Songjoon Baek, Ph.D.

Songjoon Baek, Ph.D.
Staff Scientist
Laboratory of Receptor Biology and Gene Expression

Team Member of:

Gordon L. Hager, Ph.D.
Yamini Dalal, Ph.D.

Dr. Baek’s primary research interest is in computational biology and biostatistics.  He has made a significant impact on bioinformatics and biological interpretation of research involving analysis of DnaseI hypersensitive sites, digital genomic footprinting, and comparative enrichment analysis.  His contributions have led to a better understanding of the global chromatin landscape and the elucidation of transcriptional mechanisms.  Dr. Baek is also interested in the development of a novel bioinformatics algorithm for the analysis of high-throughput multi-omics data. 

Areas of Expertise

1) computational biology, 2) biostatistics, 3) DnaseI-seq analysis, 4) RNA-seq analysis,
4) genomic classification algorithms, 5) gene expression analysis

Contact Info

Songjoon Baek, Ph.D.
Center for Cancer Research
National Cancer Institute
Building 41, Room B915
Bethesda, MD 20892-5055
Ph: 240-760-6574
baeks@mail.nih.gov

My research goal is to further the understanding of transcriptional regulation, especially the identification and characterization of chromatin modifications that lead to modifications and transitions of gene activation, repression, and epigenetic inheritance.   My specific interests include statistical and bioinformatic analysis of multi-omics data (involving ChIP-, DNase-, ATAC-, and RNA- seq) and their interpretation.  These efforts will provide novel methods for elucidation of mechanisms underlying epigenetic regulation of gene expression in cancer and also will help to improve integration of clinical data involving cancer from patient samples.

Recently, I have developed a highly sophisticated algorithm for identifying short genomic regions (footprints) which enable analysis of transcriptional activities at the nucleotide resolution.  The algorithm has been implemented in Dnase2TF, a public domain software platform used by many biology groups for high-throughput analysis of digital genomic footprinting.   I collaborate widely at NIH and with the extramural scientific community and have several publications with groups at the University of Southern Denmark, the University of Washington, The Pennsylvania State University, the University of Bristol, etc.

NIH Scientific Focus Areas:
Cancer Biology, Chromosome Biology, Computational Biology, Genetics and Genomics

Selected Publications

  1. DNase Footprint Signatures Are Dictated by Factor Dynamics and DNA Sequence.
    Sung MH*, Guertin MJ*, Baek S*, and Hager GL. (*Co-first author)
    Mol Cell. 56(2): 275-85, 2014. [ Journal Article ]
  2. Molecular Architecture of Transcription Factor Hotspots in Early Adipogenesis.
    Siersbaek R, Baek S, Rabiee A, Nielsen R, Traynor S, Clark N, Sandelin A, Jensen ON, Sung MH, Hager GL, and Mandrup S.
    Cell Rep. 7(5): 1434-42, 2014. [ Journal Article ]
  3. Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions.
    Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, and Hager GL.
    Nat Struct Mol Biol. 21(1): 73-81, 2013. [ Journal Article ]
  4. Quantitative analysis of genome-wide chromatin remodeling.
    Baek S, Sung MH, and Hager GL.
    Methods Mol Biol. 833: 433-41, 2012. [ Journal Article ]
  5. Development of Biomarker Classifiers from High-Dimensional Data.
    Baek S, Tsai CA, and Chen JJ.
    Brief Bioinform. 10(5): 537-46, 2009. [ Journal Article ]

Dr. Songjoon Baek completed his B.S and M.S. in mathematics at Sogang University in Seoul, South Korea in 1997 and obtained a Ph.D. in applied mathematics and statistics at the State University of New York at Stony Brook in 2004.  His Ph.D. studies focused on statistical analysis of high-dimensional data.  After finishing his postdoctoral training at Seoul National University and at the U.S. Food and Drug Administration (FDA), Dr. Baek joined the Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI as a Staff Scientist in 2009.