Group meeting

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==Group meeting Schedule==
==Group meeting Schedule==
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=== 2012 Schedule ===
;Rule
;Rule
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*저널발표 순서 : 고혁진-김소현-박은혜-노한성-이세영-김병호-<font color=green>김수진(가능할 때)</font>
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*저널발표 순서 (Topics: NGS & Synthetic biology applications)
-
*실험발표 순서 : 고혁진-노한성-김소현-박은혜-이세영-<font color=green>김병호/남지희/김학진/박홍재/민병남/장경우/고아름(가능할 때)</font>
+
**Synbio  김병호-고혁진-박홍재- 이세영-고아름(>매주 1명 이상) (김병호 bi-weekly)
 +
**Compbio 노한성-남지희-<font color=green>김수진(가능할 때)-민병남</font> (매주 1명씩) (남지희 bi-weekly)
*발표시간 엄수
*발표시간 엄수
<pre style=color:red>
<pre style=color:red>
리뷰논문 20분이내
리뷰논문 20분이내
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실험논문/실험결과 15분이내</pre>
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실험논문/실험결과 15분이내
 +
PPT slide 5장 이내로 만들것
 +
</pre>
*발표논문 미리 읽기 (아래 링크 PMID = pubmed id)
*발표논문 미리 읽기 (아래 링크 PMID = pubmed id)
-
----
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====2014_Spring====
-
;Schedule
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;2014/3/15
-
:
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박홍재 : RNA-guided editing of bacterial genomes using CRISPR-Cas systems PMID 23360965
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===2011 Schedule===
+
;2014/3/22
 +
고혁진 : ZFN, TALEN, and CRISPR-Cas-based methods for genome engineering PMID 23664777
 +
;2014/3/29
 +
장경우 : Processive_endoglucanases_mediate_degradation_of_cellulose_by_Saccharophagus_degradans PMID 19617364
 +
;2014/4/5
 +
민병남 : Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris PMID 21964414
 +
;2014/4/26
 +
박병혁 : Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota PMID 20376150
 +
====2013_Spring====
 +
;2013/5/13
 +
이세영 PMID 23334451
 +
김병호
 +
;2013/5/6
 +
남지희 PMID 22110030
 +
고아름 PMID 17891388
 +
;2013/4/29
 +
노한성 PMID 23185043
 +
박홍재 PMID 23475073
 +
;2013/4/22
 +
이세영
 +
김병호
-
====2011_summer====
+
;2013/4/8
-
*저널발표 시간 및 장소 : 1:00PM~2:30PM-<font color=green>  생명과학관 서관 L211호</font>
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고아름 Tuning Promoter Strengths for Improved Synthesis and Function of Electron Conduits in Escherichia coli
 +
[http://pubs.acs.org/doi/abs/10.1021/sb300119v]
 +
남지희 PMID
 +
;2013/4/1
 +
노한성 PMID 22509729, 박홍재 PMID 23258894
 +
;2013/3/18
 +
고아름 PMID 20453141, 남지희  PMID 17167517
 +
;2013/3/8
 +
노한성 PMID 22221832, 박홍재 PMID 22081564
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;2013/3/4
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이세영 PMID 23371936, 민병남 PMID 15613400
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;6-24-2011
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====2012_Winter====
-
:[실험 - 이세영, 고혁진] [저널 - 김학진]
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발표순서 : 박홍재,고아름,남지희,김병호,고혁진,이세영,민병남,노한성
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;7-7-2011
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;2013/2/13
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:[실험 - 노한성, 김소현]
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남지희 PMID 20554054, 김병호 PMID 23297225, 고혁진 PMID 23183303
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;7-21-2011
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;2013/2/4
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:[실험 - 박은혜, 이세영]
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노한성 PMID 17400247, 박홍재 PMID 23354052, 고아름 PMID 20520829
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;7-28-2011
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;2013/1/28
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:[실험 - 고혁진, 노한성]
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고혁진 PMID 23183303, 이세영 PMID 23332744,민병남 PMID 23282285
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;8-4-2011
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:[실험 - 김소현, 박은혜]
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;8-11-2011
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:[실험 - 이세영, 고혁진]
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;8-18-2011
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:[실험 - 노한성, 김소현]
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;8-25-2011
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-
:[실험 - 박은혜, 이세영]
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 +
;2013/1/21
 +
고아름 PMID 19218409, 남지희 PMID 21552257, 김병호 PMID 22957093
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;2013/1/14
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민병남 PMID 22936779, 노한성 PMID 22300632, 박홍재 PMID 20453931
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;2013/1/7
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김병호 PMID 15851066, 고혁진 PMID 22544021, 이세영 PMID 22388287
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;2012/12/31
 +
박홍재 PMID 18323808 , 고아름 PMID 22237017, 남지희 PMID 21925380
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;2012/12/24
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김병호 PMID 22676891, 이세영 PMID 23042452, 노한성 PMID 22555938
 +
;2012/12/17
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고혁진 PMID 22565964, 민병남 PMID 9381168, 남지희 PMID 21847113
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;2012/12/10
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박홍재 PMID 22895337, 고아름 PMID 23034349
 +
;Reading list
 +
<biblio>
 +
#0114-hsr pmid=22300632
 +
#0114-bnm pmid=22936779
 +
#0107-syl pmid=22388287
 +
#1231-jhn pmid=21925380
 +
#1231-ark pmid=22237017
 +
#1231-hjp pmid=18323808
 +
#1224-bhk pmid=22676891
 +
#1224-hsn pmid=23042452
 +
#1224-syl pmid=22555938
 +
#1217-jhn pmid=21847113
 +
#1217-hjk pmid=22565964
 +
#1217-bnm pmid=9381168
 +
#1210-hjp pmid=22895337
 +
#1210-ark pmid=23034349
 +
</biblio>
-
====2011_Spring====
+
====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)
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;2-21-2011
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;8-06-2012
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:[저널 - 박은혜, 이세영, 고혁진] [실험 - 김소현, 박은혜, 남지희]
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: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)
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#2-21-2011-HJKo Improving Enzymes for Biomass Conversion: A Basic Research Perspective, Banerjee, Goutami, Scott-Craig, John S., Walton, Jonathan D. BioEnergy Research. Vol. 3, no. 1, pp. 82-92. Mar. 2010
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: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)
-
;2-28-2011
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;7-30-2012
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:[저널 - 김소현, 박은혜, 김수진] [실험 - 이세영, 고혁진]
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: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)
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#2-28-2011-SHKim PMID 19756010 Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?(PMID 12209002)
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: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)
-
#2-28-2011-EHPark PMID 8905079 Microbial hydrolysis of polysaccharides
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:민병남:On the Thermodynamics of Microbial Growth Processes Biotechnology and Bioengineering. 1991. 38:697-718
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#2-28-2011-SJKim PMID 20519413 Strand-specific deep sequencing of the transcriptome
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: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)
-
;3-7-2011
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: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)
-
:[저널 - 노한성, 이세영] [실험 - 노한성, 김소현]
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;7-04-2012
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#3-7-2011-HSRoh PMID 21298028 (or PMID 21253555)
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: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)
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#3-7-2011-SYLee PMID 21173271 Experimental support for the evolution of symmetric protein architecture from a simple peptide motif.
+
-
;3-17-2011
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: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)
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:[저널 - 김병호, 고혁진] [실험 - 박은혜, 이세영]
+
-
#3-14-2011-HJKo1 PMID 20576891, (PMID 20706208, PMID 9891795 Bacteria as modular organisms)
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-
#3-14-2011-HJKo2 PMID 20206495
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-
#3-14-2011-BHKim PMID 14745042 Coauthorship networks and patterns of scientific collaboration
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-
;3-24-2011
+

-
:[저널 - 김소현, 박은혜] [실험 - 고혁진, 노한성]
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: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
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#3-24-2011-SHKim PMID 21358636 Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways
+
-
#3-24-2011-EHPark PMID 20865174 An introduction to biomolecular graphics
+
-
;3-31-2011
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: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)
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:[저널 - 노한성, 이세영, 남지희] [실험 - 김소현, 박은혜]
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;6-20-2012
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#3-31-2011-HSRoh PMID 21390271 Identifying causal genes and dysregulated pathways in complex diseases.
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: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)
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#3-31-2011-SYLee PMID 17054983 Reconstruction of functional beta-propeller lectins via homo-oligomeric assembly of shorter fragments.
+
-
#3-31-2011-JHNam PMID 20946837 The fungal genome initiative and lessons learned from genome sequencing.
+
-
;4-7-2011
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: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)
-
:[저널 - 김병호, 고혁진] [실험 - 이세영, 고혁진]
+
-
#4-7-2011-BHKim [http://www.e-epih.org/Synapse/Data/PDFData/0073KJE/kje-30-60.pdf 국내 역학 분야의 학술활동과 공저자 핵심어 네트워크]
+
-
#4-7-2011-HJKo PMID 21378968 Conversion of proteins into biofuels by engineering nitrogen flux
+
-
;4-14-2011
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:김병호 : Synthetic biology and the development of tools for metabolic engineering Keasling JD(PMID 22314049)
-
:[저널 - 김소현, 박은혜] [실험 - 노한성, 김소현]
+
-
#4-14-2011-SHKim PMID 21272631 Microbial 2,3-butanediol production: A state-of-the-art review/ PMID 19756578 Engineering Klebsiella oxytoca for efficient 2,3-butanediol production through insertional inactivation of actaldehyde dehydrogenase gene
+
-
#4-14-2011-EHPark PMID 21385722 A Virophage at the Origin of Large DNA Transposons
+
-
;4-21-2011
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;6-13-2012
-
:[저널 - 노한성, 이세영] [실험 - 박은혜, 이세영]
+
: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)
-
#4-21-2011-HSRoh PMID 21253555 Measuring the evolutionary rewiring of biological networks
+
-
#4-21-2011-SYLee PMID 21471968 Crystal structure of a phosphorylation-coupled saccharide transporter
+
-
;4-28-2011
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: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)
-
:[저널 - 김병호, 고혁진] [실험 - 고혁진, 노한성]
+
-
#4-28-2011-HJKo :[http://jxb.oxfordjournals.org/content/54/383/609.full.pdf+html]
+
-
#4-28-2011-BHKim :[http://pre.aps.org/abstract/PRE/v64/i1/e016131 Scientific collaboration networks. I.Network construction and fundamental results]
+
-
;5-4-2011 Wed (rescheduled)
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: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 
-
:[저널 - 김소현, 박은혜] [실험 - 김소현, 박은혜]
+
;6-8-2012
-
#5-4-2011 SHKim PMID 18383127 Utilization of cellulosic waste from tequila bagasse and production of polyhydroxyalkanoate (PHA) bioplastics by Saccharophagus degradans/ PMID 18193466 Biosynthesis and characterization of polyhydroxyalkanoates in the polysaccharide-degrading marine bacterium Saccharophagus degradans ATCC 43961
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:노한성 : The Tomato Genome Consortium The tomato genome sequence provides insights into flesh fruit evolution 2012, Nature
-
#5-4-2011-EHPark PMID 16690241 Outlook for cellulase improvement: screening and selection strategies
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: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 )
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;5-11-2011 Wed (rescheduled)
+
====2012_Spring====
-
:[저널 - 이세영] [실험 - 이세영, 고혁진]
+
-
#5-11-2011 SYLee PMID 20393580 A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion.
+
-
;5-19-2011
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;5-30-2012
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:[저널 - 김병호, 고혁진, 노한성] [실험 - 노한성, 김소현]
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: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)
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#5-19-2011-HJKo [http://aem.asm.org/cgi/content/abstract/76/3/971 Enhanced Display of Lipase on the Escherichia coli Cell Surface, Based on Transcriptome Analysis]
+
 
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#5-19-2011-BHKim[http://www.ncbi.nlm.nih.gov/pubmed/11461356 Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality]
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: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
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#5-19-2011-HSRoh PMID 21297116 Towards more robust methods of alien gene detection
+
-
;5-26-2011
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:[저널 - 김소현, 박은혜] [실험 - 박은혜, 이세영]
+
-
#5-26-2011-SHKim PMID 2059047 Genetic Improvement of Escherichia coli for Ethanol Production:Chromosomal Integration of Zymomonas mobilis Genes Encoding Pyruvate Decarboxylase and Alcohol Dehydrogenase Il
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-
;6-2-2011
+
-
:[저널 - 노한성, 이세영] [실험 - 고혁진, 노한성]
+
-
#6-2-2011 HSRoh PMID 21471011Alignment-free detection of local similarity among viral and bacterial genomes
+
-
#6-2-2011 SYLee PMID 21602812 Metabolic engineering of escherichia coli for direct production of 1,4-butanediol
+
-
;6-9-2011
+
-
:[저널 - 김병호, 고혁진] [실험 - 김소현, 박은혜]
+
-
#6-9-2011 HJKo PMID 19633652 Programming cells by multiplex genome engineering and accelerated evolution
+
 +
:고아름 : Slusarczyk AL, Lin A, Weiss R. Foundations for the design and implementation of synthetic genetic circuits. 2012. NATURE REVIEWS GENETICS. (PMID 22596318)
-
====[[2011_Winter|2010_2011_Winter]]====
+
: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
==Previous years==
==Previous years==
*[[Old_group_meeting_schedule|Since 2007]]
*[[Old_group_meeting_schedule|Since 2007]]
-
==Computational Biology Group Meeting==
+
<!-- ==Computational Biology Group Meeting==
===[[Computational Biology Group]]===
===[[Computational Biology Group]]===
*Textbook: Statistics Using R with Biological Examples
*Textbook: Statistics Using R with Biological Examples
Line 149: Line 243:
*2011-01-25 HS Bae, 4. Programming with R, JH Nam, 5. Exploratory Data Analysis and Graphics
*2011-01-25 HS Bae, 4. Programming with R, JH Nam, 5. Exploratory Data Analysis and Graphics
*2011-02-01 BH Kim, 6. Foundations of Probability Theory
*2011-02-01 BH Kim, 6. Foundations of Probability Theory
-
*2011-02-08
+
*2011-02-08 --!>

Latest revision as of 02:23, 26 April 2014

Contents

讀書百遍義自見

Group sister sites

Lab. Bulletin: 게시판(자료실)
Google Group Page: 메일링 리스트
Data image sharing: 데이터 사진
Connotea-kucsbl: 참고문헌 공유

Group meeting Schedule

2012 Schedule

Rule
리뷰논문 20분이내
실험논문/실험결과 15분이내
PPT slide 5장 이내로 만들것

2014_Spring

2014/3/15

박홍재 : RNA-guided editing of bacterial genomes using CRISPR-Cas systems PMID 23360965

2014/3/22

고혁진 : ZFN, TALEN, and CRISPR-Cas-based methods for genome engineering PMID 23664777

2014/3/29

장경우 : Processive_endoglucanases_mediate_degradation_of_cellulose_by_Saccharophagus_degradans PMID 19617364

2014/4/5

민병남 : Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris PMID 21964414

2014/4/26

박병혁 : Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota PMID 20376150

2013_Spring

2013/5/13

이세영 PMID 23334451 김병호

2013/5/6

남지희 PMID 22110030 고아름 PMID 17891388

2013/4/29

노한성 PMID 23185043 박홍재 PMID 23475073

2013/4/22

이세영 김병호

2013/4/8

고아름 Tuning Promoter Strengths for Improved Synthesis and Function of Electron Conduits in Escherichia coli [1]

남지희 PMID

2013/4/1

노한성 PMID 22509729, 박홍재 PMID 23258894

2013/3/18

고아름 PMID 20453141, 남지희 PMID 17167517

2013/3/8

노한성 PMID 22221832, 박홍재 PMID 22081564

2013/3/4

이세영 PMID 23371936, 민병남 PMID 15613400

2012_Winter

발표순서 : 박홍재,고아름,남지희,김병호,고혁진,이세영,민병남,노한성

2013/2/13

남지희 PMID 20554054, 김병호 PMID 23297225, 고혁진 PMID 23183303

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
Error fetching PMID 22300632:
Error fetching PMID 22936779:
Error fetching PMID 22388287:
Error fetching PMID 21925380:
Error fetching PMID 22237017:
Error fetching PMID 18323808:
Error fetching PMID 22676891:
Error fetching PMID 23042452:
Error fetching PMID 22555938:
Error fetching PMID 21847113:
Error fetching PMID 22565964:
Error fetching PMID 9381168:
Error fetching PMID 22895337:
Error fetching PMID 23034349:
  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]
All Medline abstracts: PubMed HubMed

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

Previous years


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