Monday, May 30, 2016

[Invited Lecture] Daehwan Kim, PhD.

Date: May 31, 2016
Venue: Seoul National University College of Medicine

Daehwan Kim, Ph.D.

Center for Computational Biology
McKusick-Nathans Institute of Genetic Medicine
Johns Hopkins University
Baltimore, MD, USA

Daehwan Kim is a post-doctoral research fellow in the McKusick-Nathans Institute of Genetic Medicine at Johns Hopkins University.  He received his Ph.D. in Computer Science from the University of Maryland, College Park in 2013 under the supervision of Steven Salzberg, currently Director of the Center for Computational Biology at JHU.  Dr. Kim’s expertise is in algorithms and high performance computing approaches for Next Generation Sequencing analysis, with a focus on sequence alignment and fusion gene/transcript discovery.  He is the main developer of some popular software such as TopHat2, HISAT, HISAT2, and TopHat-Fusion.  He has also been involved in the development of Bowtie2 and Cufflinks.

His HP at

Abstract of the Special Lecture

Graph-based alignment of NGS reads to a population of human genomes

In his presentation heI will first describe two popular alignment programs: (1) Bowtie2 for DNA-seq reads and (2) TopHat2 for RNA-seq reads.

He will then concentrate on discussing my new alignment programs, HISAT and its successor, HISAT2, as follows.

Since the introduction of next-generation sequencing (NGS) technologies, multiple large-scale human sequencing projects have been launched, including the 1000 Genomes Project, GTEx, and GEUVADIS.  These projects have already yielded a large and growing amount of information about human genetic variation, including >110 million SNPs (in dbSNP).  I have developed a novel indexing scheme that captures a wide representation of the human population by incorporating these variations into the reference genome.  With an index that incorporates ~12.3M common SNPs from the dbSNP database, I have built a new alignment system, HISAT2.  This system shows promise, with an index size of just 6.2 GB and among the fastest alignment programs, with greater alignment accuracy for reads containing SNPs.  HISAT2 also has the potential to genotype essentially all the genes on the human genome on a desktop within a few hours.  To demonstrate the capability of my initial genotyping work, I chose one gene family, Human Leukocyte Antigen (HLA) genes, which are among the most diverse human genes.  I incorporated these HLA alleles and variants into the index of the human genome, requiring only a small addition in computational resources.  Tests on Illumina’s Platinum Genomes data show that my method correctly identifies all 204 alleles of the six HLA genes for the 17 genomes, at a speed surpassing other currently available methods.

Wednesday, May 25, 2016

[New Presentation] 24th Federation Meeting of Korean Basic Medical Scientists 2016

Harappan Burial Sites in India: A Review Based On the Latest Anthropological Research Approaches

Astha Dibyopama1, Vasant Shinde1, Dong Hoon Shin2 and Nilesh P. Jadhav1

1Department of Archaeology, Deccan College Post Graduate and Research Institute, India
2Department of Anatomy, Institute of Forensic Science, Seoul National University, Korea

Burial is one of the important evidence to know about our ancestors. Harappan civilization flourished mainly in northwestern province of Indian subcontinent, roughly from between 4000 to 1500 BCE. There are about more than fifty burial sites of the Harappa Civilization discovered so far most of them belonging to a period between 2500-1500 BCE. Lothal, Kalibangan, Rupar, Rakhigarhi, Farmana, Tarkhanwala Dera, Sanauli, Bedwa, Puthi Seman, Bhorgarh, etc. are major sites yielding the remains of Harappan burial. Until the early 1980’s, the study of human skeletal were primarily focused to answer specific questions pertaining to establishing the ethnic or racial identity of the concerned population and was used primarily to complement archaeological hypotheses of cultural migration or diffusion. Recently, however, efforts are shifted to anthropological studies on diet, health and composition of Harappan population. Some of these issues are undertaken by high-end using Stable Isotope and DNA analyses. We intend in this presentation is to focus how these scientific methods which are freshly applied in Harappan burial research are fairly valuable for reconstruction of a variety of aspects of Harappan civilization.
Keywords: Harappan Civilization, Burial sites, Human skeletal remains, Stable Isotope, DNA study

[New Presentation] Kantikumar A. Pawar et al. for World Archaeology Congress (WAC-8)

Existence of Megalithic Dolmen in Central India and Their Cultural Comparison with Other Asian Countries

Megaliths and Megalithism are world phenomenon known for the characteristic mode of burial construction and ritualistic offerings is found all over the South Asia and also different parts of the world but their architecture, cultural  associations and chronology differs. In South Asia, concentration of these burials have been found mainly in the countries like India, China, Korea and Japan. Bewildering typology of these burials also differs and divided into two broad categories as Sepulchral and Non-Sepulchral based on their external and internal characteristic feature. The Megalithic burial tradition or this Megalithism associated with different cultural epoch in different countries. In Europe Megalithism associated with the Neolithic Age whereas in Korea it has been find as part of Bronze Age Culture. Legacy of this ancient burial tradition is still continued amongst the native tribal groups of many countries including India, Indonesia, etc. There is heated debate over the century about its origin, migration and the chorology when compare with different geographical landscapes

[New Presentation] Harappan Burial Sites of India: Recent Research Trends

Monday, May 23, 2016

[Invited Lecture] Young Explorer Grant Seminar: National Geographic

Presentation Slide

I made a speech at 
National Geographic Young Explorers Grants Seminar Seoul

● Venue: Room 101, Shinsegae Building at Ewha Womans University
● Date: Monday, May 23, 2016

15:55 Professional Grantee Presentation: Study of Rakhigarhi Site: People’s Life of Indus Valley Civilization by Dr. Dong Hoon Shin, Professor, Institute of Forensic Science at Seoul National University, NG grantee of Fall 2015

Monday, May 16, 2016

World Mummy Congress: the Program

Aug 10, 2016
Age estimation in mummies

Aug 10, 2016
Host-parasite relationships and diseases: lessons from the past

Aug 11, 2016
Ancient Bodies: the interplay between ancient culture, spiritual beliefs and mummification

Aug 11, 2016
Mummies and Textiles

Aug 12, 2016
From autopsy to diagnostic imaging and metagenomics, guidelines, levels of evidence and medical data