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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

2013/2/13

남지희, 김병호, 고혁진

2013/2/4

노한성 PMID 17400247, 박홍재 PMID 23354052, 고아름 PMID 20520829

2013/1/28

고혁진 PMID 23183303, 이세영 PMID 23332744,민병남 PMID 23282285

2013/1/21

고아름 PMID 19218409, 남지희 PMID 21552257, 김병호 PMID 22957093

2013/1/14

민병남 PMID 22936779, 노한성 PMID 22300632, 박홍재 PMID 20453931

2013/1/7

김병호 PMID 15851066, 고혁진 PMID 22544021, 이세영 PMID 22388287

2012/12/31

박홍재 PMID 18323808 , 고아름 PMID 22237017, 남지희 PMID 21925380

2012/12/24

김병호 PMID 22676891, 이세영 PMID 23042452, 노한성 PMID 22555938

2012/12/17

고혁진 PMID 22565964, 민병남 PMID 9381168, 남지희 PMID 21847113

2012/12/10

박홍재 PMID 22895337, 고아름 PMID 23034349

Reading list

1. Error fetching PMID 22300632: [0114-hsr]
2. Error fetching PMID 22936779: [0114-bnm]
3. Error fetching PMID 22388287: [0107-syl]
4. Error fetching PMID 21925380: [1231-jhn]
5. Error fetching PMID 22237017: [1231-ark]
6. Error fetching PMID 18323808: [1231-hjp]
7. Error fetching PMID 22676891: [1224-bhk]
8. Error fetching PMID 23042452: [1224-hsn]
9. Error fetching PMID 22555938: [1224-syl]
10. Error fetching PMID 21847113: [1217-jhn]
11. Error fetching PMID 22565964: [1217-hjk]
12. Error fetching PMID 9381168: [1217-bnm]
13. Error fetching PMID 22895337: [1210-hjp]
14. Error fetching PMID 23034349: [1210-ark]

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 PMID 10921867

남지희 Functional genome annotation through phylogenomic mapping PMID 15940241

박홍재 Direct cloning of large genomic sequences PMID 22565964

민병남 On the thermodynamics of microbial growth processes PMID 18600796

8-20-2012

고혁진 Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides PMID 20639866

김병호 Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems PMID 12536251

노한성 Biological network motif detection and evaluation PMID 22784624

고아름 Microbial solar cells: applying photosynthetic and electrochemically active organisms PMID 21067833

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.(PMID 21925268)

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 pr int](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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