Browsing by Author "Aach, John"

Now showing items 1-20 of 20

    • Automated Modelling of Signal Transduction Networks 

      Steffen, Martin; Petti, Allegra; Aach, John Dennis; D'haeseleer, Patrik; Church, George McDonald (BioMed Central, 2002)
      Background: Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. ...

    • Barcoding cells using cell-surface programmable DNA-binding domains 

      Mali, Prashant; Aach, John; Lee, Jehyuk; Levner, Daniel; Nip, Lisa; Church, George M. (2013)
      We develop here a novel approach to barcode large numbers of cells through cell-surface expression of programmable zinc-finger DNA-binding domains (sZFs). We show sZFs enable double-stranded DNA to sequence-specifically ...

    • CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering 

      Mali, Prashant; Aach, John; Stranges, P. Benjamin; Esvelt, Kevin M.; Moosburner, Mark; Kosuri, Sriram; Yang, Luhan; Church, George M. (2013)
      Prokaryotic type II CRISPR-Cas systems can be adapted to enable targeted genome modifications across a range of eukaryotes.1–7. Here we engineer this system to enable RNA-guided genome regulation in human cells by tethering ...

    • Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human 

      Zhang, Kun; Li, Jin Billy; Gao, Yuan; Egli, Dieter; Xie, Bin; Deng, Jie; Li, Zhe; Lee, Je-Hyuk; Aach, John Dennis; Leproust, Emily M; Eggan, Kevin Carl; Church, George McDonald (Nature Publishing Group, 2009)
      We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock captured SNPs from the transcriptome. We characterized ...

    • Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues 

      Lee, Je Hyuk; Daugharthy, Evan R; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas Charles; Terry, Richard; Turczyk, Brian M; Yang, Joyce L; Lee, Ho Suk; Aach, John Dennis; Zhang, Kun; Church, George McDonald (Springer Nature, 2015)
      RNA sequencing measures the quantitative change in gene expression over the whole transcriptome, but it lacks spatial context. On the other hand, in situ hybridization provides the location of gene expression, but only for ...

    • Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems 

      DiCarlo, James; Norville, Julie; Mali, Prashant; Rios Villanueva, Xavier; Aach, John Dennis; Church, George McDonald (Oxford University Press, 2013)
      Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems in bacteria and archaea use RNA-guided nuclease activity to provide adaptive immunity against invading foreign nucleic ...

    • Genome-wide inactivation of porcine endogenous retroviruses (PERVs) 

      Yang, Luhan; Guell, Marc; Niu, D.; George, H.; Lesha, E.; Grishin, Dennis; Aach, John Dennis; Shrock, Ellen Lee; Xu, W.; Poci, Jurgen; Cortazio, R.; Wilkinson, R. A.; Fishman, Jay Alan; Church, George McDonald (American Association for the Advancement of Science (AAAS), 2015)
      The shortage of organs for transplantation is a major barrier to the treatment of organ failure. While porcine organs are considered promising, their use has been checked by concerns about transmission of porcine endogenous ...

    • Global Gene Expression of Prochlorococcus ecotypes in Response to Changes in Nitrogen Availability 

      Tolonen, Andrew; Aach, John Dennis; Lindell, Debbie; Johnson, Zackary I; Rector, Trent; Steen, Robert G.; Chisholm, Sallie W (European Molecular Biology Organization, 2006)
      Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such as MED4 and MIT9313, ...

    • Highly Multiplexed Subcellular RNA Sequencing in Situ 

      Lee, Je Hyuk; Daugharthy, Evan; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas; Yang, Joyce; Terry, Richard; Jeanty, Sauveur; Li, Chao; Amamoto, Ryoji; Peters, Derek; Turczyk, Brian; Marblestone, Adam; Inverso, Samuel; Bernard, Amy; Mali, Prashant; Rios, Xavier; Aach, John; Church, George (American Association for the Advancement of Science, 2014-03-21)
      Understanding the spatial organization of gene expression with single nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here we describe fluorescent in situ RNA ...

    • Identification of Molecular Markers of Bipolar Cells in the Murine Retina 

      Kim, Douglas S; Ross, Sarah Elizabeth; Trimarchi, Jeffrey M; Aach, John Dennis; Greenberg, Michael Eldon; Cepko, Connie (Wiley Subscription Services, Inc., A Wiley Company, 2008)
      Retinal bipolar neurons serve as relay interneurons that connect rod and cone photoreceptor cells to amacrine and ganglion cells. They exhibit diverse morphologies essential for correct routing of photoreceptor cell signals ...

    • Improved Cell-Free RNA and Protein Synthesis System 

      Li, Jun; Gu, Liangcai; Aach, John; Church, George M. (Public Library of Science, 2014)
      Cell-free RNA and protein synthesis (CFPS) is becoming increasingly used for protein production as yields increase and costs decrease. Advances in reconstituted CFPS systems such as the Protein synthesis Using Recombinant ...

    • Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells 

      Byrne, Susan M.; Ortiz, Luis; Mali, Prashant; Aach, John; Church, George M. (Oxford University Press, 2015)
      Sequence-specific nucleases such as TALEN and the CRISPR/Cas9 system have so far been used to disrupt, correct or insert transgenes at precise locations in mammalian genomes. We demonstrate efficient ‘knock-in’ targeted ...

    • Multiplex Padlock Targeted Sequencing Reveals Human Hypermutable CpG Variations 

      Li, J. B.; Gao, Y.; Aach, John; Zhang, K.; Kryukov, G. V.; Xie, B.; Ahlford, A.; Yoon, J.-K.; Rosenbaum, A. M.; Zaranek, A. W.; LeProust, E.; Sunyaev, Shamil; Church, George (Cold Spring Harbor Laboratory, 2009-09)
      Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently ...

    • On the design of clone-based haplotyping 

      Lo, Christine; Liu, Rui; Lee, Jehyuk; Robasky, Kimberly; Byrne, Susan; Lucchesi, Carolina; Aach, John; Church, George; Bafna, Vineet; Zhang, Kun (BioMed Central, 2013)
      Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on ...

    • Optimization of scarless human stem cell genome editing 

      Yang, Luhan; Guell, Marc; Byrne, Susan; Yang, Joyce L.; De Los Angeles, Alejandro; Mali, Prashant; Aach, John; Kim-Kiselak, Caroline; Briggs, Adrian W; Rios, Xavier; Huang, Po-Yi; Daley, George; Church, George (Oxford University Press, 2013)
      Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific ...

    • Proteome-Wide Systems Analysis of a Cellulosic Biofuel-Producing Microbe 

      Tolonen, Andrew; Haas, Wilhelm; Chilaka, Amanda C; Aach, John Dennis; Gygi, Steven P.; Church, George McDonald (Nature Publishing Group, 2011)
      Fermentation of plant biomass by microbes like Clostridium phytofermentans recycles carbon globally and can make biofuels from inedible feedstocks. We analyzed C. phytofermentans fermenting cellulosic substrates by integrating ...

    • A Public Resource Facilitating Clinical Use of Genomes 

      Ball, Madeleine P.; Thakuria, Joseph V.; Zaranek, Alexander Wait; Clegg, Tom; Rosenbaum, Abraham M.; Wu, Xiaodi; Angrist, Misha; Bhak, Jong; Bobe, Jason R; Callow, Matthew J.; Cano, Carlos; Chou, Michael; Chung, Wendy K.; Douglas, Shawn M.; Estep, Preston W.; Gore, Athurva; Hulick, Peter; Labarga, Alberto; Lee, Je-Hyuk; Lunshof, Jeantine E.; Kim, Byung Chul; Kim, Jong-Il; Li, Zhe; Murray, Michael F; Nilsen, Geoffrey B.; Peters, Brock A.; Raman, Anugraha M.; Rienhoff, Hugh Y.; Robasky, Kimberly; Wheeler, Matthew T.; Vandewege, Ward; Vorhaus, Daniel B.; Yang, Joyce L.; Yang, Luhan; Aach, John; Ashley, Euan A.; Drmanac, Radoje; Kim, Seong-Jin; Li, Jin Billy; Peshkin, Leonid; Seidman, Christine; Seo, Jeong-Sun; Zhang, Kun; Rehm, Heidi; Church, George (National Academy of Sciences, 2012-07-24)
      Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of ...

    • Rational optimization of tolC as a powerful dual selectable marker for genome engineering 

      Gregg, Christopher J.; Lajoie, Marc J.; Napolitano, Michael G.; Mosberg, Joshua A.; Goodman, Daniel B.; Aach, John; Isaacs, Farren J.; Church, George M. (Oxford University Press, 2014)
      Selection has been invaluable for genetic manipulation, although counter-selection has historically exhibited limited robustness and convenience. TolC, an outer membrane pore involved in transmembrane transport in E. coli, ...

    • Systematic Management and Analysis of Yeast Gene Expression Data 

      Aach, John; Rindone, Wayne; Church, George (Cold Spring Harbor Laboratory, 2000-04)
      We report steps toward the systematic management, standardization, and analysis of functional genomics data. We developed the ExpressDB database for yeast RNA expression data and loaded it with approximately 17.5 million ...

    • Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells 

      Yang, Luhan; Grishin, Dennis; Wang, Gang; Aach, John; Zhang, Cheng-Zhong; Chari, Raj; Homsy, Jason; Cai, Xuyu; Zhao, Yue; Fan, Jian-Bing; Seidman, Christine; Seidman, Jonathan; Pu, William; Church, George (Nature Pub. Group, 2014)
      CRISPR/Cas9 has demonstrated a high-efficiency in site-specific gene targeting. However, potential off-target effects of the Cas9 nuclease represent a major safety concern for any therapeutic application. Here, we knock ...