公开(公告)号：US09243290B2

公开(公告)日：2016-01-26

申请号：US13500578

申请日：2010-10-08

Applicant: Jeremy Edwards

Inventor： Jeremy Edwards

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6869 ,  C12Q2525/155 ,  C12Q2521/313 ,  C12Q2565/518 ,  C12Q2563/131 ,  C12Q2525/191

Abstract: We describe ultra-high throughput polony genome sequencing that can permit, for example, generating raw data to re-sequencing the human genome in about one week (including library prep and sequencing) at a reasonable cost. The methods described herein include one or more of the following: (1) increasing polony sequencing read length, (2) improving library construction and emulsions protocols, (3) increasing bead density and/or moving to alternative clonal amplication strategies (other than emulsion PCR or ePCR), (4) extending software capabilities to allow SNP calls from our new sequencing raw data, (5) Dual Primer Emulsion PCR, and (6) diagnostic method exploiting one or more of the foregoing.

Abstract translation: 我们描述了超高吞吐量的基因组测序，可以以合理的成本，在大约一周内（包括文库准备和测序），生成原始数据来重新测序人类基因组。 本文描述的方法包括以下一个或多个：（1）增加血清测序阅读长度，（2）改进文库构建和乳剂方案，（3）增加珠密度和/或移动到替代克隆扩增策略（乳液除外） PCR或ePCR），（4）扩展软件功能以允许来自我们的新测序原始数据的SNP呼叫，（5）双引物乳剂PCR，和（6）利用上述一种或多种的诊断方法。

公开(公告)号：US20070016383A1

公开(公告)日：2007-01-18

申请号：US11525380

申请日：2006-09-22

Applicant: Bernhard Palsson ,  Jeremy Edwards

Inventor： Bernhard Palsson ,  Jeremy Edwards

IPC: G06F19/00 ,  C12Q1/00 ,  C12N15/09

CPC classification number: G06F19/12 ,  G06F19/18

Abstract: The present invention relates to methods for achieving an optimal function of a biochemical reaction network. The methods can be performed in silico using a reconstruction of a biochemical reaction network of a cell and iterative optimization procedures. The methods can further include laboratory culturing steps to confirm and possibly expand the determinations made using the in silico methods, and to produce a cultured cell, or population of cells, with optimal functions. The current invention includes computer systems and computer products including computer-readable program code for performing the in silico steps of the invention.

Abstract translation: 本发明涉及实现生物化学反应网络的最佳功能的方法。 该方法可以使用细胞的生化反应网络的重建和迭代优化程序在计算机中进行。 所述方法还可以包括实验室培养步骤以确认并可能扩展使用计算机方法进行的测定，并产生具有最佳功能的培养细胞或细胞群。 本发明包括计算机系统和包括用于执行本发明的计算机步骤的计算机可读程序代码的计算机产品。

公开(公告)号：US20070055457A1

公开(公告)日：2007-03-08

申请号：US11584368

申请日：2006-10-19

Applicant: Bernhard Palsson ,  Jeremy Edwards

Inventor： Bernhard Palsson ,  Jeremy Edwards

IPC: G06F19/00

CPC classification number: G06F19/12 ,  G06F19/18

Abstract: The present invention relates to methods for achieving an optimal function of a biochemical reaction network. The methods can be performed in silico using a reconstruction of a biochemical reaction network of a cell and iterative optimization procedures. The methods can further include laboratory culturing steps to confirm and possibly expand the determinations made using the in silico methods, and to produce a cultured cell, or population of cells, with optimal functions. The current invention includes computer systems and computer products including computer-readable program code for performing the in silico steps of the invention.

公开(公告)号：US20120270740A1

公开(公告)日：2012-10-25

申请号：US13500578

申请日：2010-10-08

Applicant: Jeremy Edwards

Inventor： Jeremy Edwards

IPC: C40B20/00 ,  C40B50/06 ,  C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q1/6869 ,  C12Q2525/155 ,  C12Q2521/313 ,  C12Q2565/518 ,  C12Q2563/131 ,  C12Q2525/191

Abstract: We describe ultra-high throughput polony genome sequencing that can permit, for example, generating raw data to re-sequencing the human genome in about one week (including library prep and sequencing) at a reasonable cost. The methods described herein include one or more of the following: (1) increasing polony sequencing read length, (2) improving library construction and emulsions protocols, (3) increasing bead density and/or moving to alternative clonal amplication strategies (other than emulsion PCR or ePCR), (4) extending software capabilities to allow SNP calls from our new sequencing raw data, (5) Dual Primer Emulsion PCR, and (6) diagnostic method exploiting one or more of the foregoing.

Abstract translation: 我们描述了超高吞吐量的基因组测序，可以以合理的成本，在大约一周内（包括文库准备和测序），生成原始数据来重新测序人类基因组。 本文描述的方法包括以下一个或多个：（1）增加血清测序阅读长度，（2）改进文库构建和乳剂方案，（3）增加珠密度和/或移动到替代克隆扩增策略（乳液除外） PCR或ePCR），（4）扩展软件功能以允许来自我们的新测序原始数据的SNP呼叫，（5）双引物乳剂PCR，和（6）利用上述一种或多种的诊断方法。