18
September
Next Generation Sequencing and Omics Technologies
9:30 am - 10:30 am

Session Topics: Processing NGS Data (from raw data to structured data),  Standard tools and concepts for genomics, transcriptomics, epigenomics, metagenomics. Use of NGS in...

23
September
Metagenomics
8:00 pm - 9:00 pm
Online

What is Metagenomics and why study Metagenomics Microbiome and taxonomy The Gut Microbiota and Human Health NGS of the Metagenome and 16S metagenomic data...

17
October
Machine Learning
8:00 pm - 9:00 pm
Online

What is machine learning, categories of methods Regression, factors, and features – Factor Regression Analysis Challenges associated with different kinds of machine learning

24
October
Planning a Bioinformatics project
8:00 pm - 9:00 pm
Online

  Identifying the correct dataset(s) for your bioinformatics project   Input and output of the typical processing and analysis steps   Team Project selection...

05
November
Microbiome – functional bacterial community
9:30 am - 10:30 am
Online

Session Topics: Understanding the Microbiome, Diversity, The Microbiome and Human Health, The gut microbiota, Gut health and the brain, Metabolome characterization. This is an...

05
November
Planning a Bioinformatics project
12:00 pm - 1:00 pm

Identifying the correct dataset(s) for your bioinformatics project, Input and output of the typical processing and analysis steps, Team Project selection criteria and team...

08
November
Analysis challenges – short reads, HVRs, OTUs
9:30 am - 10:30 am
Online

Session Topics:Overview of 16S metagenomics analysis, Pre-processing, data simulation, and error correction, Mapping to a reference database (Short overview), Generating the Abundance Table, Post-processing...

12
November
Mapping on databases
9:30 am - 10:30 am
Online

Session Topics: Mapping to a reference database (Detailed), Silva, Greengenes, NCBI – hypervariable regions of ribosomal RNA and full genome databases This is an...

15
November
DADA2 pipeline
9:30 am - 10:30 am
Online

Overview of DADA2, OTUs, Amplicon 16S/18S analysis algorithms, Pipeline demonstration, Data analysis and results.  This is an event from the OmicsLogic Metagenomics program, you...

15
November
Metagenomics project & multiomics approach in Bioinformatics
9:30 am - 10:30 am
Online

Project details: Project from the edu site  This is an event from the OmicsLogic Metagenomics program, you can register for the full program here: https://edu.t-bio.info/organizations/omicslogic-metagenomics/...

10
December
Bacterial populations- GWAS
9:30 am - 10:30 am
Online

Session Topics: How Genome Wide Association studies can be used to analyze microbial response to soil composition and identify other genotype-phenotype associations This is...

13
December
Viral genome detection in standard RNA-Seq
9:30 am - 10:30 am
Online

Session Topics: detection of viral genomes presence and estimation of contamination. Example: SF-9 project This is an event from the OmicsLogic Metagenomics program, you...

17
December
Phylogenetic analysis
9:30 am - 10:30 am
Online

Session Topics: Analysis of phylogenetic relationships between genomes to study evolutionary divergence based on select regions or genes. This is an event from the...

20
December
Drug resistance
9:30 am - 10:30 am
Online

Session Topics: Association of tuberculosis genomic variations with drug resistance mechanisms for antibiotic treatment This is an event from the OmicsLogic Metagenomics program, you...

23
December
Evolution, fitness and quasi species
9:30 am - 10:30 am
Online

Session Topics: Analysis of viral fitness in passages of viral populations to identify mutations responsible for adaptation. This is an event from the OmicsLogic...

01
November
Machine Learning 1
12:00 pm - 1:00 pm

Decision Trees, Discriminant Analysis and Support Vector Machines, Feature Selection and expanding the list of features, Data Visualization

01
November
16s metagenomics sequencing
9:30 am - 10:30 am
Online

Session Topics: History & Significance of 16s rRNA in Metagenomics,16S Metagenomic Sequencing Library Preparation: (Protocol Overview): Sample collection and preparation, DNA extraction, 16S rRNA...

31
October
Data Access and Project Abstract – Part 2
9:15 am - 10:15 am

Session Topics: Data processing Analysis Plan Discussion

25
October
Workshop III
8:00 pm - 9:00 pm

Multi-Omics Data Analysis in Cancer Research

25
October
Introduction to Machine Learning
12:00 pm - 1:00 pm

What is machine learning, categories of methods, Regression, factors, and features – Factor Regression Analysis, Challenges associated with different kinds of machine learning

24
October
Exemplar Projects (Microbiology)
9:15 am - 10:15 am

Session Topics: Infectious Diseases and Microorganisms Tuberculosis and Drug Resistance Ebola outbreaks in West Africa

22
October
Machine Learning 1
8:00 pm - 9:00 pm

Decision Trees, Discriminant Analysis and Support Vector Machines, Feature Selection and expanding the list of features, Data Visualization

22
October
Metagenomics 1
12:00 pm - 1:00 pm

The current research areas in Metagenomics, The biological background of the Metagenomics, Logical Steps for Metagenomics Data Analysis and associated Algorithms, Interpretation of the...

21
October
Exemplar Projects (Oncology)
9:15 am - 10:15 am

Session Topics: Oncology Projects and biomedical research MODELING PRECISION MEDICINE STUDYING NETWORKS OF CANCER REGULATION IN PATIENTS

19
October
Project Planning
9:00 am - 11:00 pm
Online

Day 1 Big Data in Life Sciences and Data mining, Pratim Chakraborty, September 9th, 2019 Big Data types in Life Sciences – public and...

17
October
Discriminant Analysis and Classification
9:30 am - 10:30 am

Session Topics: LDA, QDA, swLDA Support Vector Machines Deep Learning

15
October
Introduction to Metagenomics
12:00 pm - 1:00 pm

What is Metagenomics and why study Metagenomics, Microbiome and taxonomy, The Gut Microbiota and Human Health, NGS of the Metagenome and 16S metagenomic data,...

14
October
Decision Trees
9:30 am - 10:30 am

Session Topics: Binary Decision Trees Random Forest Random Forest Multi-run

09
October
Clustering
9:30 am - 10:30 am

Session Topics: Distances and boundaries  K-means, Hierarchical and DB-scan Heatmaps and Hierarchical Clustering

07
October
Dimensionality Reduction
9:30 am - 10:30 am

Session Topics: Curse of dimensionality Features, Objects and loadings Principal Component Analysis Improving Visual Representation of PCA using R

06
October
Visualization and Network Analysis
9:15 am - 10:15 am

Session Topics: Genome visualization Circle maps Cluster and interaction networks

30
September
Factorial Regression Analysis
9:15 am - 10:15 am

Session Topics: Least error Predictive model Fitting a regression line Factorial analysis

25
September
Data Visualization for Exploratory Analysis
9:30 am - 10:30 am

Session Topics: Boxplots, Histograms, Scatterplots Distribution and Lognormal Distribution Quantile Normalization

24
September
Metagenomics 1
8:00 pm - 9:00 pm

The current research areas in Metagenomics, The biological background of the Metagenomics, Logical Steps for Metagenomics Data Analysis and associated Algorithms, Interpretation of the results and visualization

24
September
Transcriptomics 2
12:00 pm - 1:00 pm

Filtering, removing noise and Normalization Techniques Exploring multi-dimensional data using PCA visualization Principal Components and variance – outliers, filtering, normalization

23
September
Summary Statistics and Statistical Properties
9:30 am - 10:30 am

Session Topics: Summary Statistics Mean, Median and Standard Deviation Histograms and Distribution

17
September
Next Generation Sequencing: Transcriptomics
12:00 pm - 1:00 pm

Processing Raw NGS Data (read mapping and quantification)   Analysis (differential gene expression, factor regression analysis)   Interpretation (Gene Ontologies and Gene Set Enrichment Analysis)

16
September
Program Overview
9:30 am - 10:30 am

Session Topics: High throughput data experiments,  challenges and opportunities in biomedical research Program resources

10
September
Workshop II
8:00 pm - 9:00 pm

Role of Genomics and Transcriptomics in Modern Biology.

10
September
Introduction to Genomics
12:00 pm - 1:00 pm

Cell, Nucleus and Chromosomes The DNA molecule and its structure Genome variations: A detailed understanding Targeted Sequencing, Whole Exome Sequencing and Whole Genome Sequencing...

06
September
Introduction to Big Data Bioinformatics
12:00 pm - 1:00 pm

Introduction to multi-omics (Definitions) Knowledge-Driven vs. Data-Driven Discovery and Examples Applications of Bioinformatics in Agriculture, Neuroscience, Cancer Biology, Immunology, Defense and Healthcare

06
September
Machine Learning
12:00 am - 12:00 am
Online

Day 1 Introduction to Machine Learning, Mohit Mazumder, September 2nd, 2019 What is machine learning, categories of methods Regression, factors, and features – Factor...

05
September
Transcriptomics 2
8:00 pm - 9:00 pm

Filtering, removing noise and Normalization Techniques, Exploring multi-dimensional data using PCA visualization, Principal Components and variance – outliers, filtering, normalization

03
September
Introduction to OmicsLogic Program
12:00 pm - 1:00 pm
Institute of Genetic Engineering

Introduction to OmicsLogic Program at the Institute of Genetic Engineering (IGE) Mohit Mazumder & Pratim Chakraborty, Sep 3, 2019 Workshop I Introduction and commencement...

30
August
Bioinformatics for Precision Oncology
10:00 am - 11:00 pm
Online

Online Training Program focused on oncology and bioinformatics, including bioinformatics courses in genomics and transcriptomics from processing of raw fast files to interpretation of...

29
August
Transcriptomics
8:00 pm - 9:00 pm
Online

  Processing Raw NGS Data (read mapping and quantification)   Analysis (differential gene expression, factor regression analysis)   Interpretation (Gene Ontologies and Gene Set Enrichment Analysis)

28
August
Preparing a project
11:00 am - 12:00 pm
Online

Cancer studies (several examples) Development of treatment resistance (Tuberculosis) Case-control studies, GWAS (Breast Cancer Risk)

28
August
Using Machine Learning for Genomic Data
11:00 am - 12:00 pm

Regression, factors, and features – Factor Regression Analysis Supervised Machine Learning (Classification, Discriminant Analysis) Mutational Profiling, Signatures, and biomarkers

27
August
Genomics
8:00 pm - 9:00 pm
Online

Cell, Nucleus and Chromosomes The DNA molecule and its structure Genome variations: A detailed understanding Targeted Sequencing, Whole Exome Sequencing and Whole Genome Sequencing...

26
August
Metagenomics and Microbiome
9:00 am - 11:00 pm
Online

Day 1 Introduction to Metagenomics, Pratim Chakraborty, August 19th, 2019 What is Metagenomics and why study Metagenomics Microbiome and taxonomy The Gut Microbiota and...

22
August
Introduction to Bioinformatics
8:00 pm - 9:00 pm

Introduction to multi-omics (Definitions), Knowledge-Driven vs. Data-Driven Discovery and Examples, Applications of Bioinformatics in Agriculture, Neuroscience, Cancer Biology, Immunology, Defense and Healthcare

21
August
Introduction to OmicsLogic Program
8:00 pm - 9:00 pm
Online

Introduction and commencement of the program by VC, SNU Kolkata Introduction to the Faculty & Trainers Overview of the tools and resources for this...

20
August
Annotation
11:00 am - 12:00 pm
Online

Types of variants missense, synonymous, nonsense Prediction of variant effects on protein structure/function, P-P interaction, abnormal splicing Using reference databases Population genetics – phylogeny,...

12
August
Transcriptomics
12:00 am - 12:00 am
Online

Day 1 Transcriptomics 2, Pratim Chakraborty, August 5th, 2019   Filtering, removing noise and Normalization Techniques Exploring multi-dimensional data using PCA visualization Principal Components...

09
August
Bioinformatics Hackathon
10:00 am - 1:00 pm
Online

If you ever tried running through an analysis, you know it is going to be difficult to complete it without any technical challenges. Format...

08
August
Project Design and proposal
12:00 am - 12:00 am
Online

Scientific Inquiry and Translational Value  Example 1: Breast Cancer – classification of subtypes (cell lines)  Example 2: Liver Cancer – risks and molecular factors...

07
August
Analysis of Variants
11:00 am - 12:00 pm
Online

Accurate detection – the significance of coverage distribution Filtering – limiting the number of potentially significant variants  Statistical methods for significance, stratification

06
August
Summer Bioinformatics Workshop Series
10:00 am - 4:00 pm
Online

Note: You can register for each workshop separately, or get access to all 3 for a reduced price Summer Bioinformatics Workshop series is being organized...

06
August
Single-Cell Resolution in Precision Oncology
10:00 am - 3:00 pm
Online

Cancer in organs and tissues: new opportunities and challenges with single-cell data Different cell types in tissues and organs Single cell sequencing methods (overview...

31
July
DNA Variation
11:00 am - 12:00 pm
Online

Germline variation Somatic mutations – reference and “normal” sample Non-point variations (CNV, chromosomal instability, rearrangements)

30
July
Processing of Genomic data
11:00 am - 12:00 pm

What is DNA, Variation, and Significance Next Generation Sequencing (WES, WGS, Targeted panels) Read length/quality, Mapping NGS data to a reference Genome

29
July
High throughput data, NGS
9:00 am - 11:00 pm
Online

Day 1 High Throughput Data in Life Sciences: Pratim Chakraborty, July 26th, 2019 The Central dogma of molecular biology: DNA code, Transcription, and Translation...

29
July
Data sources for raw data and databases
12:00 am - 12:00 am
Online

NCBI (cell lines, animal models) TCGA (patient cohorts) NCI, COSMIC (databases of mutations and interactions

23
July
Systems-biology and Precision Oncology
10:00 am - 3:00 pm
Online

Overview of Multi-omics integration methods in comparison to single-omics profiling DNA Variation (germline and somatic mutations, copy number variation) Transcriptome (Genes, Isoforms and non-coding...

23
July
Introduction to the Program
11:00 am - 12:00 pm
Online

Program Overview: tools and resources for successful learning Expectations, schedule review, and important deadlines Introduction to materials, speakers, and presenters

22
July
Introduction to OmicsLogic
9:00 am - 11:00 pm
Online

Day 1 Introduction to OmicsLogic at Amity University, Kolkata: Mohit Mazumder & Pratim Chakraborty, July 19th, 2019 Introduction and commencement of the program by...

22
July
RNA Seq Workshop
10:00 am - 1:00 pm
Online

In this session, we go more in-depth with our RNA-seq analysis. We will talk about differential gene expression algorithms like DESEQ and EDGER, and...

17
July
LBRN Event: Introduction to Genomics
10:00 am - 12:00 pm
Online only

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

10
July
Next Generation Sequencing and Precision Oncology
10:00 am - 3:00 pm
Online

General introduction to -omics studies in oncology: cell lines, animal models and patients DNA and RNA variation In Cancer Biology Sensitivity and Specificity using...

08
July
Introduction to RNA Seq
10:00 am - 11:00 am
Online

In this session, we will start looking at RNA-Seq analysis logic and review some of the typical steps involved in NGS data analysis: mapping,...

08
July
Next Generation Sequencing – Genomics (DNA Variants and Mutations)
12:00 am - 12:00 am
Online

Processing (germline and somatic mutations)  Analysis (mapping, detecting variants)  Interpretation (significant and insignificant mutations, etc.) Associated online course/resource: Transcriptomics 1

25
June
Next Generation Sequencing and Precision Oncology

General introduction to -omics studies in oncology: cell lines, animal models and patients DNA and RNA variation In Cancer Biology Sensitivity and Specificity using...

17
June
Introduction to Precision Oncology
12:00 am - 12:00 am
Online

Cancer biology challenges (organs, tissues, cells) Molecular factors in tumor development, growth and metastasis  Clinical and Molecular Data (phenotype-genotype relationship)  Associated online course/resource: https://www.ncbi.nlm.nih.gov/books/NBK20362/

31
May
OmicsLogic Training Program
10:00 am - 11:00 pm
Online

Join this online training program to learn about the analysis of Next Generation Sequencing data (NGS). This 3-month program will provide an in-depth overview...

23
May
Independent project work
10:00 am - 11:00 pm
Online

Students are expected to work on the independent projects. They can either choose from the list of projects provided by us or they can...

16
May
Independent project work
10:00 am - 12:00 pm

Event Details: Participants will be asked to work on the independent project which they can choose from the list of the projects or can work...

09
May
Interpretation
10:00 am - 12:00 pm

Event Details: 1. Annotation using Gene Ontology 2. Human GAGE: Gene Set Enrichment Analysis 3. Statistical Significance and Reproducibility

02
May
Using Machine Learning for Expression Data
10:00 am - 12:00 pm

Event Details: 1. Decision Trees, Discriminant Analysis and Support Vector Machines 2. Feature Selection and expanding the list of features 3. Data Visualization

25
April
Introduction to Data Mining
10:00 am - 12:00 pm

Event Details: 1. What is machine learning, categories of methods 2. Regression, factors and features – Factor Regression Analysis 3. Challenges associated with different kinds of machine...

23
April
Interpretation
10:00 am - 11:00 am
Online

Session will cover: 1. Annotation using Gene Ontology 2. Human GAGE: Gene Set Enrichment Analysis 3. Statistical Significance and Reproducibility

18
April
DNA Variation, Gene and Isoform expression, DNA Methylation and Histone Modification
10:00 am - 12:00 pm

Event Details: 1. Detecting SNVs and measuring frequency of mutations (example - Ebola) 2. Somatic Mutations in Cancer 3. Epigenetic regulation in neurodegenerative diseases 4. Multi Omics integration...

16
April
Using Machine Learning for Expression Data
10:00 am - 11:00 am
Online

Session will cover: 1. Decision Trees, Discriminant Analysis and Support Vector Machines 2. Feature Selection and expanding the list of features 3. Data Visualization

11
April
Analysis of Gene Expression – hypothesis testing and biostatistics
10:00 am - 12:00 pm

Event Details: 1. Correlation – detecting correlation of features and factors 2. Clustering of samples using gene expression profiles 3. Clustering of genes by expression profiles across...

09
April
Introduction to Supervised Data Mining
10:00 am - 11:00 am
Online

Session will cover: 1. What is machine learning, categories of methods 2. Regression, factors and features – Factor Regression Analysis 3. Challenges associated with different kinds...

06
April
Louisiana Biomedical Research Network (LBRN) Bioinformatics Training Program
10:00 am - 11:00 pm

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

04
April
Exploratory Data Analysis
10:00 am - 12:00 pm

Event Details: 1. Filtering, removing noise and Normalization Techniques 2. Exploring multi-dimensional data using PCA visualization 3. Principal Components and variance – outliers, filtering, normalization

02
April
Analysis of Gene Expression
10:00 am - 11:00 am
Online

Session will cover: 1. Correlation – detecting correlation of features and factors 2. Clustering of samples using gene expression profiles 3. Clustering of genes by expression profiles...

29
March
28
March
Processing of NGS data
10:00 am - 12:00 pm

Event Details: (Pre-processing, Alignment and Quantification - RNA-seq example) 1. Role of quality control and re-processing in standard RNA-seq pipelines (Trimmomatic/PCR-clean) 2. Mapping techniques: mapping on transcriptome,...

26
March
Exploratory Data Analysis
10:00 am - 11:00 am
Online

Session will cover: 1. Filtering, removing noise and Normalization Techniques 2. Exploring multi-dimensional data using PCA visualization 3. Principal Components and variance – outliers, filtering, normalization

22
March
LBRN Event: Machine Learning Workshop II

Machine Learning for Biomedical Data (LBRN) NOTE: This workshop is free for LBRN members, online access to non-LBRN members is available upon registration. This...

21
March
Introduction to Bioinformatics
10:00 am - 12:00 pm

Event Details: 1. Why big data in biology (“small data” vs “big data” - high throughput experiments) 2. Data driven vs. hypothesis driven (how can data...

19
March
Processing of NGS data
10:00 am - 11:00 am
Online

Session will cover: 1. Role of pre-processing in standard RNA-seq pipelines (Trimmomatic and PCR-clean) 2. Mapping techniques: mapping on transcriptome, mapping on genome and combined strategies...

14
March
Introductory meeting
10:00 am - 12:00 pm

Event Details: 1. Goal of the program and introduction 2. Overview of the tools and resources for this program (edu.t-bio.info courses, projects and datasets and the...

12
March
Introduction to the program
10:00 am - 11:00 am
Online

Session will cover: 1. Overview of the tools and resources for this program (edu.t-bio.info courses, projects and datasets and the T-BioInfo Analytics Platform) 2. Expectations and...

08
March
LBRN Event: Introduction to MetaGenomics
10:00 am - 12:00 pm
Online only

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

25
February
LBRN Event: Machine Learning Workshop

Machine Learning has become an exciting approach to extract meaningful insights from big heterogenous datasets such as those that are commonplace in biomedical research....

04
February
Hands-on Biomedical Data Science Training Program
8:30 am - 11:00 pm
Online

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

04
February
LBRN Event: Genomics Workshop

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

11
December
Hands-on Biomedical Data Science Training Program
8:30 am - 11:00 pm
Online

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

10
December
LBRN Event: RNA Seq Workshop

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

03
December
LBRN Event: Introduction to Epigenetics
10:00 am - 12:00 pm
Online only

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

09
November
LBRN Event: Introduction to RNA Seq

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

05
November
LBRN Event: Introduction to Bioinformatics

LBRN has partnered with Pine Biotech to offer an innovative curriculum that was designed to quickly introduce complex bioinformatics topics in a project-based approach.

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