NM-INBRE/NCGR Differential Gene Expression Workshop

April 8, 2019 @ 8:30 am – April 12, 2019 @ 5:30 pm
National Center for Genome Resources
2935 Rodeo Park Dr. E
Lisana Chavez
(505) 995-4487



The National Center for Genome Resources (NCGR), Santa Fe, NM


April 8 – 12, 2019


This program is geared towards training biologists (undergraduates, graduates and researchers) with minimal or no bioinformatics experience. Space is limited.


Students will acquire the skill-set to independently analyze RNA-Seq data using the command line interface, analytical workflows and current differential gene expression (DE) tools. 


DE entails examining the fraction of the genome that is responsible for making products that drive organismal function. Gene expression is influenced by various extrinsic physiological and environmental as well as several intrinsic properties of the organism. Whole transcriptome profiles are becoming increasingly popular, useful and generate large volumes of data. Knowing how to handle, analyze, and make biological inferences on this scale of data is a valuable skill-set for researchers.

Topic overview

UNIX fundamentals, RNA-Seq, data QC, alignments, read count generation, featureCounts, DE and pathway analysis will be taught. 

Workshop Rates

New Mexico Students & Academic Researchers Free
All Other Students $1,500
IDeA Researchers $1,750
Academic, Military, Government $2,250
Commercial $2,750

Lodging scholarships (for NM-INBRE students only)

If you are not an NM-INBRE student, check to see if you are from an INBRE funded state, here. If so, connect with your local INBRE Administrative Core to see if funding is available to support your educational pursuit by attending our workshop.

Application Packet due 11:59pm Feb 24, 2019 (MST)

1)  Application Form: Download and complete Fillable Application Form using Adobe Acrobat. * Save & Email as a PDF for Selection Committee to scroll through multi-line answers.

2)  UNIX prerequisite:  Please thoroughly review the following to gain a fundamental understanding of UNIX prior to the course. Indicate this has been completed on Application Form.

Review Introduction to the UNIX Operating System and Tutorials 1 – 4 http://www.ee.surrey.ac.uk/Teaching/Unix/

Review vi editor https://www.cs.colostate.edu/helpdocs/vi.html 

Late applications will not be accepted.  Selection Committee to select interns within ~2 weeks of deadline. If any questions while reviewing your application packet, a phone call will be forthcoming.

What to expect upon acceptance

1)    Email confirming acceptance into the internship program
2)    Dataset (if applicable) to be sent to Project Coordinator, Lisana Chavez by March 15, 2019

Travel & Lodging Information

Travel to and from Santa Fe, NM    The Santa Fe Regional Airport is approximately 7 miles away (15 minute drive to the hotel) and Albuquerque International Sunport is approximately 60 miles away (1 hour drive to the hotel).   Santa Fe airport is very convenient.

Lodging at Santa Fe Suites    To be coordinated through Project Coordinator at the special student rate of approximately $57.72 per night ($346.32 for 6 nights or $404.04 for 7 nights) for a single queen room.  Just around the corner from the Santa Fe Suites is an Albertson’s supermarket where students may purchase groceries.  Also, there are a number of restaurants in the area (sandwiches, Chinese food, pizza, etc.).  Additionally, the hotel serves a free continental breakfast each morning.  Santa Fe Suites is approximately ½ mile away and a 15-minute walk to NCGR.  NCGR staff can always lend a hand with transportation to and from Santa Fe Suites if needed (e.g. inclement weather) as well.

Food    The hotel serves a free continental breakfast each morning and we will occasionally organize lunch outings at local Santa Fe eateries as a group (optional).  Santa Fe has excellent food—we are known for our green and red chiles!  We estimate total food expenses to be $70 – $150.

Public transportation    Available if needed. There is a city bus stop 400 ft from NCGR and the Zia train station approximately ¼ mile from Santa Fe Suites.  These can be used to visit downtown Santa Fe, sightseeing or other destinations.


Please contact Project Coordinator, Lisana Chavez, with any additional questions you may have at lchavez@ncgr.org and we look forward to your participation!

Sponsored by New Mexico IDeA Network for Biomedical Research Excellence (NM-INBRE).

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