResearchSchool.CC1837_Y08S
The course practicals cover following topics: Database searching, Genome browsers (Ensembl and UCSC) Sequence analysis tools (nucleic acid and protein sequence analysis ...
changed on 13 Jul 2009 - 12:00 by MartinDahlo
GroupFour
in ResearchSchool.CC1837_Y08S
Group four Bioinformatics analysis of mixed lineage leukemia (MLL) Masako Harada, Department of Oncology and Pathology, CCK, KI Goncalo Castelo Branco, Department ...
changed on 13 Jul 2009 - 12:00 by MartinDahlo
WebStatistics
in ResearchSchool.CC1837_Y08S
Statistics for nop ResearchSchool/CC1837 Y08S Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors ...
changed on 01 Jul 2009 - 13:56 by TWikiAdminGroup
Resources
in ResearchSchool.CC1837_Y08S
This page contains links to important bioinformatics resources on the internet. Genomes and Gene Annotations: USCS Genome Browser Ensembl Genome Browser NCBI Genome ...
changed on 27 Apr 2009 - 13:34 by RickardSandberg
YunPing
in ResearchSchool.CC1837_Y08S
Yun Ping Lim has worked on the following projects: B. T. K. Lee, L. Liew, J. Lim, J.K.L. Tan, T.C. Lee, P.S. Veladandi, Y.P. Lim , H. Han, G. Rajagopal, N. L. Anderson ...
changed on 16 Mar 2009 - 15:03 by LimYunPing
WebPreferences
in ResearchSchool.CC1837_Y08S
nop ResearchSchool/CC1837 Y08S Web Preferences The following settings are web preferences of the ResearchSchool/CC1837 Y08S web. These preferences overwrite the ...
changed on 17 Jul 2008 - 06:40 by MartinDahlo
WebHome
in ResearchSchool.CC1837_Y08S
The course provides essential, practical knowledge about computational and bioinformatics methods in biology with focus on developmental biology. The integration of ...
changed on 16 Jul 2008 - 05:53 by MartinDahlo
Team
in ResearchSchool.CC1837_Y08S
The course team: Matti Nikkola (course director), DBRM Yun Ping Lim (course examiner), NUS Singapore Carsten Daub, RIKEN in Yokohama Erik Arner ...
changed on 10 Jul 2008 - 09:17 by MartinDahlo
Contact
in ResearchSchool.CC1837_Y08S
Contact The c ourse director is Rickard Sandberg, email rickard.sandberg #64;ki.se at the Department of Cell and Molecular Biology at Karolinska Institutet. MattiNikkola ...
changed on 08 Jul 2008 - 12:04 by MattiNikkola
Syllabus
in ResearchSchool.CC1837_Y08S
Syllabus The syllabus for the course. MattiNikkola 08 Jul 2008
changed on 08 Jul 2008 - 12:02 by MattiNikkola
SebastiansAnalysis
in ResearchSchool.CC1837_Y08S
By looking into the USCS Genome Browser (http://genome.uscs.edu/) we are able to find out general features about Notch1, such as the locus on the genome, different ...
changed on 03 Jul 2008 - 07:12 by MartinDahlo
BioinfoAnalysisCont
in ResearchSchool.CC1837_Y08S
MasakoHarada 16 May 2008 miRNAs and other class of non coding RNAs miRNA target sites Using USCS browser with TargetScan, miRNA target sites were predicted on 3 ...
changed on 03 Jul 2008 - 07:12 by MartinDahlo
Examination
in ResearchSchool.CC1837_Y08S
Information about examination The exam takes places on Tuesday, May 20 in the seminar room D224 at CMB. The exam consists of project presentations by the course students ...
changed on 03 Jul 2008 - 07:12 by MartinDahlo
SamplePage
in ResearchSchool.CC1837_Y08S
Project Title: Bioinformatics analysis on Bryostatin By: Lim Yun Ping Introduction The marine ecosystem has increasingly been the focus of interest for new discoveries ...
changed on 01 Jul 2008 - 13:14 by MartinDahlo
GroupTwo
in ResearchSchool.CC1837_Y08S
Group Two (Maria, Tony, Marina) proudly presents: The Role Of Cux2 During Development And Disease Introduction Structure of the Cux2 Gene and Protein Tissue specific ...
changed on 01 Jul 2008 - 13:14 by MartinDahlo
GroupThree
in ResearchSchool.CC1837_Y08S
Group three Notch 1 (Heather, Sana, Sebastian) Introduction Notch signalling is a very important signalling pathway in both development and disease. First identified ...
changed on 01 Jul 2008 - 13:14 by MartinDahlo
SeqAnalysisPractical
in ResearchSchool.CC1837_Y08S
ErikArner 13 May 2008 Sequence analysis tools #8211; practicalThe purpose of this practical is to give a basic understanding of common tools for similarity searching ...
changed on 01 Jul 2008 - 13:14 by MartinDahlo
SNPPractical
in ResearchSchool.CC1837_Y08S
SNP Bioinformatics lab You are studying hemochromatosis and have a candidate gene for the disease. There is an EST sequence from a patient and you are trying to find ...
changed on 01 Jul 2008 - 13:14 by MartinDahlo
HMGA2
in ResearchSchool.CC1837_Y08S
Your lab has been studying a specific lymphoma in which the chromatin associated protein High Mobility Group A2 (Hmga2) is implicated. The gene is known to be expressed ...
changed on 01 Jul 2008 - 13:14 by MartinDahlo
ReceptorExpression
in ResearchSchool.CC1837_Y08S
HeatherMain 19 May 2008 UniGene EST expression analysis Notch1 ............................................................................................... ...
changed on 20 May 2008 - 06:25 by SebastianHildebrand?
NewPage2
in ResearchSchool.CC1837_Y08S
MariaLotka 19 May 2008 Two genes, and p27Kip1 , have been shown to be directley regulated by Cux2. To search for CCAAT binding motifs in the promoter sequences ...
changed on 20 May 2008 - 06:01 by MariaLotka?
MoreDetails
in ResearchSchool.CC1837_Y08S
SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.Amino acid sequence homology of SMC proteins between species ...
changed on 20 May 2008 - 04:16 by GiuliaGaudenzi?
NewPage4
in ResearchSchool.CC1837_Y08S
AnthonyOosterveen 19 May 2008 Single Nucleotide Polymorphism We searched for variation in sequences in the Cux2 locus in the human genome. We found four polymorphisms ...
changed on 19 May 2008 - 21:36 by AnthonyOosterveen?
NewPage3
in ResearchSchool.CC1837_Y08S
AnthonyOosterveen 19 May 2008 The miRNA target sites for Cux2 To investigate if there are any miRNA against Cux2 we used the UCSC genome browser and looked at the ...
changed on 19 May 2008 - 21:24 by AnthonyOosterveen?
NewPage6
in ResearchSchool.CC1837_Y08S
MariaLotka 19 May 2008 Discussion Cux2 is a transcription factor containing four well conserved DNA binding domains, three Cut domains and one Homeodomain. ...
changed on 19 May 2008 - 19:45 by MariaLotka?
TheGene
in ResearchSchool.CC1837_Y08S
The Cux2 gene Human Cux2 is located on the strand of chromosome 12. There are two alternative splicing variants of Cux2, using different first exons. The Refseq transcript ...
changed on 19 May 2008 - 19:23 by MarinaFranck?
NewPage
in ResearchSchool.CC1837_Y08S
We used UCSC Genome B rowser to identify conserved regions and transcription factor binding sites within these. The most well conserved region is the one surrounding ...
changed on 19 May 2008 - 19:05 by MarinaFranck?
GcBExpression
in ResearchSchool.CC1837_Y08S
GoncaloCasteloBranco 17 May 2008 Gene expression In order to determine the general expression pattern of MLL in different human cell and tissues. we perform a query ...
changed on 19 May 2008 - 16:52 by GoncaloCasteloBranco?
TranscriptionFactorBindingSites
in ResearchSchool.CC1837_Y08S
HeatherMain 19 May 2008 Regulation of Notch Signalling Analysis of aligned/conserved TFBS in the first 1000bp of the Notch1 promoter using rvista 2.0. Nothing amazing ...
changed on 19 May 2008 - 16:42 by HeatherMain?
GcbCisregulatoryregions
in ResearchSchool.CC1837_Y08S
GoncaloCasteloBranco 17 May 2008 Cis regulatory regions of MLL Conservation In order to identify cis regulatory regions of the MLL genes, we first analyzed in the ...
changed on 19 May 2008 - 16:41 by GoncaloCasteloBranco?
NewPage5
in ResearchSchool.CC1837_Y08S
MariaLotka 19 May 2008 To determine the expression pattern of Cux2 in human tissue we perform a query against the protein in SymAtlas, a database for published experimental ...
changed on 19 May 2008 - 16:39 by MariaLotka?
SeeAlignment
in ResearchSchool.CC1837_Y08S
GiuliaGaudenzi 19 May 2008
changed on 19 May 2008 - 15:09 by GiuliaGaudenzi?
GcbgenomebrowserESTmRNAGene
in ResearchSchool.CC1837_Y08S
GoncaloCasteloBranco 17 May 2008 MLL transcripts The MLL gene spans approximately 89 kb of DNA and contains 36 exons exons. Analysis of MLL in the UCSC genome browser ...
changed on 19 May 2008 - 15:06 by GoncaloCasteloBranco?
GcBIntroduction
in ResearchSchool.CC1837_Y08S
GoncaloCasteloBranco 17 May 2008 Introduction MLL MLL (mixed lineage leukemia) is a large gene that spans approximately 88 kb of DNA and contains 36 exons (see ...
changed on 19 May 2008 - 15:01 by GoncaloCasteloBranco?
TheRoleOfCux2DuringDevelopmentAndDisease
in ResearchSchool.CC1837_Y08S
AnthonyOosterveen 19 May 2008 Introduction In Drosophila embryos, Cut is a Notch signaling target gene required for external sensory organ development of cells ...
changed on 19 May 2008 - 14:26 by MarinaFranck?
SequenceAlignment
in ResearchSchool.CC1837_Y08S
CharlotteKarlsson 16 May 2008 msa.pdf
changed on 19 May 2008 - 13:44 by CharlotteKarlsson?
CorneliadeLange
in ResearchSchool.CC1837_Y08S
ChristineOberg 16 May 2008 Disease linkage An X linked form of the disorder Cornelia de Lange syndrome can be caused by mutations in the SMCa1 gene (OMIM). Cornelia ...
changed on 19 May 2008 - 13:02 by ChristineOberg?
SanaSNP
in ResearchSchool.CC1837_Y08S
PNG SanaEltayeb 19 May 2008
changed on 19 May 2008 - 12:16 by SanaEltayeb?
ClickHere
in ResearchSchool.CC1837_Y08S
GiuliaGaudenzi 19 May 2008 Homo sapiens nop SMC1A Mus musculus SMC1A Saccharomyces cerevisiae SMC1
changed on 19 May 2008 - 10:44 by GiuliaGaudenzi?
CN3D
in ResearchSchool.CC1837_Y08S
GiuliaGaudenzi 19 May 2008 Homo sapiens nop SMC1A Mus musculus SMC1A Saccharomyces cerevisiae SMC1
changed on 19 May 2008 - 09:18 by GiuliaGaudenzi?
MultipleSequenceAlignment
in ResearchSchool.CC1837_Y08S
clustalw2.txt The sequences used are here. notch human.txt SanaEltayeb 19 May 2008
changed on 19 May 2008 - 07:58 by SanaEltayeb?
GoncaloCastelobranco
in ResearchSchool.CC1837_Y08S
GoncaloCasteloBranco 17 May 2008 Introduction MLL Source (Entrez Gene) MLL in disease Recurring chromosomaltranslocations involving chromosome 11, band ...
changed on 17 May 2008 - 07:03 by GoncaloCasteloBranco?
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