ils 2010 it
DESCRIPTION
KNOWLEDGE BASED PLATFORM FOR BIOTECHNOLOGY http://www.usamvcluj.ro/html/cercetare/platforma/TRANSCRIPT
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PROF. DR DORU PAMFILPROF. DR DORU [email protected]@usamvcluj.roHEAD of ILSHEAD of ILSCalea Manastur 3-5, Calea Manastur 3-5, 400372 Cluj-Napoca400372 Cluj-Napocawww.usamvcluj.rowww.usamvcluj.ro
INSTITUTE OF LIFE SCIENCE INSTITUTE OF LIFE SCIENCE ILSILS
INSTITUTE OF LIFE SCIENCE INSTITUTE OF LIFE SCIENCE ILSILS
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GeneralGeneral
Founded in 1869Faculty of AgricultureFaculty of Animal Science & BiotechnologyFaculty of HorticultureFaculty of Veterinary Medicine
INSTITUTE OF LIFE SCIENCE (ILS) - 2007
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WHYWHYWHYWHY
SPINE – Structural Proteomics IN Europe
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RationalRational Capture: best practices in the development of skill
standards, certification and curriculum in regionally
specialized biotech training centers Disseminate: make available replicable models to
community colleges across Romania
CompositionComposition Team: 24 center of Excellence/Expertise regionally Collective purpose: a national resource
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TeamTeam
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ILS Partnerships with USAMV
USAMVUSAMV
Universities at Cluj-NapocaUSAMV - ILS Grove Center
University of Medicine and Phramacy “Iuliu Hatieganu”
Technical University of Cluj-Napoca
Faculty of Veterinary Medicine
Institute of Cancer Research “dr. I. Chiricuta”
Faculty of Horticulture
Faculty of Animal Science & Biotechnology
University of Babes Bolyai
Faculty of Agriculture
Located in the heart of Transylvania
Full-time undergraduate programe, distance learning, e-learning and postgraduate program (master courses, joint doctoral)
Interdisciplinary Collaboration is a Hallmark of ILS Teaching & ResearchInterdisciplinary Collaboration is a Hallmark of ILS Teaching & Research
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Concept and Expansion of ILSINSTITUTE OF LIFE SCIENCE CLUJ-
NAPOCA
ILS – Innovation
ILS –Research & Co-operation
ILS – Facility
ILS – Factors of Success
ILS – Concept
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Demand-Driven ProcessDemand-Driven Process
opportunity
implementation
results
sustainability
needs
Approximately 90% Integration into the Workforce Approximately 90% Integration into the Workforce
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Partnerships are EssentialPartnerships are EssentialPartnerships are EssentialPartnerships are Essential
College
Workforce Development
Industry
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VISION & MISSIONVISION & MISSION
VISION
Cluj-Napoca ILS is the preferred location for new
business opportunities through knowledge creation
in the Agriculture, Food Science, Biotechnology,
Pharmaceutical, and Health Care
ILS the preferred Partner for Biotechnology
Enterprises
MISSION - The Science & Technology Development
Program works to strengthen Cluj universities
so they can serve as foundations for
biotechnology economic development by:• Enhancing the ability of universities to attract federal funding
• Funding research of commercial interest
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PRIORITIESPRIORITIES
Provide forum for integration
Promote ILS - BioTech (press, conf. etc)
Grow Biotechnology Research (pilot plant)
Educational Development (PhD, MSc., Cert.,
Awareness)
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Infrastructure for Universities
Encourage multidisciplinary
collaborative research
Support faculty
recruitment
Provide venues for intellectual exchange
Provide core facilities & equipment
Move of IP from labto commercialization
Enhance high performance computing capabilities
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om
ics
Transcriptomics
High throughput screening
Moleculebank
Genomics / proteomics
Sclerosis Multiplex, POCD, Alzheimer
Oral antidiabetics
Sa
fety p
ha
rma
colo
gy
Chemiotherapy Nanotechnology
Proteomic platform
Microbial genomics / proteomics / transcriptomics
Fermentation/Bioprotect
DNS → animal breeding
Molecular farming
Safety pharmacology
Microarray platformBio
me
dica
l m
ea
sure
me
nt
Ag
ro-b
iote
chn
olo
gy
Metabolomics
Enriched egg
Technology Transfer ManagementBiomedical Informatics
Joint technology platforms
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ORGANISATION – ILS – CORE LABORATORIESORGANISATION – ILS – CORE LABORATORIES
Cell culture
Transgenic animal model
DNA Sequencing
Post-genomic
Histology, cytology, morphology
Imaging
Glassware & Lab maintenance
Microarray laboratory
Proteomics Laboratory
Bioinformatics & Biostatistics
High throughput analytical chemistry
Translational research
System biology
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Biotechnology
Medicine:
-Therapeutics-Diagnostics
-Vaccines-Early Diagnosis
Agriculture
-GMO -Plants
-Nutrition
Environment
Detection and decompositionof pollutants
Industrial Production
-Manufacturingprocesses
-Use of naturalmaterial
Use of marine organisms
-Cosmetics-Drugs
-New materials
ILS – Research & Co-operationILS – Research & Co-operation
BIOTECHNOLOGY
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Indication areas at ILS
- Diseases of the Central Nervous System;- Inflammatory Diseases; - Cancer;- Proteomics- Probiotics, Functional Food.
Indication areas are based on:
- Regional resources, know how and research co-operations within the local institutes and companies
- Global market expectations
Focus increases the efficiency of Innovation
ILS – Research & Co-operationILS – Research & Co-operation
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Alliance of local members of the cluster by competition and supply relationships or common interests
examples at ILS:
ILS – Research & Co-operationILS – Research & Co-operation
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ILS wish to establishe a global network
ILS – Research & Co-operation
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Institutional PPPFocused managementPermanent monitoring of the life cycle of the facilityOptimized risk allocationProfit oriented facility conceptMarket orientationSpecific Know How
- Real estate- Economics- Science
Interface between politics and business
ILS – Factors of SuccessILS – Factors of Success
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R & D
Production
Human Resources
ILS
Finance & Risk Capital
Infra - structure
one stop agency
Management Services & Consulting
Political support
ILS – Factors of SuccessILS – Factors of Success
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ILS – Factors of SuccessILS – Factors of SuccessReasons for a settlement within FIZ
0,0
1,0
2,0
3,0
4,0
5,01) Infrastructure
1a) Airport / Access to motorway network
1b) Access to public transport connection
1c) Architecture
2) Financial Center
2a) Bourse
2b) VC/PE
2c) Corporate Capital
3) Research & Developement
3a) Access to academicresearch (UNI/MPI)
3b) IP/technology transfer
3c) International cooperations
in identified areas
4) Industry
4a) Production
4b) Commercialization
4c) Clustering
ILS
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POLICY MAKERS
ACADEMIC PARTNERS
ILS
University of Medicine and
Pharmacy
University of Agricultural Sciences and Veterinary Medicine
University of Babes Bolyai
Technical University
County Hospital of Cluj
Institute of Oncology
Institute of Public Health
Institute of Public Health
Veterinary State Direction
EC
NASR CNCSIS
Start-up company
Spin-off company
PUBLIC PARTNERS
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StrengthsStrengths Research connected to teaching and students
Several internationally strong research groups
Two large research units From Data to Knowledge - DtK
Institute for Information Technology - (Basic Research Unit -
BRU)
Research infrastructure
Good success in the competition of research funding
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OpportunitiesOpportunities
Still stronger networking with international scientific
community Joint European projects
International recruiting
Still stronger co-operation within Cluj campus Other departments of the Faculty, University
UMF, UBB, UT-CN,
IOCN, Hospitals, University’s Cliniques
Still stronger co-operation with other sciences Bioinformatics
Functional Genomics, Proteomics
Still stronger interaction with society Industrial innovations
open-source source
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Group Ioana Neagoe-Al. Irimia-P Virag-I Brie-C Braicu-O Tudoran
Group Doru Pamfil -Ioana Petricele-Iulia Francesca Pop-Cristian Sisea-CT Socol
Group Ramona Suharoschi- C Semeniuc-vacancy-S Andrei-V Chedea-R PetrutGroup Manuela Banciu - MT Chiriac-HL Banciu-LB Tudoran-J Endre
Group Liviu Marghitas- Dan Dezmirean-O Bobis-Laura Stan-Otilia Popescu-vacancy
Subgroup Tibor Krausz - A Gionis/SA- F Afrati/FDK- N Haiminen/FDK
Subgroup Maria Tofana -S Socaci-E Mudura-C Muresan-S Muste-R Cheleman-D Truta-D Tic-AM Pop-S Man-V Muresan
Internal collaborations
Group Laurian Vlase - DS Popa-D Muntean-AS Porfire-R Iovanov
SubgroupOvidiu Balacescu - L Balacescu
Subgroup Ioan Groza - A Gionis/SA- F Afrati/FDK- N Haiminen/FDK
Subgroup Raul Malutan -vacancy
Group Sorin Apostu - AM Rotar-C Lazar
Group Cornel Catoi - A Gal-Taulescu-I Rus
Group I Groza - I Moraru
Subgroup Carmen Socaciu- A Stanila-D Preda-D Vodnar-vacancy
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External collaborations
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Research TopicsResearch Topics
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EU projects
INTERREG IVC 0340R1 - Common Land for
sustainable management, COMMONS
7th EU Frame Programme FP7-OC-2007-2-1705 –
Molecular farming, MOLFARM
ANCS CG 8/0606/2008 – Investigation of ornamental
germplasm exchange of breeding technology
6th EU Frame Programme FP6 IRC, no. 510512 -
Inovation Relay Centre
Leonardo, RO/03/B/NT/BB/17056, Quality
Management Network for CEECs (Central and East
European Countries) - QUAMANCEEC.
5th EU Frame Programme FP5-QLK3 CT-
2002-02140 TRANSVIR
4th EU Frame Programme
FP4-INCO/COPERNICUS PL 96-6084 Study
of growth regulation in plum tree – TUTOR
Leonardo: RO/2004/PL 91176/S
Leonardo: RO/2002/PL 89074
Mondial Bank BCUM, nr. 35/2000 -
LAMARGEN
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MICROARRAY FACILITYMICROARRAY FACILITY
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Why analyze so many genes?Why analyze so many genes?
<10% of the human genome has been studied at the level of gene function. 40,000 odd genes represent the pool of remaining drug targets
Patterns/clusters of expression are more predictive than looking at one or two prognostic markers
Increased accuracy/confidence
Unbiased. Empiric. Holistic. Independent of “flawed” hypotheses
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Microarray facility: tasksMicroarray facility: tasks
Microarray production
Protocol development
User support
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User support: philosophyUser support: philosophy
CollaborationAs many groups as possibleTrain users
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Spotted cDNA microarraysSpotted cDNA microarrays
Advantages Lower price and flexibility Simultaneous comparison of two related biological
samples (tumor versus normal, treated cells versus
untreated cells) ESTs allow discovery of new genes
Disadvantages Needs sequence verification Measures the relative level of expression between 2
samples
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Spotted arraysSpotted arrays
1 nanolitre spots90-120 um diameter
384 well source plate
chemically modified slides
steel
spotting pin
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spotted material: gene specific oligos (70-mer) or cDNAs
oligos for the external controls: for various purposes
(van de Peppel et al., 2003, EMBO reports, 4, p.387-393)
User support: arraysUser support: arrays
suitable for two channel (Cy3 / Cy5) experiments; i.e. two sample comparison
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44Preluat de la J Assouline, Genome-wide measurement of gene expression
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MIAME - cADN microarrayMIAME - cADN microarray
6 STEPS of a Microarray Experiment
Array
• Array design
Hybridization protocol
• Statistical analysis • Data mining
• Image acquisition and quantification• Database building • Filtering • Normalization
HybridizationSample
(S. Sansone)
MIAME • Sample QC• Sample treatment• Metadata• mARNs Extraction protocol QC• Target preparation (labeling) - QC
QC
QC
QC
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From Macgregor and Squire, Clinical Chemistry, 2002
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RNA/DNA quality and quantity assesment
Spectrophotometer: quantitycDNA synthesis (>30 µg total RNA)
RNA amplification (> 1 µg total RNA)
Total RNA
Bioanalyzer: integrity of RNA
(labeled) cDNA
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Cy3 Cy5
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Cy-3 Cy-5 Gene D Over-expressed in normal tissue
Gene E Over-expressed in tumour
• Biomarkersof prognosis
• Genes affecting Treatment
Response
Data quality check :• QQCC: QC
NormalizedRaw data
normalisation
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Data storage and advanced analysis :• Genespring 6.0 / Genet + BASE:
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Microarray Applications (some)
Can identify new genes implicated in disease
progression and treatment response (90% of our
genes have yet to be ascribed a function) Can assess side-effects or drug reaction profiles Can extract prognostic information, e.g. classify
tumours based on hundreds of parameters rather than 2
or 3 Can detect gene copy number changes in cancer
(array CGH) Can identify new drug targets and accelerate
drug discovery and testing ???
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The challenges of microarrays
Acquisition of high quality clinical samples,
tumor and normal tissues High Quality RNA Experimental design: what to compare to what? Data analysis -1: what to do with the data? Data analysis -2: How do to it?
Very large number of data points
Size of data files
Choice of data analysis strategy / algorithm /
software
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Experimental DesignExperimental Design
Choice of reference: Common (non-biologically
relevant) reference, or paired samples? Number of replicates: how many are needed? (How
many are affordable...?). Are the replicate results going
to be averaged or treated independently? Dye switches? Choice of data base: where and how to store the data?
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What is a “dye switch”:What is a “dye switch”:What is a “dye switch”:What is a “dye switch”:
One slide with experimental sample labeled with Cy5, and reference sample labeled with Cy3 (“straight”)
Replicate slide with experimental sample labeled with Cy3, and reference sample labeled with Cy5 (“switch”)
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Data Pre-processingData Pre-processing
Filtering: background subtraction? Low intensity spots? Saturated spots? Low quality spots (ghosts spots, dust spots etc).
Filtering or flagging?
Outliers?
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Data Pre-processing : NormalizationData Pre-processing : Normalization
Housekeeping genes/ control genes
Intensity dependent (most commonly used): global intensity or global ratio, calculates a single normalization factor
Intensity independent (LOWESS – Locally Weighted Scatter plot Smoother) calculates a function
Global array or Sub-array
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Microarray data analysis Microarray data analysis
Scatter plots of intensities of tumor samples versus normal samples: quick look at the changers and overall quality of microarray
Supervised versus unsupervised analysis
Clustering: organization of genes that are similar to each other and samples that are similar to each other using clustering algorithms
Statistical analysis: how significant are the results?
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log/log
scatter plot
UP
DOWN
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2 dimensional hierarchical (“Eisen”) clustering (Eisen et al, PNAS (1998), 95, p. 14863)
2 dimensional hierarchical (“Eisen”) clustering (Eisen et al, PNAS (1998), 95, p. 14863)
Unsupervised: no assumption on samples
The algorithm successively joins gene expression profiles to form a dendrogram based on their pair-wise similarities.
Two-dimensional hierarchical clustering first reorders genes and then reorders tumors based on similarities of gene expression between samples
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Two dimensional hierarchical (“Eisen”) ClusteringTwo dimensional hierarchical (“Eisen”) Clustering
From:
Dhanasekaran et al.
Nature, 421, p.822.
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Significance Analysis of Microarrays (SAM)Significance Analysis of Microarrays (SAM)
Supervised learning software for genomic expression data mining
Developed at Stanford University, based on the paper of Tusher et al PNAS (2001) 98, p. 5116.
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What SAM does:What SAM does:
SAM assigns a score to each genes on the basis of the change in gene expression relative to the standard deviation of repeated measurements.
For genes with scores above a certain threshold (set by the user), SAM uses permutations of the repeated measurements to estimate the % of genes identified by chance = the false discovery rate (FDR).
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Every cell in the body has the same genetic constitution. In cancer cells there is usually acquired aberrant DNA
Development of “cancer genomics” to better understand the molecular basis of acquired genetic change
Breast
OvaryProstate
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TEAM WORK in prostate cancer at the IOCN-UMF-USAMVTEAM WORK in prostate cancer at the IOCN-UMF-USAMV
Clinicians / Pathologists / Basic Scientists / Computer Scientists
Tissue bank (tumor tissue and normal prostate tissue) of ~ 500 samples
New patients treated at County Clinical Hospital and IOCN for ovarian cancer (~100/ year)
Microarray Centre / Basic Research labs
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Urgent need for:Urgent need for:
Improved detectionImproved detection
Better tumor classification
Better Better evaluation of responseevaluation of response to currently to currently used and experimental chemotherapyused and experimental chemotherapy
New therapeutic targetsNew treatments
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Our lab’s approach:Our lab’s approach:
Combine the powers of protein microarrays and RNA expression (cDNA microarrays) to facilitate the identification of smaller subsets of genes pertinent to prostate cancer adenocarcinoma
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Tumor heterogeneity challengeTumor heterogeneity challenge
**Some cancers, such as prostate cancer, are multifocal / heterogeneous.
**For these tumors, “bulk” extraction of genetic material from tumor tissue will produce microarray results that are “contaminated” by normal or pre-malignant tissue
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Laser Capture Microdissection (LCM)Laser Capture Microdissection (LCM)
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Microdissected PIN
(prostatic intraepithelial
neoplasia)
Before LCM
After LCM
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Microarray data validationMicroarray data validation
cDNA microarrays: one patient - 20,000 genes
Tissue arrays: one gene -1000 patientsRT-PCRImmunohistochemistry (IHC)In situ Hybridization (ISH)
Cancer profiling arrays: one gene - 10 tumor/normal sample pairs for different tumors
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Tissue ArraysTissue Arrays
Monni et al, Seminars in Cancer Biology, (2001), 11, p.395
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Northern Blot, Tissue ArraysNorthern Blot, Tissue Arrays
a. Northern blot
b. Tissue array
c. IHC, anti-hepsin antibody (1:benign-2:cancer) X 100
d. X 400
Dhanasekaran et al, Nature, (2001) 421, p.822
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cDNA array, Northern, ISH, IHCcDNA array, Northern, ISH, IHC
Mousses et al, Cancer Research (2002), 62, p. 1256
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Cancer Profiling Array (Clontech)Cancer Profiling Array (Clontech)
Wiechen Wiechen et alet al, American , American Journal of Pathology, (2001), Journal of Pathology, (2001), 159159, p.1635, p.1635
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Predicting the FuturePredicting the FuturePredicting the FuturePredicting the Future
What is going to happen now that the human and other genomes are completed?
How quickly the next steps will happen?
What are the potential difficulties?
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PROTEOMICS FACILITYPROTEOMICS FACILITY
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Uncovering gene enhancer elements (& J Taipale, Biomedicum)
gene1 gene2 gene3 gene4DNA
RNA
transcription
translation
Proteins
transcription factors
enhancer module
APPLICATIONSAPPLICATIONS
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Model of cell type specific regulation of target gene expression
GLI X Y (tissue specific TFs)
GLI GLI Ubiquitously expressed TF
transcription
transcription
Common targets (e.g. Patched):
Cell type specific targets (e.g. N-myc):
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Binding affinity matrices
Transcription factor binding
sites represented by affinity
matrices
Discovered:
Computationally
Traditional wet lab
Microarrays
9 11 49 51 0 1 1 4 19 3 0 0 0 45 25 16 5 1 2 0 17 0 4 21 18 36 0 0 34 5 21 10
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Metabolic networks and systems biology (& J Rousu & VTT Biotech)
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From Data to Knowledge Research Unit - Information systems
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Mission and goalsMission and goals
Mission: provide methods for analysing and querying
masses of data for useful inferred knowledge.
Research on data mining Computational methods for data analysis
Theory of data mining, algorithms
Implementations and applications
Data mining in bioinformatics and language technology
Interaction of applications and theory
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Research topicsResearch topics
Non-redundant association rules Frequent Datalog patterns Fast pattern enumeration and evaluation algorithms Discovery of functional dependencies Text pattern induction by alignment Discovery of maximal frequent sequences in text Unsupervised methods for knowledge acquisition in text Methods for text segmentation and its evaluation Time series segmentation (Efficient algorithms for) variable length Markov models Bayesian model fitting using MCMC Nested permutation tests
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Research projects (grouped by applications)
Focus on selected application topics in bioinformatics and language technology
where we can have a significant impact
where we can team up with excellent application partners
Gene mapping discover genetic patterns in case-control data
Haplotyping find the highest probability strings (haplotypes) explaining
sequences of pairs (genotypes)
Information extraction from epidemiological reports
(ProMED-mail/Harvard Medical School) extract facts (disease, location, time,…) from plain text
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Relevance and interaction with society
Fielded applications in industry and public sector
Software for human genetics (HaploRec, HPM, TreeDT),
epidemiological fact base (ProMED-PLUS), technical
documentation, context analysis
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Future visionFuture vision
Continue work on important data analysis problems in
bioinformatics and language technology Applications, including fielded and commercialized ones
Theory and method development
Collaboration across units, disciplines, industry
Future emphasis on Mining rich public biological databases
- Discovery of patterns in complex irregular structures,
discovery of similarities and analogies
Methods for semantic analysis of large text collections
- language and domain-independence, efficiency
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USAMV Rector supportsUSAMV Rector supports
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Doru PAMFIL, PhD — an accomplished professor of genetics, he has expertise in the management of many national and international projects and veteran of large, public research institutions.
Throughout his career he has focused on expanding undergraduate research opportunities and improving the education and professional experience of graduate students, with a focus on underrepresented groups.
Pamfil’s academic work focuses on Biotechnology (marker assisted selection, detection of GMOs, genetic transformation, micropropagation, microbiology). The GMOs Laboratory – CERTOMG - was included in EUROPEAN NETWORK OF GMO LABORATORIES (ENGL) in 2009
"The problem solving, systems thinking, and teamwork aspects of biotechnology can benefit all students, whether or not they ever pursue an scientific career," said Doru PAMFIL, Rector of the University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, head of INSTITUTE OF LIFE SCIENCES (LIS).
"An biotechnology education and science curricula that does not include at least some exposure to biotechnology is a lost opportunity for students and for the nation."
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Helping Hands for Addressing Helping Hands for Addressing Excellence in Research, Education Excellence in Research, Education
and Training Needs for and Training Needs for BiotechnologyBiotechnology
Helping Hands for Addressing Helping Hands for Addressing Excellence in Research, Education Excellence in Research, Education
and Training Needs for and Training Needs for BiotechnologyBiotechnology
For more information on future partnerships, contact Dr. Ramona SUHAROSCHI
Email: [email protected]/fax:+40 264 425575
Calea Floresti 64400509, Cluj-Napoca
LIFE SCIENCE INSTITUTELIFE SCIENCE INSTITUTECalea Manstur 3-5Calea Manstur 3-5400372, Cluj-Napoca400372, Cluj-Napoca
For more information on future partnerships, contact Dr. Ramona SUHAROSCHI
Email: [email protected]/fax:+40 264 425575
Calea Floresti 64400509, Cluj-Napoca
LIFE SCIENCE INSTITUTELIFE SCIENCE INSTITUTECalea Manstur 3-5Calea Manstur 3-5400372, Cluj-Napoca400372, Cluj-Napoca
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Thank you – I am charmed to be your guest!Thank you – I am charmed to be your guest!
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ILS – we are looking forward to meeting You!ILS – we are looking forward to meeting You!