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Our Science – Lee Website

Byungkook Lee, Ph.D.

Selected Publications

1)  Taylor TJ, Bai H, Tai CH, Lee B.
Assessment of CASP10 contact-assisted predictions.
Proteins. 2013.
[Journal]
2)  Tai CH, Bai H, Taylor TJ, Lee B.
Assessment of template-free modeling in CASP10 and ROLL.
Proteins. 2013.
[Journal]
3)  Taylor TJ, Tai CH, Huang YJ, Block J, Bai H, Kryshtafovych A, Montelione GT, Lee B.
Definition and classification of evaluation units for CASP10.
Proteins. 2013.
[Journal]
4)  Pak Y, Zhang Y, Pastan I, Lee B.
Antigen shedding may improve efficiencies for delivery of antibody-based anticancer agents in solid tumors.
Cancer Res. 72: 3143-52, 2012.
[Journal]
5)  Tai CH, Sam V, Gibrat JF, Garnier J, Munson PJ, Lee B.
Protein domain assignment from the recurrence of locally similar structures.
Proteins. 79: 853-66, 2011.
[Journal]
6)  Kim C, Basner J, Lee B.
Detecting internally symmetric protein structures.
BMC Bioinformatics. 11: 303, 2010.
[Journal]
7)  Kim C, Tai C, Lee B.
Iterative refinement of structure-based sequence alignments by Seed Extension.
BMC Bioinformatics. 10: 210, 2009.
[Journal]
8)  Kim C, Lee B.
Accuracy of structure-based sequence alignment of automatic methods.
BMC Bioinformatics. 8: 355, 2007.
[Journal]
9)  Liu W, Onda M, Kim C, Xiang L, Weldon JE, Lee B, Pastan I.
A recombinant immunotoxin engineered for increased stability by adding a disulfide bond has decreased immunogenicity.
Protein Eng. Des. Sel. 25: 1-6, 2012.
[Journal]
10)  Samson F, Shrager R, Tai CH, Sam V, Lee B, Munson PJ, Gibrat JF, Garnier J.
DOMIRE: a web server for identifying structural domains and their neighbors in proteins.
Bioinformatics. 28: 1040-1, 2012.
[Journal]
11)  Feiglin A, Moult J, Lee B, Ofran Y, Unger R.
Neighbor overlap is enriched in the yeast interaction network: analysis and implications.
PLoS ONE. 7: e39662, 2012.
[Journal]
12)  Liu W, Onda M, Lee B, Kreitman RJ, Hassan R, Xiang L, Pastan I.
Recombinant immunotoxin engineered for low immunogenicity and antigenicity by identifying and silencing human B-cell epitopes.
Proc. Natl. Acad. Sci. U.S.A. 109: 11782-7, 2012.
[Journal]
13)  Onda M, Beers R, Xiang L, Lee B, Weldon JE, Kreitman RJ, Pastan I.
Recombinant immunotoxin against B-cell malignancies with no immunogenicity in mice by removal of B-cell epitopes.
Proc. Natl. Acad. Sci. U.S.A. 108: 5742-7, 2011.
[Journal]
14)  Yomtovian I, Teerakulkittipong N, Lee B, Moult J, Unger R.
Composition bias and the origin of ORFan genes.
Bioinformatics. 26: 996-9, 2010.
[Journal]
15)  Bera T, Lee B.
Choudhuri S, Carlson D, eds.
Mining of Genome Sequence Database to Identify New Targets for Prostate and Breast Cancer Therapy. In: Genomics: Fundamentals and Applications.
New York, NY: Informa Healthcare USA, Inc.; 2009. p. 191-205 [Book Chapter]
16)  Kaneko O, Gong L, Zhang J, Hansen JK, Hassan R, Lee B, Ho M.
A binding domain on mesothelin for CA125/MUC16.
J. Biol. Chem. 284: 3739-49, 2009.
[Journal]
17)  Hahn Y, Kim DS, Pastan IH, Lee B.
Anoctamin and transmembrane channel-like proteins are evolutionarily related.
Int. J. Mol. Med. 24: 51-5, 2009.
[Journal]
18)  Sathyanarayana BK, Hahn Y, Patankar MS, Pastan I, Lee B.
Mesothelin, Stereocilin, and Otoancorin are predicted to have superhelical structures with ARM-type repeats.
BMC Struct. Biol. 9: 1, 2009.
[Journal]
19)  Tai CH, Vincent JJ, Kim C, Lee B.
SE: an algorithm for deriving sequence alignment from a pair of superimposed structures.
BMC Bioinformatics. 10 Suppl 1: S4, 2009.
[Journal]
20)  Bera TK, Liu XF, Yamada M, Gavrilova O, Mezey E, Tessarollo L, Anver M, Hahn Y, Lee B, Pastan I.
A model for obesity and gigantism due to disruption of the Ankrd26 gene.
Proc. Natl. Acad. Sci. U.S.A. 105: 270-5, 2008.
[Journal]
21)  Goonesekere NC, Lee B.
Context-specific amino acid substitution matrices and their use in the detection of protein homologs.
Proteins. 71: 910-9, 2008.
[Journal]
22)  Chen KC, Kim J, Li X, Lee B.
Modeling recombinant immunotoxin efficacies in solid tumors.
Ann Biomed Eng. 36: 486-512, 2008.
[Journal]
23)  Bera TK, Saint Fleur A, Ha D, Yamada M, Lee Y, Lee B, Hahn Y, Kaufman DS, Pera M, Pastan I.
Selective POTE paralogs on chromosome 2 are expressed in human embryonic stem cells.
Stem Cells Dev. 17: 325-32, 2008.
[Journal]
24)  Das S, Hahn Y, Walker DA, Nagata S, Willingham MC, Peehl DM, Bera TK, Lee B, Pastan I.
Topology of NGEP, a prostate-specific cell:cell junction protein widely expressed in many cancers of different grade level.
Cancer Res. 68: 6306-12, 2008.
[Journal]
25)  Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ.
Towards an automatic classification of protein structural domains based on structural similarity.
BMC Bioinformatics. 9: 74, 2008.
[Journal]
26)  Grigoryev DN, Ma SF, Shimoda LA, Johns RA, Lee B, Garcia JG.
Exon-based mapping of microarray probes: recovering differential gene expression signal in underpowered hypoxia experiment.
Mol. Cell. Probes. 21: 134-9, 2007.
[Journal]
27)  Hahn Y, Jeong S, Lee B.
Inactivation of MOXD2 and S100A15A by Exon Deletion During Human Evolution.
Mol Biol Evol. 24: 2203-12, 2007.
[Journal]
28)  Das S, Hahn Y, Nagata S, Willingham MC, Bera TK, Lee B, Pastan I.
NGEP, a prostate-specific plasma membrane protein that promotes the association of LNCaP cells.
Cancer Res. 67: 1594-601, 2007.
[Journal]
29)  Onda M, Nagata S, FitzGerald DJ, Beers R, Fisher RJ, Vincent JJ, Lee B, Nakamura M, Hwang J, Kreitman RJ, Hassan R, Pastan I.
Characterization of the B cell epitopes associated with a truncated form of Pseudomonas exotoxin (PE38) used to make immunotoxins for the treatment of cancer patients.
J. Immunol. 177: 8822-34, 2006.
[Journal]
30)  Hahn Y, Bera TK, Pastan IH, Lee B.
Duplication and extensive remodeling shaped POTE family genes encoding proteins containing ankyrin repeat and coiled coil domains.
Gene. 366: 238-45, 2006.
[Journal]
31)  Lee Y, Ise T, Ha D, Saint Fleur A, Hahn Y, Liu XF, Nagata S, Lee B, Bera TK, Pastan I.
Evolution and expression of chimeric POTE-actin genes in the human genome.
Proc. Natl. Acad. Sci. U.S.A. 103: 17885-90, 2006.
[Journal]
32)  Egland KA, Liu XF, Squires S, Nagata S, Man YG, Bera TK, Onda M, Vincent JJ, Strausberg RL, Lee B, Pastan I.
High expression of a cytokeratin-associated protein in many cancers.
Proc. Natl. Acad. Sci. U.S.A. 103: 5929-34, 2006.
[Journal]
33)  Hahn Y, Lee B.
Human-specific nonsense mutations identified by genome sequence comparisons.
Hum. Genet. 119: 169-78, 2006.
[Journal]
34)  Gubbels JA, Belisle J, Onda M, Rancourt C, Migneault M, Ho M, Bera TK, Connor J, Sathyanarayana BK, Lee B, Pastan I, Patankar MS.
Mesothelin-MUC16 binding is a high affinity, N-glycan dependent interaction that facilitates peritoneal metastasis of ovarian tumors.
Mol. Cancer. 5: 50, 2006.
[Journal]
35)  Bera TK, Saint Fleur A, Lee Y, Kydd A, Hahn Y, Popescu NC, Zimonjic DB, Lee B, Pastan I.
POTE paralogs are induced and differentially expressed in many cancers.
Cancer Res. 66: 52-6, 2006.
[Journal]
36)  Sam V, Tai CH, Garnier J, Gibrat JF, Lee B, Munson PJ.
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification.
BMC Bioinformatics. 7: 206, 2006.
[Journal]
37)  Vincent JJ, Tai CH, Sathyanarayana BK, Lee B.
Assessment of CASP6 predictions for new and nearly new fold targets.
Proteins. 61 Suppl 7: 67-83, 2005.
[Journal]
38)  Tress M, Tai CH, Wang G, Ezkurdia I, López G, Valencia A, Lee B, Dunbrack RL.
Domain definition and target classification for CASP6.
Proteins. 61 Suppl 7: 8-18, 2005.
[Journal]
39)  Tai CH, Lee WJ, Vincent JJ, Lee B.
Evaluation of domain prediction in CASP6.
Proteins. 61 Suppl 7: 183-92, 2005.
[Journal]
40)  Hahn Y, Lee B.
Identification of nine human-specific frameshift mutations by comparative analysis of the human and the chimpanzee genome sequences.
Bioinformatics. 21 Suppl 1: i186-94, 2005.
[Journal]
41)  Graziano G, Lee B.
On the intactness of hydrogen bonds around nonpolar solutes dissolved in water.
J Phys Chem B. 109: 8103-7, 2005.
[Journal]
42)  Vasmatzis G, Essand M, Brinkmann U, Lee B, Pastan I.
Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis.
Proc. Natl. Acad. Sci. U.S.A. 95: 300-4, 1998.
[Journal]
43)  Reiter Y, Brinkmann U, Lee B, Pastan I.
Engineering antibody Fv fragments for cancer detection and therapy: disulfide-stabilized Fv fragments.
Nat. Biotechnol. 14: 1239-45, 1996.
[Journal]
44)  Lee B.
Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules.
Biopolymers. 31: 993-1008, 1991.
[Journal]
45)  Lee B, Richards FM.
The interpretation of protein structures: estimation of static accessibility.
J. Mol. Biol. 55: 379-400, 1971.
[Journal]
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This page was last updated on 1/2/2014.