Get to know us …

Bioinformatics UnitDepartment of Biological Services

Sequence analysis Biostatistical support

Image analysisNGS data analysis

Microarray analysis

Bioinformatics Team

IT & programming

Domains of Activity

Mode of work

• Consulting (first meeting free)

• Experimental design (kickoff meeting)

• Analyzing– Complete project analysis done by our team

– Guided analysis

– In your lab analysis (group meetings)

• Training, personally and in groups

• Teaching FGS courses and workshops

• Help desk

Mode of work

• Consulting

• Experimental design (kickoff meeting)

• Analyzing– Complete project analysis done by our team

– Guided analysis (for NGS)

– In your lab analysis

• Training, personally and in groups

• Teaching FGS courses and workshops

• Help desk

Guided analysis:Simplifying bioinformatics analysis

Command line operations

Graphical interface and built-in pipelines (Chipster)

Types of AnalysisAim: Find and understand the biological

meaning of the data

But.. How do we get to the aim?

We can help you -

• choose the proper tools and build proper workflows for analysis

• perform analysis using existing tools

• customize existing tools to specific data and aims

• development of new methods and algorithms

Previous achievements• Fruitful collaborations resulting in ~40 publications since

2013

• FGS courses given in 2015 (offered also in 2016):

– Statistical Principles in the Analysis of Research Data

– Practical Image Analysis for Biology

– Introduction to Deep Sequencing Analysis course

• Workshops given in 2015 (2016 to be announced):

– CRIPSR Design

– ChIP-Seq: Using Deep Sequencing to Discover Protein-DNA Interactions

– Ilastik: machine learning tool for image analysis

– Population structure

Infrastructure

• Workstations for bioinformatics applications and image analysis (@Levine bldg)

• Unix servers for intensive data analysis (local/Wexac cluster nodes)

• Software licenses for:

– Bioinformatics

– Biostatistics

– Image Analysis

• BioImg Storage Server:

– Automatically copies data from Imaging equipment & FACS at core facilities and individual labs

– Lets the users access, share, annotate the data everywhere on campus

• Managing Biological Services LIMS

BioImaging Informatics

How to store / display / enhance / quantify Image Data

Light microscopy, EM, Histology, MRI, CT

Quantitative Image Analysis

• Image data in Biology becomes larger and more important

Our aims:

• Replace subjective visual inspection and manual measurement by objective quantitative computerized image processing & analysis

• Design high throughput pipelines for image data

• Record and analyze tens of parameters per cell

• Meet reviewer requirements for quantitative measurements

Common Image Quantifications Questions

• What is the mean intensity of the green channel in wild-type and knockout ?

• What is the length or area of a structure in each cell?

• How does the intensity of the GFP change over a time course?

• How is the protein distributed, perhaps relative to a particular structure?

• How many cells, spots … are in the image?

• How fast and far does the object move ?

• How much does the green colocalize with

the red?

Biostatistical support• We provide biostatistical support at all stages of the

experiment - from planning to final analysis and presentation.• Experimental design, sample size, data organization, choosing

the proper tests, interpretation and presentation.

CyTOF analysis• CyTOF (Cytometry by Time of Flight) can characterize single

cells with dozens of probes (antibodies) per cell. • Analysis of the results requires recently developed tools for

multi-parametric data. • We provide support for these tools, either through training or

conducting the complete analysis.

Biostatistics

Possible questions:• How many samples should I use in each of my treatments?

• How do I analyze the effect of several experimental factors and/or

time points?

• Is it possible to use data from an animal that survived only half of

the experiment?

• How do I handle multiparametric data, e.g. from microarrays or

CyTOF?

Biostatistics

- Differential gene expression analysis

- Clustering of genes/conditions

- Mining and reanalysis of microarray data from published

studies (GEO)

- Comparative analysis of multiple microarray experiments at the

gene and pathway levels

Microarray Analysis

What can NGS do for you?

mRNA expression and discovery

Mutation discovery

Sequencing novel genomes

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Alternative splicing and allele specific expression

Protein-DNA interactions

Next Generation Sequencing Tools by Applications

RNA-SeqRSEM, DESeq,

CufflinksTrinity …

ChIP-SeqMACS, HOMER, Meme-

ChIP, CEAS, GREAT …

Genomic VariationIGV, VCFtools,

FreeBayes, SAMtools, GATK, Plink

MetagenomicsMetalook, Metamine, Metastats, MEGAN …

MappingBowtie, BWA, STAR, TopHat

NGS raw reads QC: fastqc, FastQ…

De novo Assembly

Velvet, Newbler …

Werner T Brief Bioinform 2010;11:499-511

CLASSICAL BIOINFORMATICS

DNA

RNA

PROTEIN

Basic Tools for all:

Database SearchesAlignments

DNA Analyses

Genome Browsers Comparative Genomics

Genomic Primer Design Gene Prediction

Gene Structure

Sanger SequenceTroubleshooting

Phylogenetics

SNP Interpretation CRISPR

RNA Analyses

siRNA

Cloning/Plasmid Design

Primer Design Restriction Mapping

Splice Variants

Sanger Sequence Troubleshooting

miRNA

Long non-coding RNA

Expression3’ UTR signals

EST/gene building

Secondary Structure

Protein Analyses

Protein-protein interactions Subcellular Localization

Antigen Design

Motif Finding/Definition Secondary Structure

Post-translational modifications

Phylogenetics

Transcriptional Control(DNA-Protein-RNA interactions)

Promoter Analyses

Transcription Start Site Definition

Transcription Factor Binding Site Prediction

Conservation

Transcription Factor Binding Site Definition

SNP Interpretation

Site-licenses for software packages

• Sequence analysis:

Lasergene, MacVector, Sequencher, SnapGene

• Promoter analysis:

Genomatix Genome Analyzer (GGA)

• Pathways and system analysis:

Ingenuity – IPA Data Analysis

• Microarray and NGS statistical analysis

PARTEK Genomics Suite

• Image Analysis

Imaris, AutoQuant, Volocity, Analyze, Avizo (by CRS), Arivis

• Tool for studying publicly available expression data (GEO)

GenVestigator

Bioinformatics Unit - Contacts

• Programming projects and programming help: Dr. Jaime Prilusky

• Genomics, Promoter analysis, Sequence analysis and Phylogenetics: Dr. Shifra Ben-Dor

• High-throughput genomics and Next-generation sequencing: Dr. Ester Feldmesser, Dr. Dena Leshkowitz and Dr. Naama Kopelman

• Microarray analysis, Sequence analysis, software installation, general issues: Irit Orr

• Biostatistical support: Dr. Ron Rotkopf

• BioImaging analysis: Ofra Golani

• Infrastructure: Ofra Golani (image related), Irit Orr (bioinformatics related), Kiril Kogan, Jaime Prilusky

Head of unit:

Dr. Dena Leshkowitz (x6330)

Project coordinator:

Irit Orr (x2470)

The End

… and hopefully the beginning of collaboration on your projects!

Links to our websites:

http://www.weizmann.ac.il/Biological_Services/bioinformatics-about

http://bip.weizmann.ac.il/

http://www.weizmann.ac.il/vet/IC/informatics/about-service

General Information:

Sequence Analysis (tools):

Image Analysis:

GCK (gene construction kit) eliminates tedious examination

of DNA sequence data by automatically identifyingopen reading frames (ORF's), keeping track of sticky ends during cutting and pasting of restriction enzyme digestionfragments, assisting withPCR primer design, and enabling comprehensive annotation of DNA sequence features. This DNA analysis software allows multiple files to be opened and displayed simultaneously, allowing DNA sequences to easily be copied and pasted between plasmids and vectors to represent real-world DNA cloning protocols. The Gene Construction Kit software is available for both Windows and Macintosh users.

MacVector Major Features:Graphical Sequence Editing, Gateway and Topo CloningAuto AnnotationPrimer DesignDNA AnalysisProtein AnalysisDatabase SearchingMultiple Sequence AlignmentSequence Assembly

Site-licenses for software packages

Sequencher features:Sequence editingSequence trimmingSequence assemblyAssemble o referenceMultiple alignmentRestriction mappingConfidence valueSNP detectionAutomated analysis

SnapGene for Cloning features:Gibson Assembly®Restriction cloningPCR & MutagenesisAgarose Gel ElectrophoresisEnzyme SitesPrimersORFsChromosome–size sequencing

Ingenuity – IPA Data Analysis IPA Core Analysis has multiple ways of relating the molecules in your dataset to the bodyof information in the Ingenuity Knowledge Base. Biological functions and diseases that are over-represented in your data, and the predicted directional effects on these functions and diseases.Signaling and metabolic canonical pathways enriched in your data.Predicted upstream regulators that might explain the changes observed in your data.Molecular networks (algorithmically generated pathways describing potential molecular interactions in your experimental system)

PARTEK Genomics SuitePartek Genomics Suite is a comprehensive suite of advanced statistics andinteractive data visualization specifically designed to reliably extract biologicalsignals from noise and includes all of the functionality of the Discovery Suite.Designed for high-dimensional genomic studies containing thousands of samples,Partek GS is fast, memory efficient and will analyze large data sets on a personalcomputer. It supports a complete workflow including convenient data access tools,identification and annotation of important biomarkers, and construction andvalidation of predictive diagnostic classification systems.

AcknowledgmentsSource of Images (slides 2,5,9)

• Confocal florescence microscopy: Source: Nature of Nature

• Histology: Source: central microscopy Iowa

• Light microscopy: Phase, DIC. Source: Nikon Microscopy

• FIB-SEM: Ilana Sabanay, Elior Peles, Alon Weiner

• MRI: Michal Neeman lab