Research Methodologies in Bioinformatics
Lecturers: Dr. Daniel Sher, Dr. Mickey Kosloff, Dr. Eyal Privman
Course 227.4020, Fall semester
Lecture: Tuesday 1215-1400, Room 128, Sala building
Tutorial Tuesdays 1415-1600, room TBD
‫שיטות מחקר בביואינפורמטיקה‬
Modern biological research relies heavily on the analysis of genes
and proteins. Recent technological advances (such as next
generation sequencing and tandem mass spectrometry) led to
exponential growth of biological databases and allow us to analyze
whole genomes, together with many thousands of gene expression
patterns, protein structures, and protein-protein interactions. Such
research requires sophisticated computational tools.
Students will learn basic concepts, approaches and tools used for
bioinformatic analysis of sequence data (DNA and protein) and
structural data (protein). We will discuss the design principles of
prokaryotic and eukaryotic genomes, as well as the environmental
and evolutionary forces shaping genomes. Technical topics covered
will include: genomic architecture, gene identification,
characterization, and annotation, sequence alignment, phylogeny
reconstruction, selection pressure on DNA, RNA and proteins, protein
3D structure visualization and comparison, quantitative methods for
protein structure analysis, structure prediction, genome/transcriptome
sequencing and assembly methods, and gene/protein networks. The
course will include lectures and hands-on computer tutorials.
Prerequisite courses include biochemistry, molecular biology and
genetics.
Grade composition: 70% final exam and 30% written tutorials (the
exam can be substituted with a final project if approved)
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il
Blue: Daniel Red - Mickey Green - Eyal
1) The genetic playing field for selection (28/10/14 - Daniel)
a. Genetic code(s)
b. The central paradigm: DNA-RNA-protein
c. Non-coding RNAs
d. Where else can selection work? Non coding regions,
codon ratios and RNA stability
e. Tutorial: sequence databases
2) From sequence to function (4/11/14 - Daniel)
a. The various flavors of BLAST, HMMs.
b. Tutorial: ncbi BLAST
3) Multiple alignment (11/11/14 - Eyal)
a. Sequence alignment the basis of evolutionary analysis
b. Multiple alignments – making and testing
c. Other binning methods: nucleotide frequencies, clustering
d. Tutorial: Multiple alignment generation, filtering and
visualization (MAFFT & PAGAN; Guidance; Jalview)
4) Phylogeny (18/11/14 - Eyal)
a. Nothing in sequence analysis makes sense except in the
light of evolutionary trees
b. Distance-based methods
c. Bootstrap confidence scores
d. Likelihood-based methods
e. Rogue taxa
f. Tutorial: Phylogeny reconstruction and visualization
(RAxML & figtree)
5) Introduction to Protein structure (25/11/14 - Mickey)
a. 3D structures of proteins – introduction
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il
b.
c.
d.
e.
Primary, secondary, tertiary, quaternary structures
Protein folding, structural domains
3D structure visualization
Tutorial: PDB, PDBe, 3D structure visualization online
6) Proteins - one segment/motif at a time (2/12/14 - Mickey)
a. Functional domains – signal peptides, transmembrane
domains, coiled coils
b. Secondary structure prediction
c. In silico motif identification
d. Tutorial: 3D structure visualization continued
7) Protein structures - quantified and predicted (Mickey 9/12/14)
a. From Structure to function
b. Energy functions for 3D structures
c. Structure comparison
d. Structure prediction
e. Tutorial: ExPASY, motif prediction servers, fold
recognition servers
8) What makes a genome and how to sequence it (16/12/14 Daniel)
a. Genome types: linear, circular, plasmids, viruses
b. Origins, operons, rRNA
c. Start and stop codons, PolyA, RBS, Shine-Delgarno
d. Introns and exons
e. Sequencing methods – their advantages and
disadvantages: Sanger, 454, Illumina, next-generation
f. Assembling a genome
g. Tutorial: Genome browsing - Microbesonline, IMG
9) Comparative genomics (23/12/14 - Daniel)
a. Homologs, Paralogs and Orthologs
b. Genome evolution: gene content vs. Synteny
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il
c. Lateral gene transfer
d. Islands in the genome
e. Tutorial (12/12/13): Comparative microbial genomics
(IMG, Microbesonline)
10)
a.
b.
c.
d.
e.
Eukaryotic genomics (30/12/14 - Eyal)
Junk DNA and repetitive elements
Assembling BIG genomes
Gene structure annotation (blast, HMM, Maker)
Mapping transcriptomes to genomes
GC bias, DNA methylation & other epigenetics
a.
b.
c.
d.
e.
The gene lives in an organism (6/1/15 - Eyal)
Functional categories (GO, COG, KEGG)
Metabolic networks
Regulatory networks
Protein-protein interaction networks
Tutorial (19/12/13):
11)
12)
Other “Omics” - transcriptomes and proteomes
(13/11/14 - Daniel)
a. Recruiting transcriptomes to genomes
b. De-novo transcriptome assembly
c. P value vs Q value
d. Tandem MS/MS and shotgun proteomics
e. Tutorial (17/1/13): Excel tricks for dealing with NGS data
13)
A very brief introduction to environmental genomics
(20/1/14 - Daniel)
a. The uncultivated majority
b. Who is there? 16S
c. What can they do? metagenomics.
d. What are they doing? metatranscriptomics,
metaproteomics
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il
e. Tutorial: IMG/M
14)
Summary lesson and teaser for further courses
(27/1/14 - all teachers)
a.
30% Exercises - Yonatan
70% Final exam; students can opt to do a research project
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il
Some examples of seminar papers (likely to be updated):
Gene and genome papers:
Sorek, R et al (2007) Genome-wide experimental determination of
barriers to horizontal gene transfer. Science 318(5855):1449-52.
Coleman, ML et al (2006) Genomic islands and the ecology and
evolution of Prochlorococcus. Science 311(5768):1768-70.
Putnam et al (2006) Sea anemone genome reveals ancestral
eumetazoan gene repertoire and genomic organization. Science
317(5834):86-94.
Beja, O et al (2000) Bacterial rhodopsin: evidence for a new type of
phototrophy in the sea. Science 289(5486):1902-6.
Sullivan, M et al (2005). Three Prochlorococcus Cyanophage
Genomes: Signature Features and Ecological Interpretations.
PLoS biology 3(5): e144
Tripp, HJ et al (2010). Metabolic streamlining in an open-ocean
nitrogen-fixing cyanobacterium. Nature 464(7285):90-4
Shrivastava, M et al (2010). The Amphimedon queenslandica
genome and the evolution of animal complexity. Nature
466(7307):720-6
Kettler, G.C. et al (2007) Patterns and Implications of Gene Gain
and Loss in the Evolution of Prochlorococcus. PLoS Genetics
3(12): e231.
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il
Metagenome and population papers:
Delong, EF et al (2005) Community Genomics Among Stratified
Microbial Assemblages in the Ocean's Interior. Science 311(
5760) 496-503
Rawis et al (2006). Reciprocal Gut Microbiota Transplants from
Zebrafish and Mice to Germ-free Recipients Reveal Host Habitat
Selection. Cell 127, 423–433
Coleman, ML and Chisholm, SW (2010). Ecosystem-specific
selection pressures revealed through comparative population
genomics. PNAS 07:18634–18639.
Campbell, BJ et al (2011) Activity of abundant and rare bacteria in a
coastal ocean. PNAS 108(31), 12776–12781
Yooseph, S. Et al (2010). Genomic and functional adaptation in
surface ocean planktonic prokaryotes. Nature 468, 60–66
___________________________________________________
Daniel Sher, PhD. The Marine Chemical Ecology lab
Department of Marine Biology, The Leon H.Charney School of Marine Science
University of Haifa, Mount Carmel, Haifa 31905, Israel
Phone:972-4-8240731 Fax: 972-4-8288267 Email: dsher@univ.haifa.ac.il