Lab Alumni

Class of
2016!
Kirsten Fischer - Kirsten’s did a Research Methods project during Fall 2015 analyzing the genome of Flavobacterium sp. ABG. Her goal was to compare the genome to what we thought were the closest relatives based on 16S rRNA sequence – Flavobacterium succinicans, glaciei and hydatis. However, when performing whole genome sequence comparisons, Flavobacterium hibernum, reichenbachii and denitrificans were the most similar. She also discovered a problem with the initial assembly of the ABG genome that caused one area of the rRNA gene to be duplicated. Because of the amount of time necessary to fix the problems, we put this on the back burner and Kirsten focused on a different organism, Flavobacterium sp KJJ. A major contribution of Kirsten’s work is a further standardization in the way we approach genome analysis for our novel species, which is outlined on our research page. Kirsten will present her work at the ASM Microbe 2016 meeting in Boston and we expect to submit the KJJ paper for publication this summer
Honors Thesis - Genomic Analysis and Classification of Novel Species Flavobacterium gabrieli KJJ
Class of
2015!
Bayly Anderson
Emily Barger
Jesse Clayton - MD Program at Commonwealth Medical College(TCMC)
Jesse took Biochemistry as a Junior, but not Microbiology, so for Research Methods he chose a more biochemistry/bioinformatics oriented project focused on comparing “true” Chryseobacterium genomes with those from organisms that started in separate genera (Kaistella and Sejongia) but were moved into the genus Chryseobacterium. Jesse discovered that all of the organisms we will propose for the reinstated Kaistella genus have Nitrous Oxide Reductase but none of the “true” Chryseobacterium have it. His Research Methods paper and poster are below.
Paper - Evidence Found Which Supports The Reinstatement of The Genus Kaistella
Poster - Presented at Research Methods poster session December 4, 2014
Andrew Gale - PhD program at Johns Hopkins University
Andrew worked in my lab starting in his freshman year and participated in a number of projects. Initially, he was trained by Jordan Krebs’13 on the HPLC and helped with developing our pigment polar lipid analysis methods. As part of the Molecular Biology course, Andrew sequenced the genome of Flavobacterium aquatile, the type species for the genus, family and order. This involved preparation of the DNA that was sent off for sequencing, then manual analysis of the initial assembly to improve it, resulting in a final assembly of just 7 contigs, GenBank WGS JRHH. Later, he was very active in our efforts to develop bioinformatics tools to compare the genome sequences of organisms. Specifically he helped develop Excel macros to take the output (*.tsv files) from the RAST sequence-based comparison tool and calculate Average Amino Acid Identity, %Bi-directional Best Hits, Orthology Score and Reciprocal Orthology Score Average (ROSA). For Andrew’s Honors Project, he examined the phylogenetic relationships among a broad range of organisms using the ROSA metric we developed. His goal was to investigate instances in which the metric was outside the range expected based on its current classification, to determine if the discrepancy reflected a problem with the metric or the classification. As part of this, Andrew worked with Tom Sontag ’14 to develop a pair of Excel files that would take RAST sequence-based comparison *.tsv files and group genes into different categories of sharing (unique, shared by 1&2, 1&3, 1&4, etc), then by performing the analysis with 5 files, would generate the data for a Venn diagram
  • Honors Thesis - Validation of Reciprocal Orthology Score Average (ROSA) Through Comparison With Other Genomic Metrics and Traditional Phenotypic Methods
  • Andrew Gale & Jeff Newman – ASM 2015 New Orleans
    Reclassification within the Genus Flavobacterium.
  • Andrew Gale, Jordan Krebs, Eileen Peluso & Jeff Newman – ASM 2014 Boston
    Integration of Average Amino Acid Identity (AAI) and Percentage of Orthologous Genes in a Single Phylogenomic Metric, the Reciprocal Orthology Score Average (ROSA)
    		•
    Miranda Giraldo
    Victoria Keyser
    Shannon Pipes – Ph.D. program for Marine Science at the University of South Carolina
    Shannon took Microbiology in spring of her junior year, and heard from her friend Samantha Stropko that I had some funding from the Fish and Boat Commission for a student to work in my lab that summer to sequence the genomes of some Large Mouth Bass Virus (LMBV) isolates collected from small mouth Bass. She had worked with the Lycoming College Clean Water Institute the previous summer and was interested in Marine Biology. During summer 2014, and continuing into her senior year, Shannon first researched LMBV and other Iridoviruses to identify primers to confirm that we actually had isolated LMBV DNA. After PCR and Sanger sequencing confirmed that we had good DNA, we sequenced, assembled and compared the genome sequences. We concluded that the 3 LMBV isolates from SMB were essentially identical to the isolate from LMB that we also sequenced. Shannon presented her work as posters at the Bucknell River Symposium in Nov 2014, and at the ASM meeting in May 2015. She and Samantha Stropko also worked together to analyze the novel species that Sam identified in the Microbiology course. In the process, we discovered that two separately published species, Bacillus cibi and Bacillus indicus, were similar enough to really be the same species. Her posters and paper are below.
  • Stropko*, SJ, Pipes*, SE, and Newman, JD. (2014) Genome-based reclassification of Bacillus cibi as a latter heterotypic synonym of Bacillus indicus and emended description of Bacillus indicus. Int. J. Syst. Evol. Microbiol. 64:3804-3809.
  • Shannon Pipes & Jeff Newman (from ASM 2015)
    Genome Sequence Analysis of Largemouth Bass Virus Isolates from Smallmouth Bass
    		•
    Abigail Smith - Dental School - Illinois
    Samantha Stropko
    Class of
    2014!
    Taylor Anspach
    Victoria Bortniak- Clinical Lab Science
    Caitlin Dougherty - Clinical Lab Science
    Ashley Gimbel
    Dillon Snyder
    Thomas Sontag
    Kyle Swovick - Ph.D program University of Rochester
    Kerry Then - Clinical Lab Science
    Class of
    2013!
    Shayn Collins - MD program St George's University
    Tri Do
    Trisha Duncan
    Lain Hostelley - Ph.D Program University of Maryland
    Honors Thesis - Sequencing, Assembly, and Annotation of the Kaistella koreensis Genome and Comparison to Closely Related Organisms
    Jordan Krebs - NIH --> MD-PhD program Penn State Hershey
    Honors Thesis - Purification and Molecular Structure Determination of Flexirubin Pigments from Chryseobacterium
    Jessica Lehman - High School Teacher
    Logan Mariano - Dental School Temple University
    Clark Thompson
    Class of
    2011!
    Melissa Cashner
    Kristen Collins
    Kevin Failor - Ph.D Programm Virginia Tech
    Katherine Smith - PA Program Lock Haven University
    Class of
    2010!
    Allison Batties – Ph.D. Program in Molecular Medicine, University of Virginia
    Damian Mariano – Dental School, Temple University
    Samantha McKenna
    Alicia Schueck - Master of Public Health (MPH) from Penn State (Hershey)
    Stephanie Woodhouse – Lab Technician
    Class of
    2009!
    Brittane Strahan – Nursing Program at Thomas Jefferson University
    Jessica Bennett – Ph.D. Program at University of Maryland
    Class of
    2008!
    Patrick Hayes – Research Technician at NYU --> Brewmaster in California
    Tyler Marcinko - Regeneron Pharmaceuticals --> Ph.D Program at Univ. of Mass.
    Brad Miller - Regeneron Pharmaceuticals --> Ph.D Program at SUNY Buffalo
    Class of
    2007!
    Kellie Cicconi - Ph.D Cornell University
    Class of
    2006!
    Andrew Lutzkanin - M.D. Penn State Hershey
    Kimberly McDowell - Ph.D. University of Maryland School of Medicine
    Elizabeth Sehi
    Class of
    2005!
    Bethany Mingle
    Wilfred Tumbusch
    Erica Walsh - Ph.D Boston University
    Class of
    2004!
    Michael Powell - Ph.D. Thomas Jefferson University
    Class of
    2003!
    Denise Greene
    Justin Jay - MS Biotechnology - Johns Hopkins --> Biotech/Project Management ((LinkedIn))
    Jennifer Kinne
    Meredith Moerschbacher
    Marla Yates - Ph.D. Purdue University
    Class of
    2002!
    Jen Leader - Ph.D in Oncology, Georgetown University
    Class of
    2001!
    Christy (Boob) Ramon --> Exygen, State College, PA --> Lawrence Livermore Lab
    Anna (Bucher) Keane - DO Philadelphia College of Osteopathic Medicine --> Practicing in Allentown
    Kevin Frederick - MD Drexel University --> Practicing with Geisinger
    Mitchell Marzo - MD University of Colorado School of Medicine --> Practicing in Hamilton, Montana
    Missy (Stokes) Pell - MD University of Virginia --> Practicing in State College, PA
    Julie Wagner
    Class of
    2000!
    Deanne Green Ph.D. University of West Virginia
    Amy Mayhew
    John Mazzullo
    Joshua Stutzman - D.O. Philadelphia College of Osteopathic Medicine (PCOM) --> Ob/Gyn Residency at Geisinger --> Practicing with Susquehanna Health, Williamsport
    Dave Wilson
    Class of
    1999!
    Jason Catanzaro
    Rachel Lawton - D.V.M. Cornell University --> Practicing in Linden, PA
    Mark McCleland - Ph.D University of Virginia --> Postdoc UCSF --> Genentech (LinkedIn)
    Kim Mistiszyn
    Lori Schultz
    Class of
    1998!
    Matthew Georgy
    Kathy Roberts
    Class of
    1997!
    Diana Burley
    Jonathan Cook
    Kevin Ferguson