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ARSHAN NASIR, Ph.D. Department of Biosciences COMSATS Institute of Information Technology Islamabad 45550, Pakistan E-mail: arshan_nasir@comsats.edu.pk; arshan.nasir@gmail.com EDUCATION Ph.D. Informatics 2012-15 Illinois Informatics Institute University of Illinois at Urbana-Champaign (UIUC), USA Dissertation: Structural and Functional Advances in the Evolutionary Studies of Cells and Viruses Advisor: Dr. Gustavo Caetano-Anollés CGPA: 3.96/4.0 M. S. Bioinformatics 2010-12 Department of Crop Sciences University of Illinois at Urbana-Champaign (UIUC), USA Thesis: Origin of Viruses Revealed by Genomic Study of Protein Structures Advisor: Dr. Gustavo Caetano-Anollés CGPA: 3.96/4.0 B.S. Bioinformatics 2004-08 Department of Biosciences COMSATS Institute of Information Technology (CIIT), Islamabad, Pakistan Thesis: Hunt for Mouse Mammary Tumor-like Viruses in the Genomes of Human and Chimpanzee Advisor: Dr. Farah Mustafa CGPA: 3.73/4.0 SELECTED PUBLICATIONS Jeong H, Sung S, Kwon T, Seo M, Caetano-Anollés K, Choi SH, Cho S, Nasir A*, Kim H*. 2015. HGTree: database of horizontally transferred genes determined by tree reconciliation. Nucleic Acids Research doi:10.1093/nar/gkv1245 (*Corresponding Authors) Nasir A, Caetano-Anollés. 2015. A phylogenomic data-driven exploration of viral origins and evolution. Science Advances 1: 1500527

http://news.discovery.com/animals/viruses-are-alive-and-are-oldest-living-creatures-150925.htm (News Release)

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Nasir A, Kim KM, Caetano-Anollés G. 2015. Lokiarchaeota: eukaryote-like missing links from microbial dark matter? Trends in Microbiology 23, 448-50 Nasir A, Sun FJ, Kim KM, Caetano-Anollés G. 2015. Untangling the origin of viruses and their impact on cellular evolution. Annals of the New York Academy of Science 1341: 61-74 Nasir A, Forterre P, Kim KM, Caetano-Anollés G. 2014. The distribution and impact of viral lineages in domains of life. Frontiers in Microbiology 5: 194 Nasir A, Kim KM, Caetano-Anollés G. 2014. Global patterns of protein domain gain and loss in superkingdoms. PLoS Computational Biology 10: e1003452 Nasir A, Kim KM, Caetano-Anollés G. 2012. Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evolutionary Biology 12: 156 (Highly Accessed)

BioMed Central Research Award, Runners-up in Microbiology, Immunology, and Inflammation category (competition involved ~20,000 articles published in 2012) http://www.sciencedaily.com/releases/2012/09/120913123520.htm (News Release) Article in the top 5% of all articles ranked by attention in 2012 (www.altmertric.com)

Nasir A, Kim KM, Caetano-Anollés G. 2014. A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life. Archaea 2014: 706468 Nasir A, Caetano-Anollés G. 2013. Comparative analysis of proteomes and functionomes provides insights into origins of cellular diversification. Archaea 2013: 648746 Nasir A, Kim KM, Caetano-Anollés G. 2012. Viral evolution: primordial cellular origins and late adaptation to parasitism. Mobile Genetic Elements 2: 247-252 Nasir A, Naeem A, Khan MJ, Nicora DH, Caetano-Anollés G. 2011. Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. Genes 2:869-911 Kim KM, Nasir A, Hwang K, Caetano-Anollés G. 2014. A tree of cellular life inferred from a genomic census of molecular functions. Journal of Molecular Evolution 79: 240-62 Kim KM, Nasir A, Caetano-Anollés G. 2014. The importance of using realistic evolutionary models for retrodicting proteomes. Biochimie 99:129-137 Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, Kim KM. 2014. Archaea: the first domain of diversified life. Archaea 2014: 590214 Yafremava LS, Wielgos M, Thomas S, Nasir A, Wang M, Mittenthal JE, Caetano-Anollés, G. 2013. A general framework of persistence strategies for biological systems helps explain domains of life. Frontiers in Genetics 4: 16

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Caetano-Anollés G, Nasir A. 2012. Benefits of using molecular structure and abundance in phylogenomic analysis. Frontiers in Genetics 3:172 RESEARCH EXPERIENCES Visiting Scholar (February-May 2014 and March-April 2015) University of Paris-Sud, Paris, France Description: The impact of gain and loss of viruses on the evolution of cells Advisor: Dr. Patrick Forterre Visiting Scholar (July 2011 and September-November 2012) Korea Research Institute of Bioscience and Biotechnology (KRIBB), South Korea Description: Comparison of gene ontology terms in completely sequenced genomes Advisor: Dr. Kyung Mo Kim Visiting Scholar (August-October 2009) UIUC, USA Description: Algorithm development to speed up the process of assigning structures to protein sequences using Python under UNIX environment Advisor: Dr. Gustavo Caetano-Anollés Research Associate (April 2009-August 2010) CIIT, Islamabad Description: Development of website and database for easy retrieval and analysis of endogenous retroviral sequences Advisor: Dr. Farah Mustafa RESEARCH GRANTS The Concept of Superorganisms: A Case Study of Humans and their Microbiomes (2015) PKR 0.5 million Awarded by the Higher Education Commission Pakistan, Project No. 519 ACADEMIC HONORS AND AWARDS Guest Editor, Special Issue on Exploring the Archaeal Hologenome and Metagenome, Archaea, 2015 Managing Editor, Lifetime Issue on Origin and Evolution of the Viral Supergroup, Frontiers in Biosciences, Starting 2017

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Dissertation Completion Fellowship, highly competitive fellowship awarded to outstanding students to help complete the doctoral degree within one year of award, awarded by the Graduate College of UIUC, 2014-15 Chateaubriand Fellowship, highly competitive award given to students studying in American universities to pursue research experience in top universities in France, awarded Summer 2013 for 6 months research training starting in February 2014 at the University of Paris-Sud, France CIIT Fellowship to pursue Master of Science degree at UIUC, awarded by CIIT, 2010-12 BioMed Central Research Award, runners up in Microbiology, Immunology, and Inflammation category (competition involved ~20,000 articles published in 2012) Awardee of NSF New International Collaborations program to travel to South Korea for 2 months research internship at Biological Resource Center, KRIBB, South Korea, 2012 Awardee of International Seeds Grant Program UIUC to travel to South Korea for 3 weeks research internship at the Korean Bioinformation Center, KRIBB, South Korea, July 2011 Institute Silver and Campus Bronze medals for undergraduate CGPA > 3.50, 2009 List of Teachers Ranked as Excellent by Their Students, Human Anatomy and Physiology II (MCB 247), UIUC, Spring 2012 TEACHING AND MENTORING Instructor, Introduction to Bioinformatics, Spring & Fall 2015 Department of Biosciences, CIIT Teaching Assistant, Human Anatomy and Physiology II, Spring 2012 School of Molecular and Cellular Biology, UIUC Research Team Leader, Summer Research Opportunities Program, Graduate College, UIUC, Summer 2013 and 2014

Assisted 10-12 undergraduate students in successful completion of their summer research projects. Served as conduit between the faculty mentor and students. Designed and organized weekly research team meetings to hold discussions on various topics in science and taught research writing skills.

ACADEMIC EMPLOYMENT Assistant Professor, Department of Biosciences, CIIT, Islamabad, Pakistan, Dec 2014 - present Research Assistant to Dr. Gustavo Caetano-Anollés, 2010 - 2015

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Duties included conducting research on the evolution of macromolecular structure and the origin of cells and viruses.

CONFERENCES AND WORKSHOPS Invited Talks “Structural and Functional Advances in the Evolutionary Studies of Cells and Viruses”, Lahore University of Management Sciences, Lahore, Pakistan, November 18, 2015 “What can informatics tell us about viral evolution?”, IEEE Frontiers in Information Technology, Islamabad, Pakistan, December 16, 2015 Poster presentations “Origin and Evolution of the Viral Supergroup”, Annual Society for Molecular Biology and Evolution (SMBE) meeting, Chicago IL, July 2013 “The Functional Makeup of Proteomes is Conserved”, IEEE International Conference on Bioinformatics and Biomedicine, Atlanta GA, November 2011 Participation “International Conference on Frontiers in Information Technology”, Abbottabad, Pakistan, December 2009 “Advances in Biochemistry and Molecular Biology”, 9th Biennial Pakistan Society for Biochemistry and Molecular Biology (PSBMB) Conference, Rawalpindi, Pakistan, December 2008 “Technology Challenges for Pakistan”, IEEE Tech Fair, Faisalabad, Pakistan, August 2008 Workshops “Teaching Orientation”, Graduate Academy for College, Urbana IL, January 2012 “Train the Trainers Workshop on Counseling Skills”, Faculty Development Program CIIT, Islamabad, Pakistan May 2009 REFERENCES Dr. Gustavo Caetano-Anollés, Professor of Bioinformatics, Department of Crop Science, UIUC

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Ph: (217) 333-8172, Email: gca@illinois.edu Dr. Patrick Forterre, Professor, Pasteur Institute, Paris, France Ph: +33 01 45 68 87 91, Email: patrick.forterre@pasteur.fr Dr. Jay E Mittenthal, Associate Professor of Cell and Developmental Biology, Emeritus, The School of Molecular and Cellular Biology, UIUC Ph: (217) 333-4846, Email: mitten@life.illinois.edu Dr. Kyung Mo Kim, Research Scientist, Biological Resource Center, KRIBB Ph: +82-10-5022-8992, Email: kmkim@kribb.re.kr