Summer internship in Bioinformatics and Computational Genomics

List of past student projects

[2016] (UG=undergraduate student, HS=high school student)

  • Barathi Aravindan (HS) - Identification of telomeric sequences in plant genome assemblies (mentor Daniela Puiu)
  • Raymon Cao (UG) - HISAT2 alignment for CYP genotyping (mentor Daehwan Kim)
  • Howard Huang (UG) - Evaluating HISAT-Genotyper for HLA alleles (mentor Daehwan Kim)
  • Raymond Huffman (HS) - Computational analysis of intron retention events in RNA-seq data (mentor Liliana Florea)
  • Jonathan Jaroslawicz (UG) - Statistical mechanics model for cancer cell invasion and dissemination (mentor Joel Bader)
  • Ashutosh Jindal (UG) - Identification of alternative splicing events from RNA-seq data (mentor Mihaela Pertea)
  • Aryaman Khandelwal (HS) - DNA methylation and mitochondrial DNA copy number (mentor Dan Arking)
  • David Miller (HS) - Using StringTie with edgeR and DESeq2 (mentor Geo Pertea)

[2015] (UG=undergraduate student, HS=high school student)

  • Shreya Bhatia (HS) - Meta-analysis of miRNA regulation, abundance, and target genes in brains of Alzheimer's patients (mentor James Taylor)
  • Kevin Huang (UG) - Improved microbial gene finding using large protein sequence data sets (mentor Steven Salzberg)
  • Emily Herring (UG) - Metagenomics classification with untranslated versus translated search (mentor Ben Langmead)
  • Emma Jin (HS) - Clustering of repetitive genomic sequences (mentor Ben Langmead)
  • Nishiki Karbhari (UG) - SRA trait prediction using genomic data (mentor Jeff Leek)
  • Joseph Paggi (UG) - Graph-based alignment of DNA sequence to a population of genomes (mentor Daehwan Kim)
  • Shivani Pandey (HS) - Methods for Aegilops tauschii BAC pool assembly validation (mentor Daniela Puiu)
  • Rebecca Panitch (UG) - Replication of schizophrenia and bipolar disorder RNA-seq analysis (mentor Dan Arking)
  • Robert Phillips (UG) - SRA trait prediction using genomic data (mentor Jeff Leek)
  • Shannon Rainsford (UG) - From A to B: an enrichment analysis of subcompartments in topologically associated domains (mentor James Taylor)
  • Annika Salzberg (HS) - R for the Intimidated, an online course (mentors Jeff Leek and Steven Salzberg)
  • Alison Samsel (UG) - Metagenomics classification with untranslated versus translated search (mentor Ben Langmead)
  • Kayla Scharfstein (HS) - Identifying microbes from rRNA in whole genome sequencing experiments (mentor Florian Breitwieser)
  • Dhruv Shankar (UG) - Evaluating the accuracy of genome assembly with RNA-seq data (mentor Liliana Florea)
  • Ankur Sundara (HS) - Detecting splicing events in plants using splice graphs (mentor Liliana Florea)
  • Sara Wang (UG) - SRA sex prediction using genomic data (mentor Jeff Leek)


  • Andre Reis - Studying regulatory aspects of melanoma by combining GWAS and epigenetic data (mentor Andy McCallion)
  • Samier Merchant - Taxonomic classification of DNA sequences and applications (mentor Steven Salzberg)
  • Michael McConville - Repeat sequences and read alignment (mentor Ben Langmead)
  • Linda Gai - A search engine for proteins and researchers (mentor Joel Bader)
  • Kyle Hirschfelder - Modeling dynamic transcription factor binding and gene expression in development (mentor James Taylor)
  • Daniela Perry - Statistically modeling RNA-seq simulations comparing two spliced isoforms (mentors Liliana Florea and Stefan Canzar)
  • Edward Pang - Correlation between mtDNA copy number and mitochondrial gene expression (mentor Dan Arking)
  • Jonah Langlieb - Finishing the sugar pine and Douglas fir chloroplast (mentor Daniela Puiu)
  • Steffen Cornwell - Prediction of Myc binding sites from ChIP-seq profiles (mentor Hongkai Ji)


  • James Miller - Visualizing DNA methylation in autism (mentor Dan Arking)
  • Andrew Wang - Metagenomics analysis of arctic peat and agricultural filed samples (mentor Daniela Puiu)
  • Philip Yu - Alternative splicing of human B-cells (mentor Liliana Florea)
  • Veronica Lee - Evaluating errors in RNA-seq analyses (mentor Stefan Canzar)
  • Jaime Morton - Myrna2: Differiential gene expression (mentor Ben Langmead)
  • Sid Nanda - Transcription of Alu repeat sequences in the human genome (mentor Steven Salzberg)


  • Dhruv Shankar - A comparison of repeat finding software for the Pinus taeda genome (mentor Daniela Puiu)
  • Leslie Myint - Battle of the aligners (mentor Steven Salzberg)
  • Casey Lim - 'Seq'-ing the best annotation (mentor Tanja Magoc)
  • Shmuale Mark - RNA-seq mapping challenges and pseudogenes (mentor Dan Arking)
  • Kalliopi Drakos - Analysis of intron retention in the human genome (mentor Liliana Florea)
  • Alex Smith - Analyzing MYC targets (mentor Hongkai Ji)
  • Lani Matthews - Copy number variation in cancer (mentor Rob Scharpf)