BMB 402 and BMB 502 Syllabus: Spring 2025

Introduction to Bioinformatics

Course Location and Times

Stevens Hall 365 and by Zoom

Tuesdays and Thursdays, 2:00 pm - 3:15 pm

Course Instructors and Contact Information

BMB 402 and BMB 502 (section 0001)

Benjamin L. King, Ph.D.

Office: 290 Hitchner Hall
Office hours: By appointment
E-mail: [email protected]

BMB 502 (section 0990)

Laura Jackson, Ph.D.

Office: 434 Corbett Hall
Office hours: By appointment
E-mail: [email protected]

Course Description

A multidisciplinary study of fundamental biological questions through the organization,

integration and analysis of increasingly large and complex datasets. Topics include
primary data repositories, data integration and curation, sequence analysis methods,
functional annotation, high-throughput sequence analysis workflows, statistical analysis
of gene expression data, clustering methods and modeling biological networks. BMB 502
cannot both be taken for credit consecutively after BMB 402.

Number of credit hours: 3

Prerequisites: BMB 280 (Introduction to Molecular and Cellular Biology) or instructor’s

permission.

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Course Goals

The primary goal of the course is to provide a broad overview of how bioinformatics is
used to advance the study of biological questions through the organization, integration
and analysis of datasets. A secondary goal of the course is to obtain practical knowledge
on how to begin to apply bioinformatics resources, methods and tools to specific
questions in molecular genetics.

The goals for each of the four units in both BMB 402 and BMB 502 are as follows.
1. Describe the scope of major primary data repositories for nucleotide, protein and
functional genomic data and how data are represented in those repositories.
2. Explain common data integration methods that have been employed in major
bioinformatics resources, such as genome browsers, and curated resources,
such as model organism databases.
3. Describe common sequence analysis algorithms and apply them to functionally
annotate sequences.
4. Describe and compare common workflows for high-throughput sequence
analysis and implement a workflow for gene expression studies conducted using
high-throughput RNA sequencing.

An additional goal for BMB 502 is as follows:

1. Critique analysis methods from publications that describe a gene expression
dataset.

Course Learning Objectives

At the completion of BMB 402 and BMB 502, students will:

1. Describe the basic principles of bioinformatics that includes the organization,
integration and analysis of biological datasets.
2. Define the major primary data sources that have transformed biology into a data-
intensive science.
3. Demonstrate working knowledge of a selection of major bioinformatics resources
and tools.
4. Describe the basic principles of data integration.
5. Describe basic programming concepts.
6. Describe how to critically evaluate data and analysis results using diagnostic
plots and visualization methods.
7. Demonstrate working knowledge of common analysis workflows for high-
throughput sequence data.
8. Describe best practices for experimental design of genome-wide gene
expression experiments.
9. Demonstrate basic working knowledge of the R statistical computing
environment.
10. Describe several commonly used clustering methods.
11. Describe how networks can be used to represent different biological datasets.
12. Describe ethical considerations for biomedical datasets.

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At the completion of BMB 502, students will also:
1. Contrast the strengths and weaknesses for analysis methods described in a
publication that presents a gene expression dataset.

Student Learning Outcomes

By the end of the course, students will be able to:

1. Name the major primary data repositories for:
a. Nucleotide sequence data
b. Protein sequence data
c. Sequence variation data
d. Functional genomics data
e. Proteomic data
2. Find genomic, transcript and protein sequences for a gene in multiple organisms.
3. List all characterized sequence variants for a given gene and the allele frequency
of each variant in a population.
4. Provide an example of how accession numbers from one resource may be
mapped to another resource.
5. Generate sets of protein sequences with common functions using Gene Ontology
annotations.
6. Functionally annotate protein sequences using protein sequence similarity,
domains and secondary structure.
7. Provide examples for how data is integrated within a genome browser.
8. List genes annotated within a given region of a genome assembly.
9. Find syntenic regions between genomes. For example, find the syntenic region in
the zebrafish genome for a given chromosomal region in the human genome.
10. Provide examples of curated bioinformatics resources.
11. List phenotypes observed for mutant alleles for mouse and zebrafish genes.
12. List chemicals described to alter the function or expression of a gene.
13. Provide examples for how each of the BLAST programs (blastn, blastx, blastp,
tblastn and tblastx) are used.
14. Demonstrate how to use a scoring matrix to evaluate a pairwise sequence
alignment.
15. Find primary sequence data (FASTQ) files for a published RNA sequencing
dataset.
16. Describe how sequence composition and k-mer content are used to evaluate
sequence bias in high-throughput sequence data.
17. Describe normalization techniques commonly used for gene expression data.
18. Describe how diagnostic plots are used to evaluate gene expression data.
19. Describe how heatmaps are used to summarize gene expression profiles and
what dendrograms generated by two-dimensional hierarchical clustering
represent.
20. Explain what nodes and edges represent when gene expression data are
visualized as a network.

Instructional Materials and Methods

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Optional Textbook:

Introduction to Bioinformatics (5th edition) - by Arthur M. Lesk

(ISBN-13: 978-0198794141)

List of references:

Electronic copies (PDFs) of selected papers will be provided through Fogler

Library. Included in these papers are the following:

● Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y. Identifying

personal genomes by surname inference. Science. 2013 Jan
18;339(6117):321-4. doi:10.1126/science.1229566. PubMed PMID:
23329047.
● Erlich Y, Shor T, Pe'er I, Carmi S. Identity inference of genomic data using
long-range familial searches. Science. 2018 Nov 9;362(6415):690-694.
doi: 10.1126/science.aau4832. Epub 2018 Oct 11. PubMed PMID:
30309907.
● Jensen RA, Thompson ME, Jetton TL, Szabo CI, van der Meer R, Helou
B, Tronick SR, Page DL, King MC, Holt JT. BRCA1 is secreted and
exhibits properties of a granin. Nat Genet. 1996 Mar;12(3):303-8. PubMed
PMID: 8589722.
● Koonin EV, Altschul SF, Bork P. BRCA1 protein products ... Functional
motifs... Nat Genet. 1996 Jul;13(3):266-8. PubMed PMID: 8673121.
● Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G. BLOSUM62
miscalculations improve search performance. Nat Biotechnol. 2008
Mar;26(3):274-5. doi: 10.1038/nbt0308-274. PubMed PMID: 18327232.
● Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level
expression analysis of RNA-seq experiments with HISAT, StringTie and
Ballgown. Nat Protoc. 2016 Sep;11(9):1650-67. doi:
10.1038/nprot.2016.095. PubMed PMID: 27560171; PubMed Central
PMCID: PMC5032908.
● Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W,
Robinson MD. Count-based differential expression analysis of RNA
sequencing data using R and Bioconductor. Nat Protoc. 2013
Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. PubMed PMID:
23975260.

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 Required technology:

1. BrightSpace – all students must have access to and use BrightSpace

using a web browser. BrightSpace may be accessed through
https://my.umaine.edu.
2. Zoom – all students who cannot attend in person must have access to and
use Zoom to participate in the course.
3. Laptop with Camera – students will need a laptop with a camera and the
following free software installed:
a. Current version of a web browser
b. Current version of the R statistical computing environment
c. Current version of RStudio
d. Plain text editor: BBEdit (Mac) or Sublime Text (Windows)
4. Electronic journals – UMaine’s Fogler Library provides electronic access
to journals.

Schedule (SUBJECT TO CHANGE)

(Dates for Spring 2024)

Date Topics Learning Assignments Unit Activities

activities & Project

Week 1. Course introduction Gymrek et al. Assignment 1:

Jan. 21 Unit 1: Overview of Science (2013) Read Gymrek et al.
bioinformatics and Erich et al. Science (2013) and
● Need Science (2018) Erich et al. Science
● Scope papers (2018) papers, and
● Data sharing answer questions.
● Controlled Lesk Chapters 1
vocabularies and 2 (optional)
● Data integration
● Ethical
considerations of
data sharing

Week 2. Unit 1: Primary data Readings Assignment 2: The Jan. 30 –

Jan. 28 types: “omics” ENCODE Project Assignment 1
approaches to Lesk Chapter 3 Due
characterize biological (optional)
systems
● Genomics
● Transcriptomics
● Epigenetics
● Proteomics
● Metabolomics

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Week 3. Unit 1: Primary data Readings Unit 1 Take Home Feb. 6 -
Feb. 4 repositories Exam Assignment 2
● Sequence Lesk Chapter 4 Due
● Sequence variation (optional) Term project
● Protein structure concept (due Feb.
● Identifiable human 20)
genomic data
Functional
annotation
● Nomenclature
● Gene Ontology

Week 4. Unit 2: High-throughput Readings Unit 1 Take Home Feb. 13 - Unit

Feb. 11 sequence analysis Exam 1 Take Home
workflows Exam Due
● RNA sequencing Term project
concept (due Feb.
15)
Week 5. Unit 2: Introduction to R Readings Assignment 3: Feb. 20 - Term
Feb. 18 statistical computing Basic R plotting project
environment script concept due
● Scripts
● Variables Term project
● Data structures concept (due Feb.
● Common operations 20)
● Plotting

Week 6. Unit 2: RNA-Seq data Readings Assignment 3: Feb. 27 –

Feb. 25 analysis in R Basic R plotting Assignment 3
● Diagnostic analysis script Due
● Statistical modeling
● Differential Term project outline
expression testing (due Mar. 6)
● Multiple testing
adjustment
● Data visualization

Week 7. Unit 2: Clustering Readings Unit 2 Take Home Mar. 6 –

Mar. 4 methods with application Exam Term project
to RNA-Seq data outline due
● Hierarchical Term project outline
clustering (due Mar. 6)
● k-means
● Principal Component
Analysis
● Support Vector
Machines

Week 8. Unit 3: Sequence Lesk Chapter 4 Unit 2 Take Home Mar. 13 – Unit
Mar. 11 alignment methods (optional) Exam 2 Take Home
● Local, global Exam Due
● Pairwise, multiple Assignment 4:
● BLAST, BLAT Hunting for genes
● Repeatmasking

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 Unit 3: High-throughput
sequence analysis
workflows
● Sequence variation

SPRING BREAK
Mar. 17-21
Week 9. Unit 3: Data integration Readings Assignment 4:
Mar. 25 Genome browsers Hunting for genes
● UCSC Genome
Browser
● Ensembl

Week 10. Unit 3: Leveraging data Readings Unit 3 Take Home Apr. 3 -
Apr. 1 integration Exam Assignment 4
● Genome-wide Due
analysis (BioMart)
● Gene interactions
(STRING)

Week 11. Unit 4: Curated data Readings Unit 3 Take Home Apr. 10 – Unit
Apr. 8 integration Exam 3 Take Home
● Model organism Exam Due
databases Assignment 5: Data
● Mouse Genome Integration
Informatics (MGI)
● Zebrafish
Information Network
(ZFIN)
Week 12. Unit 4: Introduction to Readings Assignment 5: Data Apr. 17 – Term
Apr. 15 data modeling integration Project Update
● Example: integrate Due
gene expression BMB 502: Critique
datasets Assignment: Write
critique of
published gene
expression study
(to be announced).

Week 13. Unit 4: Curated data Readings Unit 4 Take Home Apr. 24 –
Apr. 22 integration Exam
● Comparative BMB 402/502:
Toxicogenomics Assignment 5
Database
BMB 502:
Critique
Assignment
Due
Week 14. Unit 4: Biological Readings Unit 4 Take Home May 9 – Term
Apr. 29 networks with application Exam project due
to RNA-Seq data Lesk Chapter 8
● Correlation (optional) May 9 – Unit 4
● Adjacency matrix Take Home
● Data visualization Exam Due

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Grading and Course Expectations

Components of the final course grade for BMB 402:

Requirement % Grade
Participation 5
Assignments 30 (5 assignments @ 6% each)
Exams 40 (4 exams @ 10% each)
Term Project 25
Total 100

Components of the final course grade for BMB 502:

Requirement % Grade
Participation 5
Assignments 20 (5 assignments @ 4% each)
Critique Assignment 10
Exams 40 (4 exams @ 10% each)
Term Project 25
Total 100

Exam schedule:

1. Unit 1: End of week 4 (Feb. 13)

2. Unit 2: End of week 8 (Mar. 13)
3. Unit 3: End of week 11 (Apr. 10)
4. Unit 4: End of week 14 (May 9)

Letter grading is determined using the following range.

A = 93 - 100 B- = 80 - 82 D+ = 67 - 69
A- = 90 - 92 C+ = 77 - 79 D = 63 - 66
B+ = 87 - 89 C = 73 - 76 D- = 60 - 62
B = 83 - 86 C- = 70 - 72 F = below 60

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Participation

Participation is required and accounts for 5% of your final grade. Excused absences are only
permitted with prior notification to the instructor and official documentation. Participation will be
graded using activities held during class and on the discussion board within Brightspace.

Assignments and Exams

All four units of the course have one or more assignments and a take home exam. The
assignments will require students to write a short summary of a paper, answer questions or
complete specific activities. Students will need to integrate new and past knowledge and then
apply it to new problems or questions. Working in groups on assignments is encouraged. Take
home exams are to be completed individually. All assignments and take-home exams are to be
submitted through Brightspace. Assignments and exams are due by the start of class on the
due date.

Term Project

Students are required to complete a term project on a bioinformatics topic that will be
summarized in a written report, presentation slides and recorded presentation. Each student
must submit a one paragraph project proposal by the end of week 5. This proposal will be
reviewed by the instructor. The instructor may require the student to refine or redirect their topic
so that the scope is appropriate. The project may be on a variety of topics relevant to the course
and may include an analysis component. Term projects will be graded based on the depth and
level of critical and independent thinking demonstrated in the report.

Course Policies

● Attendance and class participation are required and a major component of your grade.
● Grades for late submissions of assignments will be penalized by 10% for each day the
assignment is late.
● Late submissions of exams or term projects will not be accepted and assigned a score of
zero.
● Extra credit assignments are not available.
● Incomplete work will be graded based on the portion that has been completed.
● Final date for all work to be in, unless other arrangements have been made with the
instructor, is 5:00pm Friday of the last week of scheduled classes for the semester.

Artificial Intelligence

All coding, written or other work submitted for this course must be completed by you, personally.
Use of artificial intelligence (AI) to generate language coding, text, or assignment answers is
strictly prohibited. Submission of work generated by AI will be considered a violation of
academic integrity, including AI-generated responses that you have summarized or edited.

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Academic Honesty Statement

Academic Honesty Statement: Academic honesty is very important. It is dishonest to cheat on exams, to
copy term papers, to submit papers written by another person, or generated by software or systems
without the explicit approval of the instructor, to fake experimental results, or to copy or reword parts of
books or articles into your own papers without appropriately citing the source. Students committing or
aiding in any of these violations may be given failing grades for an assignment or for an entire course, at
the discretion of the instructor. In addition to any academic action taken by an instructor, these violations
are also subject to action under the University of Maine Student Conduct Code. The maximum possible
sanction under the student conduct code is dismissal from the University. Please see the University of
Maine System’s Academic Integrity Policy listed in the Board Policy Manual as Policy 314 (*Date Issued:
September 1, 2020): https://www.maine.edu/board-of-trustees/policy-manual/section-314/

Course Schedule Disclaimer

Course Schedule Disclaimer (Disruption Clause): In the event of an extended disruption of normal
classroom activities (due to COVID-19 or other long-term disruptions), the format for this course may be
modified to enable its completion within its programmed time frame. In that event, you will be provided an
addendum to the syllabus that will supersede this version.

Students Accessibility Services Statement

If you have a disability for which you may be requesting an accommodation, please contact Student
Accessibility Services, located at the Center for Accessibility and Volunteer Engagement at the UCU, 139
Rangeley Rd, [email protected], 207.581.2319, as early as possible in the term. Students may begin
the accommodation process by submitting an accommodation request form online and uploading
documentation at https://umaine-accommodate.symplicity.com/public_accommodation/. Once students
meet with SAS and eligibility has been determined, students submit an online request with SAS each
semester to activate their approved accommodations. SAS creates an accessibility letter each semester
which informs faculty of potential course access and approved reasonable accommodations; the letter is
sent directly to the course instructor. Students who have already been approved for accommodations by
SAS and have a current accommodation letter should meet with Dr. Benjamin King or Dr. Laura Jackson
(depending on the course/section you are enrolled) privately as soon as possible.

Observance of Religious Holidays/Events

Observance of Religious Holidays/Events: The University of Maine recognizes that when students are
observing significant religious holidays, some may be unable to attend classes or labs, study, take tests,
or work on other assignments. If they provide adequate notice (at least one week and longer if at all
possible), these students are allowed to make up course requirements as long as this effort does not
create an unreasonable burden upon the instructor, department or University. At the discretion of the
instructor, such coursework could be due before or after the examination or assignment. No adverse or
prejudicial effects shall result to a student’s grade for the examination, study, or course requirement on
the day of religious observance. The student shall not be marked absent from the class due to observing
a significant religious holiday. In the case of an internship or clinical, students should refer to the
applicable policy in place by the employer or site.

Classroom Environment

This class is premised on the belief that we all work together to promote an inclusive learning
environment for all and that the use of gross generalizations, stereotypes, and
derogatory/oppressive language are not conducive to inclusivity. Elevating practices of
supportive communication and learning from one another, we commit to naming instances of

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using derogatory and/or oppressive communication in our shared classroom (including by the
instructor or directed toward them). If oppressive communication is called out, we will stop,
listen with empathy and expand the learning opportunity for everyone. You may not agree with
the views expressed by others (and you shouldn’t), but we must all agree to make space for
difference. Listening to the perspectives of others creates greater understanding of the diversity
of experiences, knowledge, and ways of being in society.

Sexual Discrimination Reporting

The University of Maine is committed to making campus a safe place for students. Because of this
commitment, if you tell a teacher about an experience of sexual assault, sexual harassment, stalking,
relationship abuse (dating violence and domestic violence), sexual misconduct or any form of
gender discrimination involving members of the campus, your teacher is required to report this
information to Title IX Student Services or the Office of Equal Opportunity.

If you want to talk in confidence to someone about an experience of sexual discrimination, please
contact these resources:

For confidential resources on campus: Counseling Center: 207-581-1392 or Northern Light Primary
Care, University of Maine: at 207-581-4000. Confidential Resource Advisor: 207-571-5372 (call or
text). Or see the Confidential Resource Advisor website for a complete list of services and resources
(open in a new window).

For confidential resources off campus: Rape Response Services: 1-800-871-7741 or Partners for
Peace: 1-800-863-9909.

Other resources: The resources listed below can offer support but may have to report the incident to
others who can help:

For support services on campus: Title IX Student Services: 207-581-1406, Office of Community
Standards: 207-581-1409, University of Maine Police: 207-581-4040 or 911. Or see the Title IX
Student Services website for a complete list of services (open in a new window) . Also, Student Wellness
Resource Center (opens in a new window).

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