19
February
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...

09
December
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...

03
June
Processing NGS data: Mutation Variants, Gene Expression, Metagenomics
10:00 am - 11:00 am
Online

Understanding bioinformatics processing pipelines to convert raw NGS data to structured data and steps for data normalization, filtering and annotation. Standard algorithms, tools and...

04
June
Host-pathogen interaction
10:30 am - 11:30 am
Online

In the tenth session of the Bioinformatics for Infectious Diseases, we will discuss about Host-pathogen interaction. Protein-protein interaction and host response Immune response (adaptive,...

05
June
Statistical Analysis, Data Mining and Machine learning for NGS data
10:00 am - 11:00 am
Online

Using statistical approaches to study processing pipeline outputs, perform exploratory data analysis, hypothesis testing, data mining and classification. Methods on comparative data analysis, association...

08
June
Sequencing Viral Genomes
10:00 am - 11:00 am
Online

Using Next Generation Sequencing to Study Viral Genomes

10
June
Annotation and Biological Interpretation
10:00 am - 11:00 am
Online

Relating organism/genome-level, gene-level and mutation-level information in a biologically relevant way by annotating results. Association between genes, ontology and gene set or pathway mapping....

12
June
Detecting VIRAL Genomes in Animals and Patients using NGS
10:00 am - 11:00 am
Online

Bioinformatics techniques for finding viral genomes in host samples

15
June
Using Genomic Reference Databases of Viral Sequences
10:00 am - 11:00 am
Online

Detection of Viral Genomes in Host Samples (Part 2)

16
June
Bioinformatics in Translational Oncology Research
10:00 am - 11:00 am
Online

Cancer biology: changes in organs, tissues, and cells, Molecular factors in tumor development and metastasis, Clinical and molecular data in oncology studies, Analyzing the...

18
June
Next Generation Sequencing: Analysis of DNA Variation
10:00 am - 11:00 am
Online

Processing (germline and somatic mutations) Analysis (mapping, detecting variants) Interpretation (variant types and significance)

19
June
Multiple Sequence Alignment Similarity and Consensus
10:00 am - 11:00 am
Online

Comparing Sequences and Finding a Consensus

22
June
NCBI Virus: High-quality COVID-19 Genomic Data
10:00 am - 11:00 am
Online

Finding and preparing files for analysis on NCBI Virus

23
June
Processing Next Generation Sequencing Data
10:00 am - 11:00 am
Online

Quality Control and the role of pre-processing, Mapping strategies: alignment to transcriptome or genome Quantification and Visualization of Gene Expression

25
June
Machine Learning for Gene Expression Data
10:00 am - 11:00 am
Online

Data exploration using dimensionality reduction and clustering, Classification and discriminant analysis for labeled datasets, Unsupervised & Supervised Machine Learning

26
June
Phylogenetic Analysis
10:00 am - 11:00 am
Online

Identifying relationships between viral sequences

29
June
Hands-on Session: Preparing and Running your pipeline
10:00 am - 11:00 am
Online

Multiple sequence alignment of viral genomes, Preparing a full pipeline of MSA and Phylogeny

30
June
Oncology Data sources: Raw data and Public databases
10:00 am - 11:00 am
Online

National Center for Biotechnology Information (NCBI)Sequence Read Archive (SRA), Gene Expression Omnibus (GEO)The Cancer Genome Atlas (TCGA), COSMIC

02
July
Next-generation sequencing – viral genomes in the host transcriptome
10:00 am - 11:00 am
Online

Overview of NGS: reads, sequences, file formats, alignment, annotation, and non-mapped reads, Alignment to databases of viral genomes

03
July
Q&A on Pipeline Outputs
10:00 am - 11:00 am
Online

Using Bioinformatics Pipelines for Big Data, Preparing a Workflow based on data type, Selecting the right references and databases, Interpreting evolutionary relationships, Visualizing and...

06
July
Program Review
10:00 am - 11:00 am
Online

Evaluating the program timeline, Support and topics, Discussion about resources needed to improve course delivery.

07
July
Multiple Sequence Alignment and Phylogeny
10:00 am - 11:00 am
Online

Multiple sequence alignment and Phylogenetic Analysis, Preparation of data: assembled genome sequences, Selecting appropriate genomic sequences for a full pipeline

09
July
Q&A Session and Discussion of pipeline results
10:00 am - 11:00 am
Online

The logic behind various Workflows and Pipelines, Finding and using the right References & Databases Approaches to Interpretation of Visual Outputs

10
July
Applying bioinformatics to the vaccine and drug design
10:00 am - 11:00 am
Online

Bioinformatics in translational research: vaccine and drug design

14
July
From Infection to Pandemic: viral adaptation
10:00 am - 11:00 am
Online

Example Project: the origin of Coronavirus pandemics: MERS, SARS, and SARS-2 outbreaks

16
July
Host-pathogen interaction
10:00 am - 11:00 am
Online

Interaction between pathogen and host response, Analysis of gene expression to capture immune responses, Implications for vaccine design: factors for consideration.

02
June
Mutation Annotation & Significance for analysis
10:30 am - 11:30 am
Online

In the ninth session of the Bioinformatics for Infectious Diseases, we will discuss about Mutation Annotation & Significance for analysis. Codon/amino-acid and chemical properties...

29
May
OmIcs & Big Data
10:00 am - 11:00 am
Online

Overview of data repositories and bioinformatics project management:  NCBI: National Center for Biotechnology Information – SRA, GEO, RefSeq and other repositories of publicly available...

28
May
Rate of Mutation – mutation variant types
10:30 am - 11:30 am
Online

In the eighth session of the Bioinformatics for Infectious Diseases, we will discuss about the Rate of Mutation – mutation variant types. Point mutations,...

27
May
High-throughput “omics” data: The T-Bioinfo Platform
10:00 am - 11:00 am
Online

Overview of analytical and theoretical resources for the program: T-BioInfo: an intuitive and user-friendly interface for analysis of big data: NGS genomics and transcriptomics,...

26
May
EXAMPLE: the origin of human infection with MERS, SARS, and SARS-2 pandemics
10:30 am - 11:30 am
Online

In the seventh session of the Bioinformatics for Infectious Diseases, we will discuss about the origin of human infection with MERS, SARS, and SARS-2...

21
May
Symptom severity: Disease progression and outcomes
10:30 am - 11:30 am
Online

In the sixth session of the Bioinformatics for Infectious Diseases, we will discuss about disease progression and outcomes. Viral proteins Replication Immune evasion Register...

19
May
From Infection to Pandemic: Viral Adaptation
10:30 am - 11:30 am
Online

In the fifth session of the Bioinformatics for Infectious Diseases, we will discuss about viral adaptation. Hosts and origins Transmission Cell entry and tissue...

14
May
Q&A and DISCUSSION of pipeline results
10:30 am - 11:30 am
Online

In the fourth session of the Bioinformatics for Infectious Diseases, we will have a Q&A and DISCUSSION of pipeline results. Workflows: what to do...

12
May
Hands-on session – Preparing and Running Your pipeline: multiple sequence alignment of viral genomes and building a phylogenetic tree
10:30 am - 11:30 am
Online

In the third session of the Bioinformatics for Infectious Diseases, we will learn about Preparing and Running Your pipeline: multiple sequence alignment of viral...

10
May
LBRN Event: Bioinformatics 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.

07
May
Multiple Sequence Alignment and Phylogeny
10:30 am - 11:30 am
Online

In the second session of the Bioinformatics for Infectious Diseases, we will learn about Multiple Sequence Alignment and Phylogeny. Comparing sequences (Multiple Sequence Alignment)...

04
May
Next-generation sequencing: Viral Genomes in Host Transcriptome
10:30 am - 11:30 am
Online

In the first session of the Bioinformatics for Infectious Diseases, we will learn about Viral Genomes in Host Transcriptome. Overview of NGS: reads, sequences,...

16
April
13
April
09
April
06
April
02
April
TCGA (patient cohorts)
9:30 am - 10:30 am
Online

30
March
NCBI (cell lines, animal models)
9:30 am - 10:30 am
Online

26
March
23
March
Analysis (differential gene expression, factor regression analysis)
9:30 am - 10:30 am
Online

PCA T-Test and DIff. Expression Regression and Factor Analysis

19
March
Functional Annotation and Biological Interpretation
11:30 am - 12:30 pm
Online

Session Topics: Gene annotation using databases, pathway analysis, linking phenotype and genotype Outcome: Learn to infer biological insight from data and learn about project examples...

19
March
Processing (mapping, quantification)
9:30 am - 10:30 am
Online

With and without pre-processing Bowtie 2t and bowtie 2g Quantification Normalization

16
March
Data Mining and Machine Learning
11:30 am - 12:30 pm
Online

Session Topics:  Data Mining, Machine learning and their application to high throughput data Outcome: learn to differentiate between various clustering and classification techniques, understand how...

16
March
Next Generation Sequencing – Genomics (DNA Variants and Mutations)
9:30 am - 10:30 am
Online

Processing (germline and somatic mutations)  Analysis (mapping, detecting variants) Interpretation (significant and insignificant mutations, etc.)

12
March
Biostatistics and Data Science
11:30 am - 12:30 pm
Online

Session Topics: Biostatistical tools and exploratory data analysis concepts for working with NGS data Outcome: Learn about commonly used statistical tests and associated terminology. Learn...

12
March
Introduction to Big Data Bioinformatics
9:30 am - 10:30 am
Online

From Hypothesis Testing to Data Mining  Statistics and Algorithms  T-BioInfo Platform and relevant analysis methods

09
March
Examples of NGS data: Mutation Variants, Gene Expression, Metagenomics
11:30 am - 12:30 pm
Online

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

09
March
Introduction to Oncology
9:30 am - 10:30 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/

05
March
Big Data Challenges and Opportunities (4 Vs)
11:30 am - 12:30 pm
Online

Session Topics: What is Bioinformatics, Knowledge-Driven vs. Data-Driven Discovery, Examples of Data-Driven Discoveries, Applications of Bioinformatics in Agriculture, Neuroscience, Cancer Biology, Immunology, Defense, and...

02
March
History of Omics Data and its significance
11:30 am - 12:30 pm
Online

Session Topics: History of Omics Data and its significance, Overview of the entire course, Overview of the tools and resources for this program (edu.t-bio.info...

27
February
Planning your Project: Educational Project
9:00 am - 10:00 am
Online

Planning your project, Projects on the Educational Platform. One-on-One interactions: Data access and project abstract Case Studies & Publications Datasets Independent Projects* (Requires Research...

14
February
Independent project work
9:30 am - 10:30 am
Online

Planning your project, 2 Q&A sessions, 1 Presentation Case Studies & Publications Datasets

13
February
ScRNA Transcriptomics Data Analysis
9:30 am - 10:30 am
Online

ScRNA data analysis, Publication & projects: Drop-seq data from Ye et al., 2017, Results & Interpretation.

13
February
Biological Interpretation
9:00 am - 10:00 am
Online

Annotation using Gene Ontology Human GAGE: Gene Set Enrichment Analysis Statistical Significance and Reproducibility

11
February
Single-Cell Transcriptomics
9:30 am - 10:30 am
Online

Single-cell transcriptomics (SCT) Introduction to SCT, History of SCT, NGS Techniques, Capture techniques, Quantification, scRNA-seq data preparation & Counts

10
February
Using Machine Learning for Expression Data
9:00 am - 10:00 am
Online

Review Supervised ML Discriminant Analysis (LDA, SwLDA, QDA) and Support Vector Machines Data Visualization and classification

07
February
Interpretation
9:30 am - 10:30 am
Online

Annotation using Gene Ontology Human GAGE: Gene Set Enrichment Analysis Statistical Significance and Reproducibility

06
February
Data Mining using the Random forests
9:00 am - 10:00 am
Online

Review of unsupervised machine learning methods  Decision Trees, Random Forest  Challenges associated with different kinds of machine learning

04
February
Machine Learning for Expression Data
9:30 am - 10:30 am
Online

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

03
February
Introduction to RNA-seq
10:00 am - 12:00 pm

03
February
Exploratory Data Analysis: PCA, K-Means and H-clustering
9:00 am - 10:00 am
Online

Review of Factor Regression Analysis  Unsupervised machine learning (PCA, H-Clust, K-means,) Case study & Hands-on using Cell line project

31
January
Data Mining using the Multi-Dimensional Expression Data
9:30 am - 10:30 am
Online

Supervised Machine learning techniques  Factor Regression Analysis, Decision Trees, Random Forest  Challenges associated with different kinds of machine learning

28
January
Analysis of Gene Expression
9:30 am - 10:30 am
Online

Unsupervised machine learning (PCA, H-Clust, K-means) Clustering of samples using gene expression profiles Clustering of genes by expression profiles across samples

24
January
Exploratory Data Analysis
9:30 am - 10:30 am
Online

Filtering, removing noise and Normalization Techniques Correlation – detecting correlation of features and factors Regression, factors, and features – Factor Regression Analysis overview

23
January
Processing of NGS data and differential gene expression
9:00 am - 10:00 am
Online

Filtering, removing noise and Normalization Techniques Least error Predictive model, Fitting a regression line Regression, factors, and features – Factor Regression Analysis

20
January
High throughput: Omics Data Processing
9:00 am - 10:00 am
Online

Role of pre-processing in standard RNA-seq pipelines (Trimmomatic and PCR-clean) Mapping techniques: mapping on the transcriptome, mapping on the genome and combined strategies (Bowtie,...

17
January
Processing of Gene expression NGS data
9:30 am - 10:30 am
Online

Role of pre-processing in standard RNA-seq pipelines (Trimmomatic and PCR-clean), Mapping techniques: mapping on the transcriptome, mapping on the genome and combined strategies (Bowtie, BWA,...

16
January
Next-Generation Sequencing and Omics technologies
9:00 am - 10:00 am
Online

Overview of Processing NGS Data (from raw data to structured data),  Standard tools and concepts for genomics, transcriptomics, epigenomics, metagenomics. What kinds of challenges...

14
January
Session 1 – Introduction
9:30 am - 10:30 am
Online

Overview of the entire course, Overview of the tools and resources for this program (edu.t-bio.info courses, projects and datasets, and the T-BioInfo Analytics Platform),...

13
January
Program Overview
9:00 am - 10:00 am
Online

Overview of the entire course, Overview of the tools and resources for this program (edu.t-bio.info courses, projects and datasets, and the T-BioInfo Analytics Platform),...

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
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

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)

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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