Mapping of RNAseq reads for the purpose of transcriptional profiling

PI – Jeramiah Smith

Aaron K West, Fellowship, Institutional Diversity - Vice President, Added 08/31/2021

Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa), and sequence assemblers (minia package, Trinity).

Grad Students

Joseph Herdy
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Melissa Keinath
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Stephanie Bryant
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Lisa Taylor
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Sarah Whelan
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Postdoc

Vladimir Timoshevskiy
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Staff Scientist

Nataliya Timoshevskaya
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Collaborators

(and possible collaborators who have not yet generated data) – Ona Bloom (Feinstein Institute for Medical Research), Brian Stevenson (UKy Med School), Stacia Sower (University of New Hampshire)

Assembly of small/low complexity vertebrate genomes (e.g. Zebra Finch).

PI – Jeramiah Smith

Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Grad Students

Joseph Herdy
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Melissa Keinath
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Stephanie Bryant
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Lisa Taylor
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Sarah Whelan
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).

Postdoc

Vladimir Timoshevskiy
Programs (All freeware) used include RSEM (RNA-Seq by Expectation-Maximization), sequence aligners (blast, bowtie, bwa) and sequence assemblers (minia package, Trinity).



Students

Joseph Herdy, Graduate Student
Melissa Keinath, Graduate Student
Stephanie Bryant, Graduate Student
Maria Torres Sanches, Postdoc
Varun Dwaraka, Graduate Student

Mirindi Kabangu, Added 03/05/2021

Alexander Stewart, Postdoc, Plant Pathology, LCC Added 05/18/2021 **MCC Added 01/03/2022

Kaan Ihsan Eskut, Graduate, Added 11/13/2021 on MCC cluster

Kasturi Rajandran, Graduate, Added 03/14/2022, on MCC cluster

Kara S Jones, Graduate, Added 03/24/2022 on MCC cluster

Tyler J Spear, Postdoc, Spinal Cord and Brain Injury, Added 05/31/2023 on MCC cluster

Software

Programs used include RSEM (RNA-Seq by Expectation-Maximization), custom perl scripts and sequence aligners (blast, bowtie, trinity).

Collaborators

(possible collaborators not yet generated data) –
Ona Bloom (Feinstein Institute for Medical Research)
Brian Stevenson (UKy Med School)
Stacia Sower (University of New Hampshire)

We also request permission to use the resource as part of the BIO520 course (Fall Semester Annually) and further request that this allocation be separated from Dr. Smith’s research allocation.

Our active research project involves mapping of RNAseq reads for the purpose of transcriptional profiling.

Syallbus BIO520

BIO 520 Bioinformatics
Instructor: Dr. Jeramiah J Smith
Email: jjsmit3@uky.edu
Office Phone: 257-­‐0124
Office Hours: Tuesday 1:00 to 2:00PM

Course Description:

BIOINFORMATICS

Prerequisites: BIO315 or BIO304 or BCH304 or BCH401 or BCH501 or BCH502 or BIO510 or consent of instructor.

Student Learning Outcomes:
After completing this course, the student will be able to:
1. Interact with the terminal, install and use programs.
2. Perform analyses of large datasets (millions to billions of sequences).
3. Write and edit Perl scripts Course goals or objectives:
To achieve proficiency on computational analysis of large biological datasets.

Required Materials:
TITLE: Beginning Perl for Bioinformatics

AUTHOR: Tisdall COPYRIGHT YEAR: 2001
PUBLISHER: O'Reilly & Associates

ISBN: 9780596000806
Course Assignments 3 Quizzes 150 points total
Class Participation 150 points total
1 Final Presentation 100 points
1 Final Written Assignment 100 points
Total 450

Class - BIO520F18-001

Class - BIO520F17-001

Students:

BIO 520 Section 001
Name Username
Byrd, Aria
Chalfant, Jeffrey Martin
Chen, Fan
Chereddy, Shankar Chaitanya Rami Reddy
Donohue, Mariah
Durham, Cody Caine
Ferrell, Sarah Ruth
Filipek, Derek Michael
Gunnell, Jacob
Heckler, Steven Luke
Jin, Huan
Jones, Casey
Krueger, Laura Anne
LaRue, Kristen
Lacey, Jonathan V
Law, Audrey Dale
Linhares Boakari, Yatta
Omotola, Oluwabukola Bosede
Scott, Langston Marshall
Sovacool, Kelly Lin
Thomas, Megan Lee
Titialii, Kayla Fogasina
Verges, Virginia Laura
XIE, YUXUAN

Class - BIO520F16-001

Amos, B Kirtley
Avery, Cecile Nena
Bland, Sarah Jo
Butsch, Tyler James
Cassone, Charles Vincent
Cirulli, Michael Christopher
Dadkhah, Sepideh
Giordano, James Joseph
Graniczkowska, Kinga
Grohs, Gillian
Gunnell, Jacob
Karunadasa, Sumudu Sandeepani
Meierotto, Sarah
SAXENA, SANDEEP
Shi, Jizhe
Shull, Timothy Eric
Sosso, Anna
Waterbury, Courtney Kayla Marie
Weaver, Chelsea Christina
Young, Elizabethe Jane

Class - BIO520F15-001

Al Haj Baddar, Nour WaleedN
Araujo, Nathalia Vitoria Pereira
Biswas, Shishir Kumar
Carrara, Nicholas William
Coomer, Cagney E.
D. Mahmood, Dlovan Faiq D. Mahmood
De Freitas Clementino, Marco Antonio
Dwaraka, Varun Bhamidipati
Grewelle, Richard Ernest
Guerriero, Lauren
Hansen, Thorsten Einar
Hurst, Melanie Noelle
Jones, Kara Suzanne
Maigret, Thomas
Morris, James Wesley
Pereira Piedade, Warlen
Petersen, Rebecca Ann
Saraceno, Cody
Sears, Connor Rianne
Shaw, Douglas Mistral
Van Der Meulen, Kristyn Lee
Weaver, Megan Leigh

Students from BIO520-001: Bioinformatics (Fall 2015) request access to the DLX system in order to gain training in high performance computing, perform computational analyses of large sequence datasets, including: transcriptome assemblies (e.g. Trinity or Velvet), read mapping (e.g. Bowtie, BWA), transcript quantitation (e.g. RSEM and statistical analyses R).

Request permission to use the resource as part of the BIO520 course and further request that this allocation be separated from Dr. Smith’s research allocation.

Class - BIO520F14-001

Bendall, Emily Elizabeth
Dunoyer, Luc Arnaud
Gjevre, Alexandra N
Holscher, Kendall
Lichtenberg, Stuart Siegfried
Malik, Manasi
Osterhaus, Patrick
Pook, Victoria Gillian
Potts, Douglas Brackston
Qiu, Qingchao
Roller, Nicholas Taylor
Savage, Christina Renee
Schroder, Kristofer Robert
Smith, Alexander Michael
Wente, Rebecca Lauren
Whelan, Sarah Elizabeth
Young, Allison Mitchell


Students from BIO520-001: Bioinformatics (Fall 2014) request access to the DLX system in order to gain training in high performance computing, perform computational analyses of large sequence datasets, including: transcriptome assemblies (e.g. Trinity or Velvet), read mapping (e.g. Bowtie, BWA), transcript quantitation (e.g. RSEM and statistical analyses R).

Request permission to use the resource as part of the BIO520 course and further request that this allocation be separated from Dr. Smith’s research allocation.

Class - BIO520F13-001

Students from BIO520-001: Bioinformatics (Fall 2013) request access to the DLX system in order to gain training in high performance computing, perform computational analyses of large sequence datasets, including: transcriptome assemblies (e.g. Trinity or Velvet), read mapping (e.g. Bowtie, BWA), transcript quantitation (e.g. RSEM and statistical analyses R).

Request permission to use the resource as part of the BIO520 course and further request that this allocation be separated from Dr. Smith’s research allocation.

Students 2013

Alhakeem, Sara S.
Arnold, Will K
Cook, Adam B
Creekmore, Christopher C
Dillard, Jacqueline R.
Gormley, Stephen J.
Horbinski, Craig M
Karovnos, Christopher H
Lawrence, Stephen R
Malloy, Cole A
Marks, Rose A
Pook, Victoria G.
Sanchez-Barrios, Andrea Marisa
Wang, Chanung
White, Jennifer A
Wulff, Jason A.
Xia, Ye
Zhou, Yuting
Zhu, Yan
Zhu, Yuechen

Publications

2013

1.Amemiya, CT ;Alföldi, J.;Lee, AP ;Fan, S.;Philippe, H.;Maccallum, I.;Braasch, I.;Manousaki, T.;Schneider, I.;Rohner, N.;Organ, C.;Chalopin, D.;Smith, JJ ;Robinson, M.;Dorrington, RA ;Gerdol, M.;Aken, B.;Biscotti, MA ;Barucca, M.;Baurain, D.;Berlin, AM ;Blatch, GL ;Buonocore, F.;Burmester, T.;Campbell, MS ;Canapa, A.;Cannon, JP ;Christoffels, A.;De Moro, G.;Edkins, AL ;Fan, L.;Fausto, AM ;Feiner, N.;Forconi, M.;Gamieldien, J.;Gnerre, S.;Gnirke, A.;Goldstone, JV ;Haerty, W.;Hahn, ME ;Hesse, U.;Hoffmann, S.;Johnson, J.;Karchner, SI ;Kuraku, S.;Lara, M.;Levin, JZ ;Litman, GW ;Mauceli, E.;Miyake, T.;Mueller, MG ;Nelson, DR ;Nitsche, A.;Olmo, E.;Ota, T.;Pallavicini, A.;Panji, S.;Picone, B.;Ponting, CP ;Prohaska, SJ ;Przybylski, D.;Saha, NR ;Ravi, V.;Ribeiro, FJ ;Sauka-Spengler, T.;Scapigliati, G.;Searle, SM ;Sharpe, T.;Simakov, O.;Stadler, PF ;Stegeman, JJ ;Sumiyama, K.;Tabbaa, D.;Tafer, H.;Turner-Maier, J.;Heusden, P.;White, S.;Williams, L.;Yandell, M.;Brinkmann, H.;Volff, JN ;Tabin, CJ ;Shubin, N.;Schartl, M.;Jaffe, DB ;Postlethwait, JH ;Venkatesh, B.;Di Palma, F.;Lander, ES ;Meyer, A.;Lindblad-Toh, K. "The African coelacanth genome provides insights into tetrapod evolution." Nature 496, 7445 (2013): 311-6. Details. Full text
2.Smith, JJ ;Kuraku, S.;Holt, C.;Sauka-Spengler, T.;Jiang, N.;Campbell, MS ;Yandell, MD ;Manousaki, T.;Meyer, A.;Bloom, OE ;Morgan, JR ;Buxbaum, JD ;Sachidanandam, R.;Sims, C.;Garruss, AS ;Cook, M.;Krumlauf, R.;Wiedemann, LM ;Sower, SA ;Decatur, WA ;Hall, JA ;Amemiya, CT ;Saha, NR ;Buckley, KM ;Rast, JP ;Das, S.;Hirano, M.;McCurley, N.;Guo, P.;Rohner, N.;Tabin, CJ ;Piccinelli, P.;Elgar, G.;Ruffier, M.;Aken, BL ;Searle, SM ;Muffato, M.;Pignatelli, M.;Herrero, J.;Jones, M.;Brown, CT ;Chung-Davidson, YW ;Nanlohy, KG ;Libants, SV ;Yeh, CY ;McCauley, DW ;Langeland, JA ;Pancer, Z.;Fritzsch, B.;Jong, PJ ;Zhu, B.;Fulton, LL ;Theising, B.;Flicek, P.;Bronner, ME ;Warren, WC ;Clifton, SW ;Wilson, RK ;Li, W. "Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution." Nature genetics 45, 4 (2013): 415-21, 421e1-2. Details. Full text

2012

1.Smith, JJ ;Baker, C.;Eichler, EE ;Amemiya, CT "Genetic consequences of programmed genome rearrangement." Current biology : CB 22, 16 (2012): 1524-9. Details. Full text
2.Smith, JJ ;Sumiyama, K.;Amemiya, CT "A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome." Molecular biology and evolution 29, 3 (2012): 985-93. Details. Full text

2011

1.Smith, JJ ;Stuart, AB ;Sauka-Spengler, T.;Clifton, SW ;Amemiya, CT "Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution." Chromosoma 119, 4 (2010): 381-9. Details. Full text

2010

1.Smith, JJ ;Saha, NR ;Amemiya, CT "Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes." Integrative and comparative biology 50, 1 (2010): 130-7. Details. Full text

2009

1.Smith, JJ ;Antonacci, F.;Eichler, EE ;Amemiya, CT "Programmed loss of millions of base pairs from a vertebrate genome." Proceedings of the National Academy of Sciences of the United States of America 106, 27 (2009): 11212-7. Details. Full text

Grants

Smith, Jeramiah 5R01GM104123-02 Functional Analysis of programmed genome rearrangement National Institute of General Medical Sciences 9/1/2013 - 8/31/2018 $629,901
Smith, Jeramiah FY14197601 Germline sequence resources & analyses in a vertebrate model that undergoes PGR Benaroya Research Institute 4/1/2012 - 3/31/2015 $63,950
Smith, Jeramiah 1R01GM104123-01A1 Functional Analysis of programmed genome rearrangement $270,644 National Instit