genome.gov | Genome Technology Program Bibliography: Publications and Patents

NHGRI launched an ambitious program in 2004 to reduce the cost of full genome sequencing initially by 100-fold and subsequently by an additional 100-fold. Below, listed by Principal Investigator, are citations and links to many of the articles and patents resulting from this and closely related programs.

Benner, Steven A.

Yang Z, Sismour AM, Sheng P, Puskar NL, Benner SA.
Enzymatic incorporation of a third nucleobase pair. Nucleic Acids Res, 2007;35(13):4238-49. Epub 2007 Jun 18
PubMed

Yang Z, Sismour AM, Benner SA.
Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages. Nucleic Acids Res,, 2007;35(9):3118-27. Epub 2007 Apr 22
PubMed

patents

Akeson M, Branton D, Deamer DW, Sampson JR, inventors.
Methods and apparatus for characterizing polynucleotides. Issued July 3, 2007
Methods and apparatus for characterizing polynucleotides

Church, George

Varley KE, Mitra RD.
Nested Patch PCR Enables Highly Multiplex Mutation Discovery in Candidate Genes (submitted). Genome Res, (2008)
PubMed

Lunshof JE, Chadwick R, Vorhaus DB, Church GM.
From genetic privacy to open consent. Nat Rev Genet, (2008)
PubMed

Dantas G, Sommer MOA, Oluwasegun RD, Church GM.
Functional Microbiomics: bacteria subsisting on antibiotics in soil. Science, (2008)
PubMed

Sherley JL.
All good cells come from cells. Nat Cell Biol, 10, 248 (2008)
PubMed

Shendure JA, Porreca GJ, Church GM.
Overview of DNA sequencing strategies. Curr Protoc Mol Biol, Chapter 7, Unit 7 1 (2008)
PubMed

Nardi V, Raz T, Cao X, Wu CJ, Stone, RM, Cortes J, Deininger MW, Church G, Zhu J, Daley GQ.
Quantitative monitoring by polymerase colony assay of known mutations resistant to ABL kinase inhibitors. Oncogene, 27, 775-82 (2008)
PubMed

Kim DS, Ross SE, Trimarchi JM, Aach J, Greenberg ME, Cepko CL.
Identification of molecular markers of bipolar cells in the murine retina. J Comp Neurol, 2008 Apr 10;507(5):1795-810
PubMed

Rieger C, Poppino R, Sheridan R, Moley K, Mitra R, Gottlieb D.
Polony analysis of gene expression in ES cells and blastocysts. Nucleic Acids Res, 2007;35(22):e151. Epub 2007 Dec 10
PubMed

Leparc GG, Mitra RD.
A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples. Nucleic Acids Res, 2007;35(21):e146. Epub 2007 Nov 13
PubMed

Wang H, Johnston M, Mitra RD.
Calling cards for DNA-binding proteins. Genome Res, 2007 Aug;17(8):1202-9. Epub 2007 Jul 10
PubMed

Leparc GG, Mitra RD.
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Nucleic Acids Res, 2007;35(10):3192-202. Epub 2007 Apr 22
PubMed

Lee HS, Crane GG, Merok JR, Tunstead JR, Hatch NL, Panchalingam K, Powers MJ, Griffith LG, Sherley JL..
Clonal expansion of adult rat hepatic stem cell lines by suppression of asymmetric cell kinetics (SACK). Biotechnol Bioeng, 83, 760-71 (2003)
PubMed

Willerth SM, Faxel TE, Gottlieb DI, Sakiyama-Elbert SE.
The effects of soluble growth factors on embryonic stem cell differentiation inside of fibrin scaffolds. Stem Cells, 25, 2235-44 (2007)
PubMed

Sherley JL.
Commentary: Facing up to the feasibility of ANT-OAR. Stem Cell Rev, 3, 66-7 (2007)
PubMed

Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J.
Multiplex amplification of large sets of human exons. Nat Methods, 4, 931-6 (2007)
PubMed

Kim JB, Porreca GJ, Song L, Greenway SC, Gorham JM, Church GM, Seidman CE, Seidman JG.
Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science, 316, 1481-4 (2007)
PubMed

Conrad C, Zhu J, Conrad C, Schoenfeld D, Fang Z, Ingelsson M, Stamm S, Church G, Hyman BT.
Single molecule profiling of tau gene expression in Alzheimer's disease. J Neurochem, 103, 1228-36 (2007)
PubMed

Bakal C, Aach J, Church G, Perrimon N.
Quantitative morphological signatures define local signaling networks regulating cell morphology. Science, 316, 1753-6 (2007)
PubMed

Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM.
Long-range polony haplotyping of individual human chromosome molecules. Nat Genet, 38, 382-7 (2006)
PubMed

Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM.
Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol, 24, 680-6 (2006)
PubMed

Willerth SM, Arendas KJ, Gottlieb DI, Sakiyama-Elbert SE.
Optimization of fibrin scaffolds for differentiation of murine embryonic stem cells into neural lineage cells. Biomaterials, 27, 5990-6003 (2006)
PubMed

Turner DJ, Shendure J, Porreca G, Church G, Green P, Tyler-Smith C, Hurles ME.
Assaying chromosomal inversions by single-molecule haplotyping. Nat Methods, 3, 439-45 (2006)
PubMed

Tannenbaum E, Sherley JL, Shakhnovich EI.
Semiconservative quasispecies equations for polysomic genomes: the haploid case. J Theor Biol, 241, 791-805 (2006)
PubMed

Porreca GJ, Shendure J, Church GM.
Polony DNA sequencing. Curr Protoc Mol Biol. Chapter 7, Unit 7 8 (2006)
PubMed

Pare JF, Sherley JL.
Biological principles for ex vivo adult stem cell expansion. Curr Top Dev Biol, 73, 141-71 (2006)
PubMed

Lee SI, Pe'er D, Dudley AM, Church GM, Koller D.
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A, 103, 14062-7 (2006)
PubMed

Church GM.
Genomes for all. Sci Am, 294, 46-54 (2006)
PubMed

Xian HQ, Werth K, Gottlieb DI.
Promoter analysis in ES cell-derived neural cells. Biochem Biophys Res Commun, 155-62 (2005)
PubMed

Wei L, Cui L, Snider BJ, Rivkin M, Yu SS, Lee CS, Adams LD, Gottlieb DI, Johnson EM Jr., Yu SP, Choi DW.
Transplantation of embryonic stem cells overexpressing Bcl-2 promotes functional recovery after transient cerebral ischemia. Neurobiol Dis, 19, 183-93 (2005)
PubMed

Tannenbaum E, Sherley JL, Shakhnovich EI.
Evolutionary dynamics of adult stem cells: comparison of random and immortal-strand segregation mechanisms. Phys Rev E Stat Nonlin Soft Matter Phys, 71, 041914 (2005)
PubMed

Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM.
Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-32 (2005)
PubMed

Rambhatla L, Ram-Mohan S, Cheng JJ, Sherley JL.
Immortal DNA strand cosegregation requires p53/IMPDH-dependent asymmetric self-renewal associated with adult stem cells. Cancer Res, 3155-61 (2005)
PubMed

Lee HS, Sherley JL, Chen JJ, Chiu CC, Chiou LL, Liang JD, Yang PC, Huang GT, Sheu JC.
EMP-1 is a junctional protein in a liver stem cell line and in the liver. Biochem Biophys Res Commun, 334, 996-1003 (2005)
PubMed

Lee CS, Tee LY, Dusenbery S, Takata T, Golden JP, Pierchala BA, Gottlieb DI, Johnson EM Jr., Choi DW, Snider BJ.
Neurotrophin and GDNF family ligands promote survival and alter excitotoxic vulnerability of neurons derived from murine embryonic stem cells. Exp Neurol, 191, 65-76 (2005)
PubMed

Church GM.
The personal genome project. Mol Syst Biol, 1, 2005 0030 (2005)
Pubmed

Xian H, Gottlieb DI.
Dividing Olig2-expressing progenitor cells derived from ES cells. Glia, 47, 88-101 (2004)
PubMed

Tannenbaum E, Sherley JL, Shakhnovich EI.
Imperfect DNA lesion repair in the semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape. Phys Rev E Stat Nonlin Soft Matter Phys, 70, 061915 (2004)
PubMed

Shendure J, Mitra RD, Varma C, Church GM.
Advanced sequencing technologies: methods and goals. Nat Rev Genet, 5, 335-44 (2004)
PubMed

Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS.
Digital quantitative measurements of gene expression. Biotechnol Bioeng, 86, 117-24 (2004)
PubMed

Aach J, Church GM.
Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J Theor Biol, 228, 31-46 (2004)
PubMed

Zhu J, Shendure J, Mitra RD, Church GM.
Single molecule profiling of alternative pre-mRNA splicing. Science, 301, 836-8 (2003)
PubMed

Xian HQ, McNichols E, St Clair A, Gottlieb DI.
A subset of ES-cell-derived neural cells marked by gene targeting. Stem Cells, 21, 41-9 (2003)
PubMed

Qu Y, Vadivelu S, Choi L, Liu S, Lu A, Lewis B, Girgis R, Lee CS, Snider BJ, Gottlieb DI, McDonald JW.
Neurons derived from embryonic stem (ES) cells resemble normal neurons in their vulnerability to excitotoxic death. Exp Neurol, 184, 326-36 (2003)
PubMed

Mitra RD, Shendure J, Olejnik J, Edyta Krzymanska O, Church GM.
Fluorescent in situ sequencing on polymerase colonies. Anal Biochem, 320, 55-65 (2003)
PubMed

Mitra RD, Butty VL, Shendure J, Williams BR, Housman DE, Church GM.
Digital genotyping and haplotyping with polymerase colonies. Proc Natl Acad Sci U S A, 100, 5926-31 (2003)
PubMed

Merritt J, DiTonno JR, Mitra RD, Church GM, Edwards JS.
Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. Nucleic Acids Res, 31, e84 (2003)
PubMed

Collins, Scott D.

Gierhart BC, Howitt DG, Chen SJ, Smith RL, Collins SD.
Frequency dependence of gold nanoparticle superassembly by dielectrophoresis. Langmuir, Nov 20;23(24):12450-6. Epub 2007 Oct 27
PubMed

Egholm, Michael

Leamon JH, Rothberg JM.
Cramming more sequencing reactions onto microreactor chips. Chem Rev., 2007 Aug;107(8):3367-76. Epub 2007 Jul 10. Review. No abstract available
PubMed

Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH.
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics, 2006 Aug 23;7:216
PubMed

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM.
Genome sequencing in microfabricated high-density picolitre reactors. Nature, 2005 Sep 15;437(7057):376-80. Epub 2005 Jul 31. Erratum in: Nature. 2006 May 4;441(7089):120. Ho, Chun He [corrected to Ho, Chun Heen]
PubMed

Fair, Richard

Fair RB.
Integrated Digital Microfluidic Functions for Chemical and Biological Applications. Materials Research Society Meeting, San Francisco, CA April 13, 2007

Fair RB.
Digital Microfluidics: is a true lab-on-a-chip possible?. J. Microfluidics and Nanofluidics, vol. 3, 245-281 (2007)
FullText

Fair RB, Khylstov A, Tailor TD, Ivanov I, Evans RD, Srinivasan V, Pamula VK, Pollack MG, Griffin RB, Zhou J.
Chemical and Biological Applications of Digital Microfluidic Devices. IEEE Design and Test of Computers, Design and Test of Computers, 24, No. 1, pp.10-24, Jan-Feb (2007)
FullText

Fair, RB.
Digital Microfluidic Biochips. Boston, Nov. 27, 2007

Griffin PB, Fair RB.
A Continuous Flow Microchannel-based DNA Sequencing Scheme. Marco Island, FL, Feb. 9, 2006

patents

Pollack MG, Pamula VK, Allen DJ, Fair RB, Griffin PB.
Droplet-Based Pyrosequencing. Oct. 25, 2007
Droplet-Based Pyrosequencing (WO2007120240)

Ghadiri, M. Reza

Cockroft SL, Chu J, Amorin M, Ghadiri MR.
A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J Am Chem Soc, Jan 23;130(3):818-20. Epub 2008 Jan 1
PubMed

Wu HC, Astier Y, Maglia G, Mikhailova E, Bayley H.
Protein nanopores with covalently attached molecular adapters. J Am Chem Soc, 2007 Dec 26;129(51):16142-8. Epub 2007 Nov 30
PubMed

Astier Y, Kainov DE, Bayley H, Tuma R, Howorka S.
Stochastic detection of motor protein-RNA complexes by single-channel current recording. Chemphyschem, Oct 22;8(15):2189-94. 2007
PubMed

Ashkenasy N, Sánchez-Quesada J, Bayley H, Ghadiri MR.
Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew Chem Int Ed Engl, Feb 18;44(9):1401-4. 2005.
PubMed

Sánchez-Quesada J, Saghatelian A, Cheley S, Bayley H, Ghadiri MR.
Single DNA rotaxanes of a transmembrane pore protein. Angew Chem Int Ed Engl, Jun 7;43(23):3063-7. 2004.
PubMed

Golovchenko, Jene A.

Hornblower B, Coombs A, Whitaker RD, Kolomeisky A, Picone SJ, Meller A, Akeson M..
Single-molecule analysis of DNA-protein complexes using nanopores. Nat Methods, 2007 Apr;4(4):315-7. Epub 2007 Mar 4.
PubMed

Gershow M, Golovchenko JA.
Recapturing and trapping single molecules with a solid-state nanopore. Nature Nanotechnology, 2: 775-779. 2007.
FullText

****Fologea D, Brandin E, Uplinger J, Branton D, Li J..
DNA conformation and base number simultaneously determined in a nanopore. Electrophoresis, 28: 3186-3192. 2007
PubMed

Hoogerheide DP, Golovchenko JA.
Dynamics of ion beam stimulated surface mass transport to nanopores. Edited by D. Ila, J. Baglin, N. Kishimoto, P.K. Chu (Mater. Res. Soc. Symp. Proc. Volume 1020, Warrendale, PA, 2007), paper number 1020-GG-02-01
****Ion-Beam-Based Nanofabrication

Hughes ME, Brandin E, Golovchenko JA.
Optical absorption of DNA-carbon nanotube structures. Nano Letters, 7: 1191-1194. 2007
PubMed

****DeGuzman VS, Lee CC, Deamer DW, Vercoutere WA.
Sequence-dependent gating of an ion channel by DNA hairpin molecules. Nucleic Acids Res, 2006;34(22):6425-37. Epub 2006 Nov 27.
PubMed

Peng HB, Hughes ME, Golovchenko JA.
Room-temperature single-charge sensitivity in carbon nanotube field-effect transistors. Appl. Phys. Lett, 89: 243502-1 243502-3. 2006
****FullText

****Kim Y-R, Chen P, Aziz MJ, Branton D, Vlassak JJ..
Focused ion beam induced deflections of freestanding thin films.. J. Appl. Phys, 100: 104322-1 - 104322-9 (2006)
****FullText

****Park SY, Russo CJ, Branton D, Stone HA.
Eddies in a bottleneck: An arbitrary Debye length theory for capillary electroosmosis.. J. Colloid Interface Sci, 297: 832-839 (2006)
PubMed

Mitsui T, Stein D, Kim Y-R, Hoogerheide D, Golovchenko JA.
Nanoscale volcanoes: Accretion of matter at ion-sculpted nanopores.. Phys. Rev. Lett, 96: 036102-1 - 036102-4. 2006
****FullText

King GM, Golovchenko JA.
Probing nanotube-nanopore interactions. Phys. Rev. Lett., 95: 216103-1 - 216103-42005 (2005)
****FullText

Fologea D, Gershow M, Ledden B, McNabb DS, Golovchenko JA, Li J..
Detecting single stranded DNA with a solid state nanopore.. Nano Letters, 5: 1905-1909. 2005
****Abstract

King GM, Schürmann G, Branton D, Golovchenko JA..
Nanometer patterning with ice. Nano Letters, 5: 1157-1160 (2005).
****Abstract

Ristroph T, Goodsell A, Golovchenko JA, Hau LV.
Detection and quantized conductance of neutral atoms near a charged carbon nanotube. Phys. Rev. Lett., 94: 066102-1 - 066102-4. 2005
****FullText

Chen P, Gu J, Brandin E, Kim Y-R, Wang Q, Branton D.
Probing single DNA molecule transport using fabricated nanopores. Nano Letters, 4: 2293-2298. 2004
****Abstract

Chen P, Gu J, Brandin E, Kim Y-R, Wang Q, Branton D..
Probing single DNA molecule transport using fabricated nanopores. Nano Letters, 4: 2293-2298. 2004
****Abstract

****Wang H, Dunning JE, Huang AP, Nyamwanda JA, Branton D..
DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis. Proc. Natl. Acad Sci. USA, 101: 13472-13477. 2004
PubMed

Peng HB, Golovchenko JA.
Coulomb blockade in suspended Si3N4-coated single-walled carbon nanotubes.. App. Phys. Lett, 84: 5428-5430. 2004
****FullText

Chen P, Mitsui T, Farmer DB, Golovchenko JA, Gordon RG, Branton D.
Atomic layer deposition to fine-tune the surface properties and diameters of fabricated nanopores. Nano Letters, 4:1333-1337. 2004
FullText

patents

Li J, Stein D, Schurmann G, King G, Golovchenko J, Branton D, Aziz M, iventors.
Ion beam sculpting of multiple distinct materials. Issued 21 August 2007
Ion beam sculpting of multiple distinct materials

Golovchenko J, Peng H, inventors.
Suspended carbon nanotube field effect transistor. Issued August 7, 2007
Suspended carbon nanotube field effect transistor

****Akeson M, Branton D, Deamer DW, Sampson JR, inventors.
Methods and apparatus for characterizing polynucleotides. Issued July 3, 2007.
Methods and apparatus for characterizing polynucleotides

****Akeson M, Branton D, Church G, Deamer D, inventors.
Characterization of individual polymer molecules based on monomer-interface interactions. Issued March 13, 2007
Characterization of individual polymer molecules based on monomer-interface interactions

Golovchenko J, Stein D, Li J, inventors.
Pulsed ion beam control of solid state features. Issued October 10, 2006
Pulsed ion beam control of solid state features

Golovchenko J, Chopra N, Basile D, inventors.
System with nano-scale conductor and nano-opening. Issued March 22, 2005
System with nano-scale conductor and nano-opening

Gorfinkel, Vera

Stepukhovich A, Tsupryk A, Kosobokova O, Gavrilov DN, Gorbovitski B, Gudkov G, Tyshko G, Tcherevishnik M, Gorfinkel V.
Analysis of DNA Sequencing Systems Based on Capillary Electrophoresis. Technical Physics, Vol. 78, Issue 6 pp.90-102. 2008

Dhulla V, Gudkov G, Gavrilov D, Stepukhovich A, Tsupryk A, Kosobokova O, Borodin A, Gorbovitski B, Gorfinkel V.
Single Photon Counting Module Based On Large Area APD And Novel Logic Circuit For Quench And Reset Pulse Generation. Journal of Selected Topics in Quantum Electronics, v.13,NO 4, 926-933. 2007
FullText

Kosobokova O, Gavrilov DN, Khozikov V, Stepukhovich A, Tsupryk A, Pan'kov S, Somova O, Abanshin N, Gudkov G, Tcherevishnik M, Gorfinkel V.
Electrokinetic injection of DNA from gel micropads: basis for coupling polony technology with CE separation. Electrophoresis, Nov. 28(21):3890-900. 2007
PubMed

Gavrilov D, Gorbovitski B, Gudkov G, Stepukhovich A, Tcherevishnik M, Tyshko G, Tsupryk A, Gorfinkel V.
Highly sensitive single photon detection system for multi-lane DNA sequencer. Proc.of SPIE, Vol.6372, 63720C, Boston, Massachusetts, USA. Oct. 1-4, 2006
FullText

Gudkov G, Dhulla V, Borodin A, Gavrilov D, Stepoukhovitch A, Tsupryk A, Gorbovitski B, Gorfinkel V.
32-channel single-photon counting module for ultrasensitive detection of DNA sequences. Conference on Advanced Photon Counting Techniques, Proc.of SPIE, Vol.6372, 63720C, Boston, Massachusetts, USA Oct. 1-4, 2006
FullText

Tsupryk M, Gorbovitski B, Kabotyanski E, Gorfinkel V.
Novel design of multi-capillary arrays for high throughput DNA sequencing. Electrophoresis, 27, Issue 14, 2869-2879, 2005.
PubMed

Gavrilov DN, Kosobokova O, Khozikov V, Stepuhovitch A, Gorfinkel V.
Electrophoresis in capillary cells with detection gap. Electrophoresis, Vol. 26, 3430-3437. 2005.
PubMed

Khozikov V, Kosobokova O, Citver G, Tyshko G, Gavrilov DN, Gudkov G, Gorfinkel V.
Experimental study of the formation of high resistivity zones at the gel/buffer interface in capillary electrophoresis. Accepted to Electrophoresis, Volume 28, Issue 3, Date: No. 3 February 317-321. 2007
PubMed

Harris, Timothy

Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavskyi I, Causey M, Colonell J, DiMeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, and Xie Z.
Single-Molecule DNA Sequencing of a Viral Genome. Science, 320, 106-109. 2008.
PubMed

Hung, Xiaohua

Chaisson MJ, Pevzner PA.
Short read fragment assembly of bacterial genomes. Genome Res, Feb;18(2):324-30. 2008. Epub Dec 14, 2007.
PubMed

Barbee KD, Huang X.
Magnetic assembly of high-density DNA arrays for genomic analyses. Anal Chem, Mar 15;80(6):2149-54. 2008. Epub Feb 9, 2008.
PubMed

Jovanonich, Stevan

patents

Stevan Jovanovich, Iuliu Blaga, David Rank.
Microfluidic Devices. February 2, 2007
US Patent Application 20080014576

****Mattias Vangbo, William Nielsen, Iuliu Blaga, Joanne Horn, Michael Nguyen, Stevan Jovanovich.
Universal sample preparation system and use in an integrated analysis system. US Patent Application

Ju, Jingyue

Wu J, Zhang S, Meng Q, Cao H, Li Z, Li X, Shi S, Kim DH, Bi L, Turro NJ, Ju J.
3'-O-modified nucleotides as reversible terminators for pyrosequencing. Proc Natl Acad Sci U S A, Oct 16, 2007;104(42):16462-7. Epub Oct 8, 2007.
PubMed

Ju J, Kim DH, Bi L, Meng Q, Bai X, Li Z, Li X, Marma MS, Shi S, Wu J, Edwards JR, Romu A, Turro NJ.
Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A, Dec 26, 2006;103(52):19635-40. Epub Dec 14, 2006.
PubMed

Meng Q, Kim DH, Bai X, Bi L, Turro NJ, Ju J.
Design and synthesis of a photocleavable fluorescent nucleotide 3'-O-allyl-dGTP-PC-Bodipy-FL-510 as a reversible terminator for DNA sequencing by synthesis. J Org Chem, Apr. 14;71(8):3248-52. 2006.
PubMed

Bi L, Kim DH, Ju J.
Design and synthesis of a chemically cleavable fluorescent nucleotide, 3'-O-allyl-dGTP-allyl-bodipy-FL-510, as a reversible terminator for DNA sequencing by synthesis. Am Chem Soc, Mar 1, 2006;128(8):2542-3
PubMed

Bai X, Edwards J, Ju J.
Molecular engineering approaches for DNA sequencing and analysis. Expert Rev Mol Diagn, Sep. 2005;5(5):797-808. Review.
PubMed

Ruparel H, Bi L, Li Z, Bai X, Kim DH, Turro NJ, Ju J.
Design and synthesis of a 3'-O-allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis. Proc Natl Acad Sci U S A, Apr 26, 2005;102(17):5932-7. Epub Apr 13, 2005.
PubMed

Seo TS, Bai X, Kim DH, Meng Q, Shi S, Ruparel H, Li Z, Turro NJ, Ju J.
Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides. Proc Natl Acad Sci U S A, Apr 26, 2005;102(17):5926-31. Epub Apr 13, 2005.
PubMed

Lee, James W.

Zhao X, Payne CM, Cummings P.
Controlled Transport of DNA segments through nano gaps. J. Phys. Chem. C, Vol. 112, 1712-1717. 2008.
Abstract

Zhao X, Krstic PS.
Molecular dynamics simulation study on trapping ions in a nanoscale Paul trap. Nanotechnology, Vol. 19, 195702. 2008.
Abstract

Meunier V, Krsti PS.
Enhancement of the transverse conductance in DNA nucleotides. J Chem Phys, Jan. 28, 2008;128(4):041103.
PubMed

Payne CM, Zhao X, Vlcek L, Cummings PT.
Molecular dynamics simulation of ss-DNA translocation between copper nanoelectrodes incorporating electrode charge dynamics. J Phys Chem B, Feb 14, 2008;112(6):1712-7. Epub Jan 23, 2008.
PubMed

Zhao X, Payne CM, Cummings PT, Lee JW.
Single stranded DNA molecules translocation through nanoelectrode gaps. Nanotechnology, Vol. 18, 424018. 2007.
Abstract

Lee JW, Meller A.
Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA chains. Perspectives in BioPhysics, Vol. 2: New High Throughput Technologies for DNA Sequencing and Genomics. ed. K. Mitchelson, Elsevier Scientific Publishing, New York, p. 245-263. 2007.
FullText

Lee JW.
Nanoelectrode-gated detection of individual molecules with potential for rapid DNA sequencing. Solid state Phenomena, 121-123, 1379. 2007.
FullText

Krsti PS, Wells JC, Fuentes-Cabrera M, Xu D, and Lee JW.
Toward Electronic Conductance Characterization of DNA Nucleotide Bases. Solid State Phenomena, 121-123, 1387. 2007.
FullText

Fuentes-Cabrera M, Meunier V, Sumpter BG.
Benzo-homologated nucleobases in a nanotube-electrode set-up for DNA sequencing. Nanotechnology, 18 424019. 2007.
Abstract

Zikic R, Krsti PS, Zhang XG, Fuentes-Cabrera M, Wells J, Zhao X.
Characterization of the tunneling conductance across DNA bases. Phys Rev E Stat Nonlin Soft Matter Phys, Jul 2006;74(1 Pt 1):011919. Epub Jul 28, 2006.
PubMed

Zhang XG, Krsti PS, Ziki R, Wells JC, Fuentes-Cabrera M.
First-principles transversal DNA conductance deconstructed. Biophys J, Jul 1, 2006;91(1):L04-6. Epub May 5, 2006. Erratum in: Biophys J. Jul 15, 2006;91(2):777
PubMed

patents

Krstic PS, Meunier V.
Sensing Single Molecules between Doped Carbon Nanotubes. Filed on 01/25/2008.

Reed MA, Krstic PS.
Control of motion of single atoms/molecules in an aqueous and vacuum 3D nanoscale Paul trap. Filed on 03/25/2008
Abstract

Lindsay, Stuart M.

Qamar S, Williams PM, Lindsay SM..
Can an atomic force microscope sequence DNA using a nanopore?. Biophys J, 2008 Feb 15;94(4):1233-40. Epub 2007 Oct 26.
PubMed

He J, Lin L, Zhang P, Lindsay S. .
Identification of DNA basepairing via tunnel-current decay.. Nano Lett, 2007 Dec;7(12):3854-8. Epub 2007 Nov 28
PubMed

Mandecki, Wlodek

Mandecki W, Bharill S, Borejdo J, Cabral D, Cooperman BS, Farrell I, Fetter L, Goldman E, Gryczynski Z, Jakubowski H, Liu H, Luchowski R, Matveeva E, Pan D, Qin H, Tennant D, Gryczynski I. .
Fluorescence enhancement on silver nanostructures: studies of components of ribosomal translation in vitro.. Proc. SPIE, Vol. 6862, 68620T. Feb. 15, 2008.
Full Text

patents

Wlodek Mandecki.
Single molecule fluorescence assay. USPO Application Number 20050282173
USPO Application Number 20050282173

Margulies, Marcel

Margulies M, Jarvie TP, Knight JR, Simons JF.
The 454 Life Sciences Picoliter Sequencing System, in New High Throughput Technologies for DNA Sequencing and Genomics. Edited by Keith R. Mitchelson, Chapter 5, p. 153-186.
Science Direct

Leamon JH, Rothberg JM. .
Cramming more sequencing reactions onto microreactor chips.. Chem Rev, Aug 2007;107(8):3367-76. Epub Jul 10, 2007
PubMed

Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH..
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics, Aug 23, 2006;7:216.
PubMed

Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM..
Genome sequencing in microfabricated high-density picolitre reactors.. Nature, 4;441(7089):120
PubMed

patents

Nobile J, et al..
Thin-Film Coated Microwell Arrays and Methods of Making Same, United States Patent. 11/102,075, filed on 04/07/05.
U.S. Patent Number 20060228716

Kim JB, et al..
Thin-Film Coated Microwell Arrays and Methods of Making Same,. 11/215,458, filed on 08/30/05
20060228722

Leahmon JH, et al..
Methods for Determining Sequence Variants Using Ultra-Deep Sequencing. 11/104,781, filed on 04/12/05
20060228721

Berka J.
Paired End Sequencing,. filed on 06/06/06.
Paired end sequencing

Marziali, Andre

Tropini C, Marziali A..
Multi-nanopore force spectroscopy for DNA analysis. Biophys J., Mar 1;92(5):1632-7. 2007
Multi-nanopore force spectroscopy for DNA analysis

Tabard-Cossa V, Trivedi D, Wiggin M, Jetha NN, Marziali A..
Noise analysis and reduction in solid-state nanopores. Noise analysis and reduction in solid-state nanopores, 18 (2007) 305505.
Noise analysis and reduction in solid-state nanopores

Nakane J, Wiggin M, Marziali A..
A nano-sensor for trans-membrane capture and identification of single nucleic acid molecules. Biophysical Journal, Biophysical Journal, 87: 615-621 July 2004
PubMed

Nakane J, Akeson M, and Marziali A..
Nanopore sensors for macromolecule analysis. Journal of Physics: Condensed Matter, 15: R1365R1393. 2003.
Abstract

Vercoutere WA, Winters-Hilt S, DeGuzman VS, Deamer D, Ridino S, Rodgers JT, Olsen HE, Marziali A, Akeson M..
Discrimination Among Individual Watson-Crick Base-Pairs at the Termini of Single DNA Hairpin Molecules. Nucleic Acids Research, Vol. 31, 4, 1311-1318. 2003.
PubMed

Nakane J, Akeson M, Marziali A..
Evaluation of nanopores as candidates for electronic analyte detection.. Electrophoresis, 23, 25922601. 2002.
PubMed

Blazej RG, Kumaresan P, Mathies RA..
Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing.. Proc Natl Acad Sci U S A., 2006 May 9;103(19):7240-5.
PubMed

Mastrangelo, Carlos

Chen L, Wang Y, Mastrangelo C..
Microfabrication of nanopore devices without nanolithography.. 21st IEEE International Conference on Micro Electro Mechanical Systems, Jan: 701-704. 2008.
Abstract

Mathies, Richard A.

Kumaresan P, Yang CJ, Cronier SA, Blazej RG, Mathies RA..
High-throughput single copy DNA amplification and cell analysis in engineered nanoliter droplets.. Anal. Chem., May 15;80(10):3522-9. 2008.
PubMed

Emrich CA, Medintz IL, Chu WK, Mathies RA..
Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling. Analytical Chemistry, 79, 7360-7366. 2007.
PubMed

Toriello NM, Liu CN, Blazej RG, Thaitrong N, Mathies RA..
Integrated Affinity Capture, Purification and Capillary Electrophoresis Microdevice for Quantitative Double-Stranded DNA Analysis.. Anal. Chem., 79, 8549-8556. 2007.
PubMed

Blazej RG, Kumaresan P, Cronier SA, Mathies RA..
Inline injection microdevice for attomole-scale sanger DNA sequencing.. Anal Chem., Jun 15;79(12):4499-506. 2007.
PubMed

Liu CN, Toriello NM, Mathies RA..
Multichannel PCR-CE Microdevice for Genetic Analysis.. Anal. Chem., 78, 5474-5479. 2006.
PubMed

Toriello NM, Liu CN, Mathies RA.
Multichannel Reverse Transcription-PCR Microdevice for Rapid Multiplex Gene Expression Analysis. Vol. II, November 5-9, 2006, Tokyo, Japan, eds. T. Kitamori, H. Fujita, S. Hasebe, pp. 1453-1455.

Tian H, Emrich CA, Scherer JR, Mathies RA, Andersen PS, Larsen LA, Christiansen M..
High Throughput Single-Strand Conformation Polymorphism Analysis on a Microfabricated Capillary Array Device. Electrophoresis, 26, 1834-1842. 2005.
PubMed

Kamei T, Toriello NM, Lagally ET, Blazej RG, Scherer JR, Street RA, Mathies RA.
Microfluidic Genetic Analysis with an Integrated a-Si:H Detector. Biomedical Microdevices, 7, 147-152. 2005.
PubMed

Toriello NM, Douglas ES, Mathies RA.
Microfluidic Device for Electric-Field Driven Single-Cell Capture and Activation. Analytical Chemistry, 77, 6935-6941. 2005.
PubMed

Meller, Amit

Wanunu M, Meller A..
Single Molecule Analysis of Nucleic Acids and DNA-protein Interactions using Nanopores. Eds. T. Ha and P. Selvin. Cold Spring Harbor Press (2008).
Scion Publishing

Soni GV, Meller A..
Progress toward ultrafast DNA sequencing using solid-state nanopores.. Clin Chem., 53(11):1996-2001. 2007.
PubMed

Wanunu M, Meller A..
Chemically modified solid-state nanopores. Nano Lett., 7(6):1580-5. 2007.
PubMed

Dudko O, Mathé J, Szabo A, Meller A, Hummer G..
Extracting kinetics from single-molecule force spectroscopy: Nanopore unzipping of DNA hairpins.. Biophys. J., 92, 4188-4195. 2007.
PubMed

Kim M-J, McNally B, Murata K, Meller A..
Characteristics of solid-state nanometer pores fabricated using transmission electron microscope (TEM).. Nanotechnology, 18, 205302. 2007.
Abstract

Kim M-J, Wanunu M, Bell CD, Meller A..
Rapid Fabrication of Uniform Size Nanopores and Nanopore Arrays for Parallel DNA Analysis.. Adv. Mater., 18, 3149-3153. 2006.
Abstract

Lee JW, Meller A..
Rapid DNA Sequencing by Direct Nanoscale Reading of Nucleotide Bases on Individual DNA chains.. Perspectives in Bioanalysis., K. Mitchelson (Ed.), Elsevier. 2006.
Abstract

Metzker, Michael L

Metzker ML..
Emerging technologies in DNA sequencing.. Genome Res., 15(12):1767-76. 2005.
PubMed

Lewis EK, Haaland WC, Nguyen F, Heller DA, Allen MJ, MacGregor RR, Berger CS, Willingham B, Burns LA, Scott GB, Kittrell C, Johnson BR, Curl RF, Metzker ML..
Color-blind fluorescence detection for four-color DNA sequencing.. Proc Natl Acad Sci U S A., 102(15):5346-51.2005.
PubMed

Wu W, Stupi BP, Litosh VA, Mansouri D, Farley D, Morris S, Metzker S, Metzker ML..
Termination of DNA synthesis by N6-alkylated, not 3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates.. Nucleic Acids Res., 35(19):6339-49. 2007.
PubMed

Lu G, Burgess K..
A diversity oriented synthesis of 3'-O-modified nucleoside triphosphates for DNA 'sequencing by synthesis'. Bioorg Med Chem Lett., 1;16(15):3902-5. 2006.
PubMed

Oliver, John S.

Preparata FP, Oliver JS..
DNA sequencing by hybridization using semi-degenerate bases.. J Comput Biol., 11(4):753-65. 2004.
PubMed

Quake, Stephen

Fu AY, Chou HP, Spence C, Arnold FH, Quake SR..
An integrated microfabricated cell sorter.. Anal Chem., 1;74(11):2451-7. 2002.
PubMed

Kartalov EP, Quake SR..
Microfluidic device reads up to four consecutive base pairs in DNA sequencing-by-synthesis.. Nucleic Acids Res., 32(9):2873-9. 2004.
PubMed

Kartalov EP, Unger MA, Quake SR..
Polyelectrolyte surface interface for single-molecule fluorescence studies of DNA polymerase.. Biotechniques., 34(3):505-10. 2003.
PubMed

Zhong JF, Song Y, Du J, Gamache C, Burke KA, Lund BT, Weiner LP..
Gene regulation networks related to neural differentiation of hESC.. Gene Expr., 14(1):23-34. 2007.
PubMed

Marcy Y, Ishoey T, Lasken RS, Stockwell TB, Walenz BP, Halpern AL, Beeson KY, Goldberg SM, Quake SR..
Nanoliter reactors improve multiple displacement amplification of genomes from single cells.. PLoS Genet, 3(9):1702-8. 2007.
PubMed

Marcy Y, Ouverney C, Bik EM, Lösekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA, Quake SR..
Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth.. Proc Natl Acad Sci U S A., 104(29):11889-94. 2007.
PubMed

Zhong JF, Weiner LP, Burke K, Taylor CR..
Viral RNA extraction for in-the-field analysis.. J Virol Methods., 144(1-2):98-102. 2007.
PubMed

Melin J, Quake SR..
Microfluidic large-scale integration: the evolution of design rules for biological automation.. Annu Rev Biophys Biomol Struct, 36:213-31. 2007.
PubMed

Ottsen EA, Hong JW, Quake SR, Leadbetter JR..
Microfluidic digital PCR enables multigene analysis of individual environmental bacteria.. Science, 1;314(5804):1464-7. 2006.
PubMed

Kartalov EP, Anderson WF, Scherer A..
The analytical approach to polydimethylsiloxane microfluidic technology and its biological applications.. J Nanosci Nanotechnol., 6(8):2265-77. 2006.
PubMed

Kartalov EP, Walker C, Taylor CR, Anderson WF, Scherer A..
Microfluidic vias enable nested bioarrays and autoregulatory devices in Newtonian fluids.. Proc Natl Acad Sci U S A., 15;103(33):12280-4. 2006.
PubMed

Barbic M, Scherer A..
Stray field magnetic resonance tomography using ferromagnetic spheres.. J Magn Reson, 181(2):223-8. 2006.
PubMed

Marcus JS, Anderson WF, Quake SR..
Microfluidic single-cell mRNA isolation and analysis.. Anal Chem., 1;78(9):3084-9. 2006.
PubMed

Liu J, Williams BA, Gwirtz RM, Wold BJ, Quake S..
Enhanced signals and fast nucleic acid hybridization by microfluidic chaotic mixing.. Angew Chem Int Ed Engl., 26;45(22):3618-23. 2006.
PubMed

Kartalov EP, Zhong JF, Scherer A, Quake SR, Taylor CR, Anderson WF..
High-throughput multi-antigen microfluidic fluorescence immunoassays.. Biotechniques., 40(1):85-90. 2006.
PubMed

Marcus JS, Anderson WF, Quake SR..
Parallel picoliter rt-PCR assays using microfluidics.. Anal Chem., 1;78(3):956-8. 2006.
PubMed

Hansen CL, Classen S, Berger JM, Quake SR..
A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination. J Am Chem Soc., 15;128(10):3142-3. 2006.
PubMed

Garg NK, Woodroofe CC, Lacenere CJ, Quake SR, Stoltz BM..
A ligand-free solid-supported system for Sonogashira couplings: applications in nucleoside chemistry.. Chem Commun (Camb)., 28;(36):4551-3. 2005.
PubMed

Ramsey, John M.

Zwolak M, Di Ventra M..
Physical approaches to DNA sequencing and detection.. Rev. Mod. Phys., 80, 141. 2008.
Abstract

Lagerqvist J, Zwolak M, Di Ventra M..
Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport.. Biophys. J., 93, 2384. 2007.
PubMed

Lagerqvist J, Zwolak M, Di Ventra M..
Comment on Characterization of tunneling conductance across DNA bases. Phys. Rev. E, 76, 013901. 2007.
PubMed

Last Updated: June 4, 2008

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