Final Projects

Bio131 final projects touch on numerous topics throughout the course. These projects range from from investigating specific proteins and genes, to identifying patterns in genome rearrangements, to implementing more advanced algorithms described in the textbook. Materials are provided based on the students' consent.

* The project was related to the student's thesis, summer research, or independent project in another course.

Spring 2020

This semester ended online, and projects were a bit smaller in scope than previous years.

Sequence Alignment

Affine Gap Alignment - Iki Edreva
Modifying the Local Alignment Algorithm to Return Multiple Alignments - Madeleine Fenner [report.pdf]
Grantham Scores of Orthologs from Closely-Related Species - Kai Hakomori [report.pdf]
* Global and Local Protein Sequence Alignments of Selected Pathogenic Substrate Binding Proteins - Ipsita Krishnamurthy [report.pdf]
Sequence Alignment with Affine Gap Penalties - Hannah Meier
Multiple Sequence Alignment - Nicole Xu

Motif Finding

Randomized Motif Search and Gibb's Sampling - Arthi Haripriyan [report.pdf]
Random Motif Searching - Max Johnson
A Parallel Greedy Motif Finder - Robert McCaull [report.pdf]
Biological vs. Algorithmic Efficiency in the Motif Finding Problem- Stella Wroblewski [report.pdf]

Cyclopeptide Sequencing

Ananke Garani-Krishnan [report.pdf]
Carli Newman [report.pdf]
Julia Yuan [report.pdf]
Verona Yue [report.pdf]

SARS-Cov2 (COVID19) Projects

COVID-19 and MERS-CoV ORF1a Protein Sequence Alignment - Priya Narain [report.pdf]
Comparative Study on Spike Glycoprotein Structure Between Different Clades of SARS-Cov2 - Frank Zhuang

Programming the Central Dogma

The Central Dogma for Neurofibromatosis Type 1 - Erica Leif
Translating Different MYBPC3 Gene Variants - Leila Sinclair
Asymmetric DNA Replication - Maham Zia

De Bruijn Graphs

Finding an Eulerian Cycle in a De Bruijn Graph - Shawn Owens [report.pdf]

Spring 2018

Molecular Structures and Signatures

Greedy Folding Algorithm for RNA Secondary Structure Prediction - Kieran Andrews [slides.pptx][report.pdf][code]
Identifying Multiple Candidate OriCs in Bacterial Genomes - Javin deMello Folsom [slides.pdf][report.pdf][code]
* Quantifying DNA Methylation - Kat Kessler and James Vesto [slides.pptx][report.pdf][code]
Location of the Evening Element Binding Site in Promoter Sequences - Leila Shokat [slides.pptx][report.pdf][code]
Frameshift Alignment - Theresa Steele [slides.pdf][report.pdf][code]
Predicting Protein Tertiary Structure - Luke Steigler

De Novo Assembly Tasks

A Linear-Time Algorithm for Finding Eulerian Cycles - Usman Hafeez
Alignment-Free Assembly - Chris Henn [report.pdf][code][visualization]
Finding Eulerian Cycles in Graphs - Natasha Baas-Thomas [slides.pptx][report.pdf]
Identifying Contigs from De Bruijn Graphs - Jacques Trautman

Comparative Genomics

Similarities Between Humans and Bananas: A Comparison of Housekeeping Genes Between Two Species - Madeline Doak [slides.pptx][report.pdf][code]
* Local Alignment of TerD paralogs - Akanksha Majumadar
* Analysis of Heat Shock Protein sequences in Camellia sinensis - Hannah McConnell
* Interspecies Comparisons of ADAMTS13 Using Global and Local Alignments - Katie McPherson and Matthew Muller
Aligning Grass Protein Sequences Using PAM-Modified Global Alignment - Yifei Zhang [slides.pptx][report.pdf][code]

Affine Gap Alignment (textbook problems)

Ian MacCourt
Marcus Bamberger [slides.pptx][report.pdf]
Laurel Schuster [slides.pptx][report.pdf]

Cyclopeptide Sequencing (textbook problems)

Corinna Del Val
Camille Hendry [slides.pptx][report.pdf]
Tayla Isensee [slides.pptx][report.pdf]
Sol Taylor-Brill [slides.pptx][report.pdf]
Annie Peng

Spring 2017

Motif Finding

* Finding Motifs in Restriction Enzyme Sequences - August Staubus [slides.pptx][report.pdf]

Sequence Alignment

Three sequence alignment - Hayden Adoff
* Telomerase biology with A. burtoni: measuring identity with global alignment and affine gap penalties - Alexa Buckner [slides.pptx][report.pdf]
* Presence of E. coli in the rat intestinal microbiome before and after antibiotics - Yasemin Lopez
Heat shock analysis using the affine gap penalty - Hannah Sophia Mead
Affine gap alignment: an improved global alignment - Yu Fu [slides.pptx][report.pdf]

Sequence Conservation

Recreating the PAM250 matrix - Miriam Bern [slides.pptx][report.pdf]
* Identifying regions of high conservation to design degenerate primers - Alli Fatone
Automated design and scoring of degenerate primers From multiple taxon-specific Primers - Den Ivanov [slides.pdf][report.pdf]
Navigating phylogenetic trees using graphing algorithms - Giorlando Ramirez [slides.pdf][report.pdf]
Measuring relatedness between strands of DNA - Aaron Till
* Studying the conservation of PinX1 - Evan Welch [slides.pptx][report.pdf]

De novo Genome Assembly

Breaking De Bruijn graphs - Noah Radetsky
Overlapping to order: computing Eulerian cycles - Richard Pham [slides.pptx][report.pdf]

Non-Ribosomal Proteins

Sequencing cyclic peptides - Shayan Abtahi [slides.pptx][report.pdf]
Sequencing non-ribosombal proteins - Gwen Miller

Miscellaneous Topics

Dynamically Rearranging Synteny Blocks in Comparative Genomes - Nick Egan [slides.pptx][report.pdf]
* Speeding up the process of genome annotation - Eliotte Garling [slides.key][report.pdf]
Visual(eyes)ing predicted phenotypic probabilities - Simue' Isabel [slides.pptx][report.pdf]
Alternative splicing of the human POL2RB gene - Madhav Pulle
Predicting the secondary structure of RNA - Mitra Shokat [slides.pptx][report.pdf]

Spring 2016

Motif Finding

* Identification and characterization of pre-miRNA candidates in the C. mitchellii genome - Madeline Dinsdale [slides.pptx][report.pdf]
* Aromatase regulation: transcription factor binding sites - Rose Driscoll
A Gibbs Sampler for motif finding - Caleb Kalisher [report.pdf]
* Searching for 6-mers in pre-miRNAs - Elaine Kushkowski
Identifying origins of replication in circular genomes using a scoring method - Yurel Watson [slides.pdf][report.pdf]

Sequence Alignment

* Comparing crosslinkers: sequence conservation of Drosophila Short Stop and its homologs - Mari Cobb [slides.pptx][report.pdf]
Global alignment with affine gap penalties - Jocelyn Hansson [slides.pdf][report.pdf]
CAMKII sequence conservation across chicken, rat, and human - Alexander King [slides.pdf][report.pdf]
Comparing Blast alignments of mouse genes and human chromosomes - Amy Rose Lazarte [slides.pptx][report.pdf]
* Comparing mitochondrial DNA - Mina Marden [slides.pptx]

Non-Ribosomal Proteins

Non-Ribosomal Peptides: Sequencing Antibiotics - Kimmie McGowen [slides.pdf][report.pdf]

Fall 2015

Motif Finding

* AT-rich regions in promoter regions of Enteropathogenic E. coli - Lily Ben-Avi [slides.pptx][report.pdf]
Multiple replication origins in the archaeon Sulfolobus solfataricus - Ami Cooper [report.pdf]
* Splicing factor motifs in the alternatively-spliced D2 receptor gene - Danny Heinz [slides.pptx][report.pdf]
* Prospero binding site motifs in notch gene promoter regions - Emily Merfeld [slides.pptx][report.pdf]

Sequence Alignment and Assembly

* Primary and secondary structure comparison of PinX1 sequences from frogs, mice, and humans - Ajit Elhance [slides.pptx][report.pdf]
Affine gap alignment of ATF3 and PCDH15 isoforms - Erin Howell [slides.pptx][report.pdf]
De novo assembly of Candidatus Carsonella Ruddii from simulated paired-read data - Carol Iglesias Otero [slides.pptx][report.pdf]

Genome Rearrangements

Conserved synteny blocks from mouse, chimp, and human ChrX - Karl Menzel [slides.pptx][report.pdf]
Synteny block clustering and comparison of mouse, monkey, and human HOX genes - Madeline Robin [slides.pptx][report.pdf]

Non-Ribosomal Proteins

Cyclopeptide sequencing from mass spectra - Abrar Abidi [report.pdf]
A-domain sequence classification - Nick Till [slides.pptx][report.pdf]

Miscellaneous Topics

High-dimensional clustering of time series gene expression data - Aristomenes Spanos [slides.pptx]
Ancestral reconstruction of hypothetical proteins - Jazz Weisman [slides.ppt][report.pdf]