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Group meeting Schedule
2012 Schedule
- Rule
- 저널발표 순서 (Topics: NGS & Synthetic biology applications)
- Synbio 김병호-고혁진-박홍재- 이세영-고아름(>매주 1명 이상) (김병호 bi-weekly)
- Compbio 노한성-남지희-김수진(가능할 때)-민병남 (매주 1명씩) (남지희 bi-weekly)
- 발표시간 엄수
리뷰논문 20분이내 실험논문/실험결과 15분이내 PPT slide 5장 이내로 만들것
- 발표논문 미리 읽기 (아래 링크 PMID = pubmed id)
2012_winter
발표순서 : 박홍재,고아름,남지희,김병호,고혁진,이세영,민병남,노한성
2012_Summer
발표 순서 :(이세영,박홍재,민병남,남지희)(고혁진,노한성,김병호,고아름)
- 8-27-2012(예정)
- 이세영
- Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism
- 남지희
- Functional genome annotation through phylogenomic mapping
- 박홍재
- Direct cloning of large genomic sequences
- 민병남
- On the thermodynamics of microbial growth processes
- 8-20-2012
- 고혁진
- Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
- 김병호
- Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems
- 노한성
- Biological network motif detection and evaluation
- 고아름
- Microbial solar cells: applying photosynthetic and electrochemically active organisms
- 8-13-2012
- 이세영:
- Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate
- Andberg M, Maaheimo H, Boer H, Penttilä M, Koivula A, Richard P.
- (PMID 22493433)
- 노한성:
- Exhaustive enumeration of protein domain families.
- Heger A, Holm L.
- (PMID 12706730)
- 남지희:
- Wisdom of crowds for robust gene network inference.
- Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR; The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G.
- (PMID 227996662)
- 민병남:
- On the thermodynamics of microbial growth processes.
- Sandler SI, Orbey H.
- (PMID 18600796)
- 박홍재:
- Direct cloning of large genomic sequences.
- Cobb RE, Zhao H.
- (PMID 22565964)
- 8-06-2012
- 고혁진:
- Shotgun DNA synthesis for the high-throughput construction of large DNA molecules.
- Kim H, Han H, Ahn J, Lee J, Cho N, Jang H, Kim H, Kwon S, Bang D
- (PMID 22705793)
- 김병호:
- High-throughput protein expression screening and purification in Escherichia coli
- Vincentelli R, Cimino A, Geerlof A, Kubo A, Satou Y, Cambillau C.
- 고아름
- Growth of non-phototrophic microorganisms using solar energy through mineral photocatalysis
- Lu A, Li Y, Jin S, Wang X, Wu XL, Zeng C, Li Y, Ding H, Hao R, Lv M, Wang C, Tang Y, Dong H.
- (PMID 22473012)
- 7-30-2012
- 이세영:
- remodeling bacterial polysaccharides by metabolic pathway engineering
- Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4207-12. Epub 2009 Feb 26.
- Yi W, Liu X, Li Y, Li J, Xia C, Zhou G, Zhang W, Zhao W, Chen X, Wang PG.
- (PMID 19251666)
- 박홍재 :
- Science. 2011 Aug 26;333(6046):1151-4.
- Expanding the genetic code of Escherichia coli with phosphoserine.
- Park HS, Hohn MJ, Umehara T, Guo LT, Osborne EM, Benner J, Noren CJ, Rinehart J, Söll D.
- (PMID 21868676)
- 민병남:
- On the Thermodynamics of Microbial Growth Processes
- Biotechnology and Bioengineering. 1991. 38:697-718
- 남지희 :
- Nat Biotechnol. 2009 Oct;27(10):946-50. Epub 2009 Oct 4.
- Automated design of synthetic ribosome binding sites to control protein expression.
- Salis HM, Mirsky EA, Voigt CA.
- 7-23-2012
- 고혁진 :
- Nucleic Acids Res. 2012 Feb;40(3):e24. Epub 2011 Nov 29.
- Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination.
- Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, Head SR.
- (PMID 22127871)
- 노한성:
- Curr Opin Chem Biol. 2012 Jun 20. [Epub ahead of print]Computational methods in synthetic biology: towards computer-aided part design.
- Wu K, Rao CV.
- (PMID 22727029)
- 김병호 :
- Engineering the robustness of industrial microbes through synthetic biology
- authors: Zhu L, Zhu Y, Li Y
- PMID: 22264657
- 고아름:
- Annu Rev Genet. 2008;42:211-33.
- The organization of the bacterial genome.
- Rocha EP.
- (PMID 18605898)
- 7-18-2012
- 이세영 : A simple method for directional transcriptome sequencing using
- Illumina technology.
- Croucher NJ, Fookes MC, Perkins TT, Turner DJ, Marguerat SB, Keane T,
- Quail MA, He M, Assefa S, Bähler J, Kingsley RA, Parkhill J, Bentley
- SD, Dougan G, Thomson NR.
- (PMID 19815668)
- 박홍재: Tends Biotechnol. 2012 Feb;30(2):65-70. Epub 2011 Oct 29.
- Bacterial inclusion bodies: making gold from waste.
- García-Fruitós E, Vázquez E, Díez-Gil C, Corchero JL, Seras-Franzoso
- J, Ratera I, Veciana J, Villaverde A.
- (PMID 22037492)
- 민병남:On the Thermodynamics of Microbial Growth Processes
- Biotechnology and Bioengineering. 1991. 38:697-718
- 남지희: FEBS Lett. 2012 Jul 16;586(15):2037-42. Epub 2012 Feb 27.
- Perspectives on the automatic design of regulatory systems for
- synthetic biology.
- Rodrigo G, Carrera J, Landrain TE, Jaramillo A.
- (PMID 22710180)
- 7-09-2012
- 김병호: Pathway engineering and synthetic biology using acetogens.
- Bettina Schiel-Bengelsdorf
- FEBS Lett. 2012 May 3. [Epub ahead of print]
- (PMID 22710156)
- 고아름: Protein secretion and surface display in Gram-positive bacteria.
- Schneewind O, Missiakas DM.
- Philos Trans R Soc Lond B Biol Sci. 2012 Apr 19;367(1592):1123-39
- (PMID 22411983)
- 7-04-2012
- 고혁진 : FLASH assembly of TALENs for high-throughput genome editing
- Deepak Reyon, Shengdar Q Tsai, Cyd Khayter, Jennifer A Foden, Jeffry D Sander & J Keith Joung
- Nat Biotechnol. 2012 May;30(5):460-5.
- (PMID 22484455)
- 박홍재 : Genome-scale promoter engineering by coselection MAGE.
- Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM.
- Nat Methods. 2012 Apr 8. doi: 10.1038/nmeth
- (PMID 22484848)
- 민병남 : Rethinking glycolysis: on the biochemical logic of metabolic pathways.
- Arren Bar-Even, Avi Flamholz, Elad Noor & Ron Milo.
- Nat Chem Biol. 2012. 8(6):509-17.
- PMID:22596202
- 남지희 : Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals.
- Ju YS, Kim JI, Kim S, Hong D, Park H, Shin JY, Lee S, Lee WC, Kim S, Yu SB, Park SS, Seo SH, Yun JY, Kim HJ, Lee DS, Yavartanoo M, Kang HP, Gokcumen O, Govindaraju DR, ::Jung JH, Chong H, Yang KS, Kim H, Lee C, Seo JS.
- Nature Genetics 43,745–752(2011)doi:10.1038/ng.872
- (PMID 21725310)
- 6-20-2012
- 고아름 : Systems metabolic engineering of microorganisms for natural and non-natural chemicals.
- Lee JW, Na D, Park JM, Lee J, Choi S, Lee SY.
- Nat Chem Biol. 2012 May 17;8(6):536-46. doi: 10.1038/nchembio.970.(PMID 22596205)
- 노한성 : The layout of a bacterial genome.
- Képès F, Jester BC, Lepage T, Rafiei N, Rosu B, Junier I.
- The layout of a bacterial genome.(PMID 22483986)
- 김병호 : Synthetic biology and the development of tools for metabolic engineering
- Keasling JD(PMID 22314049)
- 6-13-2012
- 고혁진 : Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS.
- Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
- Nat Commun. 2012 Jun 6;3:886. doi: 10.1038/ncomms1878.(PMID 22673913)
- 박홍재 : King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D.
- Computational design of self-assembling protein nanomaterials with atomic level accuracy.
- Science. 2012 Jun 1;336(6085):1171-4.(PMID 22654060)
- 남지희: Vikas Rao Pejaver, Heewook Lee, and Sun Kim.
- Gene Cluster Prediction and Its Application to Genome Annotation.
- 2011. Protein Function Prediction for Omics Era pp. 35-54
- 6-8-2012
- 노한성 : The Tomato Genome Consortium
- The tomato genome sequence provides insights into flesh fruit evolution
- 2012, Nature
- 이세영 : Simon Auslander, David Auslander, Marius Muller, Markus Wieland & Martin Fussenegger
- Programmable single-cell mammalian biocomputers
- 2012, Nature
- 김병호 : Siying Ma, Nicholas Tang and Jingdong Tian
- DNA synthesis, assembly and applications in sythetic biology
- 2012, Nature (PMID 22633067 )
2012_Spring
- 5-30-2012
- 고혁진 : Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, Liao JC
- Integrated electromicrobial conversion of CO2 to higher alcohols.
- 2012. Science.( PMID 22461604)
- 남지희: Vikas Rao Pejaver, Heewook Lee, and Sun Kim.
- Gene Cluster Prediction and Its Application to Genome Annotation.
- 2011. Protein Function Prediction for Omics Era pp. 35-54
- 고아름 : Slusarczyk AL, Lin A, Weiss R.
- Foundations for the design and implementation of synthetic genetic circuits.
- 2012. NATURE REVIEWS GENETICS. (PMID 22596318)
- 민병남 : John W. Davey, Paul A. Hohenlohe, Paul D. Etter, Jason Q. Boone, Julian M. Catchen and Mark L. Blaxter
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing
- 2011. NATURE RIVEWS GENETICS. PMID:21681211
- 박홍재 :Jay Shendure & Hanlee Ji
- Next-generation DNA sequencing
- 2008. Nature Biotechnology. doi:10.1038/nbt1486
- 5-23-2012
- 고혁진 : Li H, Opgenorth PH, Wernick DG, Rogers S, Wu TY, Higashide W, Malati P, Huo YX, Cho KM, Liao JC
- Integrated electromicrobial conversion of CO2 to higher alcohols.
- 2012. Science. (PMID 22461604)
- 김병호 : Lee CK, Araki N, Sowersby DS, Lewis LK.
- Factors affecting chemical-based purification of DNA from Saccharomyces cerevisiae.
- 2011.Yeast. (PMID 22134898)
- 노한성: K?nig J, Zarnack K, Luscombe NM, Ule J.
- Protein?RNA interactions: new genomic technologies and perspectives.
- 2012. Nature Reviews Genetics. (PMID 22251872)
- 5-17-2012
- 이세영 : Wang T, Ma X, Zhu H, Li A, Du G, Chen J
- Available methods for assembling expression cassettes for synthetic biology.2012. Appl Microbiol Biotechnol.(PMID 22311648)
- 남지희: Vikas Rao Pejaver, Heewook Lee, and Sun Kim.
- Gene Cluster Prediction and Its Application to Genome Annotation.2011. Protein Function Prediction for Omics Era pp. 35-54
- 고아름 : Sinha S, Redfield RJ.Natural DNA Uptake by Escherichia coli.2012. PLoS One. (PMID 22532864)
- 5-10-2012
- 고혁진 : Jun Fu, et. al.Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting.
- 2012. Nature Biotechnology doi:10.1038/nbt.2183(PMID 22544021)
- 노한성 : Schraga Schwartz, Ram Oren, Gil Ast.Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads.
- 2011. PLoS ONE. PMID: 21304912(PMID 21304912)
- 5-3-2012
- 김병호 Zerbino DR, Paten B, Haussler D. Integrating genomes. 2012. Science. (PMID 22499938)
- 남지희 Vikas Rao Pejaver, Heewook Lee, and Sun Kim. Gene Cluster Prediction and Its Application to Genome Annotation.
- 4-26-2012
- 고아름:Rice KC, Bayles KW. Molecular control of bacterial death and lysis. 2008. Microbiol Mol Biol Rev. (PMID 18322035)
- 이세영:Callura JM, Cantor CR, Collins JJ. Genetic switchboard for synthetic biology applications. 2012. Proc Natl Acad Sci U S A. (PMID 22454498)
- 김병호:Tsvetanova B. et al. Genetic assembly tools for synthetic biology. 2011. Methods Enzymol. (PMID 21601684)
- 4-19-2012
- 박홍재 Synthetic biology: applications come of age. PMID 20395970
- 노한성 Insights into the bovine rumen plasmidome. PMID 22431592
- 4-10-2012
- 고혁진 Regulation of arabinose and xylose metabolism in Escherichia coli PMID 20023096
- 4-05-2012
- 민병남 Next-generation transcriptome assembly PMID 21897427
- 김병호 Minimum length of sequence homology required for in vivo cloning by homologous recombination in yeast PMID 9339466
- 김병호 Genetic assembly tools for synthetic biology PMID 21601684
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