Nafiz Hamid

I am a PhD student in Bioinformatics at Iowa State University. I am in the Computational Biology lab, advised by Iddo Friedberg. Before this, I received a Bachelors in CS from Islamic University of Technology(IUT), Bangladesh in 2012. I worked as a software engineer at Samsung Bangladesh R&D Institute, Bangladesh after that before joining Iowa State.

My current research is in using machine learning to find new bacteriocins, as well as in antibiotic resistance prediction. I am also interested in machine learning for natural language processing. It seems a lot of the new techniques in deep learning for natural language processing can also be applied to genomics to reveal interesting insights we did not have before. We also have a ton of unlabelled data in biology. I am deeply interested in unsupervised learning techniques to make sense of these data.

My Erdos number is 4.

Email / PhD Thesis / Google Scholar / Github / Blog

Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks
Md-Nafiz Hamid, Iddo Friedberg
biorxiv, 2018
[paper] / [code]

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Hosein Mohimani, Alexey Gurevich, Kelsey L Alexander, C Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo AS Benitez, Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C Dorrestein, Pavel A Pevzner

biorxiv, 2017
[paper]

Bacteriocin detection with distributed biological sequence representation
Md-Nafiz Hamid, Iddo Friedberg 
ICML Computational Biology workshop, 2017
[paper] / [poster]

Bacteriocin detection with distributed biological sequence representation
Md-Nafiz Hamid, Iddo Friedberg 
Great Lake Bionformatics Conference, 2017 (contributed talk)
[slides]

Chikungunya Virus in Febrile Humans and Aedes aegypti Mosquitoes, Yucatan, Mexico

Nohemi Cigarroa-Toledo, Bradley J. Blitvich, Rosa C. Cetina-Trejo, Lourdes G. Talavera-Aguilar, Carlos M. Baak-Baak, Oswaldo M. Torres-Chablé, Md-Nafiz Hamid, Iddo Friedberg, Pedro González-Martinez, Gabriela Alonzo-Salomon, Elsy P. Rosado-Paredes, Nubia Rivero-Cárdenas, Guadalupe C. Reyes-Solis, Jose A. Farfan-Ale, Julian E. Garcia-Rejon, and Carlos Machain-Williams

Emerging infectious diseases, 22.10 (2016): 1804 
[paper]

Using gene neighborhoods to mine for bacteriocins
Md-Nafiz Hamid, James T Morton, Stefan D Freed, Shaun W Lee, Iddo Friedberg
American Society for Microbiology North Central Branch Meeting, 2016 (poster)
[poster]

(Stolen from this website)