Works by Aach, John

Results: 30

Iterative transcription factor screening enables rapid generation of microglia-like cells from human iPSC.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-59596-3

By:

Liu, Songlei;
Li, Li;
Zhang, Fan;
Garcia-Corral, Mariana;
Meyer, Katharina;
Fortuna, Patrick R. J.;
van Sambeek, Björn;
Appleton, Evan;
Ng, Alex H. M.;
Khoshakhlagh, Parastoo;
Lu, Yuancheng Ryan;
Cameron, James;
Ramirez, Ricardo N.;
Chen, Yuting;
Wu, Chun-Ting;
Huang, Jeremy Y.;
Tan, Yuqi;
Chao, George;
Aach, John;
Lim, Elaine T.

Publication type:

Article

Long-range polony haplotyping of individual human chromosome molecules.

Published in:

Nature Genetics, 2006, v. 38, n. 3, p. 382, doi. 10.1038/ng1741

By:

Kun Zhang;
Jun Zhu;
Shendure, Jay;
Porreca, Gregory J.;
Aach, John D.;
Mitra, Robi D.;
Church, George M.

Publication type:

Article

Minimum information about a microarray experiment (MIAME)?toward standards for microarray data.

Published in:

Nature Genetics, 2001, v. 29, n. 4, p. 365, doi. 10.1038/ng1201-365

By:

Brazma, Alvis;
Hingamp, Pascal;
Quackenbush, John;
Sherlock, Gavin;
Spellman, Paul;
Stoeckert, Chris;
Aach, John;
Ansorge, Wilhelm;
Ball, Catherine A.;
Causton, Helen C.;
Gaasterland, Terry;
Glenisson, Patrick;
Holstege, Frank C.P.;
Kim, Irene F.;
Markowitz, Victor;
Matese, John C.;
Parkinson, Helen;
Robinson, Alan;
Sarkans, Ugis

Publication type:

Article

Surface attachment chemistry for in situ probe DNA amplification.

Published in:

1999

By:

Steffen, Martin;
Mitra, Rob;
Huang, Xiaohua;
Aach, John;
Church, George

Publication type:

Abstract

Aligning gene expression time series with time warping algorithms.

Published in:

Bioinformatics, 2001, v. 17, n. 6, p. 495, doi. 10.1093/bioinformatics/17.6.495

By:

Aach, John;
Church, George M.

Publication type:

Article

Improved Cell-Free RNA and Protein Synthesis System.

Published in:

PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0106232

By:

Li, Jun;
Gu, Liangcai;
Aach, John;
Church, George M.

Publication type:

Article

Proteome‐wide systems analysis of a cellulosic biofuel‐producing microbe.

Published in:

Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2010.116

By:

Tolonen, Andrew C;
Haas, Wilhelm;
Chilaka, Amanda C;
Aach, John;
Gygi, Steven P;
Church, George M

Publication type:

Article

Proteome-wide systems analysis of a cellulosic biofuel-producing microbe.

Published in:

Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/MSB.2010.116

By:

Tolonen, Andrew C;
Haas, Wilhelm;
Chilaka, Amanda C;
Aach, John;
Gygi, Steven P;
Church, George M

Publication type:

Article

Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability.

Published in:

Molecular Systems Biology, 2006, v. 2, n. 1, p. 1, doi. 10.1038/msb4100087

By:

Tolonen, Andrew C;
Aach, John;
Lindell, Debbie;
Johnson, Zackary I;
Rector, Trent;
Steen, Robert;
Church, George M;
Chisholm, Sallie W

Publication type:

Article

Highly efficient Cas9-mediated transcriptional programming.

Published in:

Nature Methods, 2015, v. 12, n. 4, p. 326, doi. 10.1038/nmeth.3312

By:

Chavez, Alejandro;
Scheiman, Jonathan;
Vora, Suhani;
Pruitt, Benjamin W;
Tuttle, Marcelle;
P R Iyer, Eswar;
Lin, Shuailiang;
Kiani, Samira;
Guzman, Christopher D;
Wiegand, Daniel J;
Ter-Ovanesyan, Dmitry;
Braff, Jonathan L;
Davidsohn, Noah;
Housden, Benjamin E;
Perrimon, Norbert;
Weiss, Ron;
Aach, John;
Collins, James J;
Church, George M

Publication type:

Article

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

Published in:

Nature Methods, 2013, v. 10, n. 5, p. 403, doi. 10.1038/nmeth.2407

By:

Mali, Prashant;
Aach, John;
Lee, Je-Hyuk;
Levner, Daniel;
Nip, Lisa;
Church, George M

Publication type:

Article

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

Published in:

Nature Methods, 2009, v. 6, n. 8, p. 613, doi. 10.1038/nmeth.1357

By:

Kun Zhang;
Li, Jin Billy;
Yuan Gao;
Egli, Dieter;
Bin Xie;
Jie Deng;
Zhe Li;
Je-Hyuk Lee;
Aach, John;
Leproust, Emily M.;
Eggan, Kevin;
Church, George M.

Publication type:

Article

Computational comparison of two draft sequences of the human genome.

Published in:

Nature, 2001, v. 409, n. 6822, p. 856, doi. 10.1038/35057055

By:

Aach, John;
Bulyk, Martha L.;
Church, George M.;
Comander, Jason;
Derti, Adnan;
Shendure, Jay

Publication type:

Article

Corrigendum: Engineering and optimising deaminase fusions for genome editing.

Published in:

Nature Communications, 2017, v. 8, n. 10, p. 16169, doi. 10.1038/ncomms16169

By:

Yang, Luhan;
Briggs, Adrian W.;
Chew, Wei Leong;
Mali, Prashant;
Guell, Marc;
Aach, John;
Goodman, Daniel Bryan;
Cox, David;
Kan, Yinan;
Lesha, Emal;
Soundararajan, Venkataramanan;
Zhang, Feng;
Church, George

Publication type:

Article

Engineering and optimising deaminase fusions for genome editing.

Published in:

Nature Communications, 2016, v. 7, n. 11, p. 13330, doi. 10.1038/ncomms13330

By:

Yang, Luhan;
Briggs, Adrian W.;
Chew, Wei Leong;
Mali, Prashant;
Guell, Marc;
Aach, John;
Goodman, Daniel Bryan;
Cox, David;
Kan, Yinan;
Lesha, Emal;
Soundararajan, Venkataramanan;
Zhang, Feng;
Church, George

Publication type:

Article

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

Published in:

Nature Communications, 2014, v. 5, n. 11, p. 5507, doi. 10.1038/ncomms6507

By:

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

Publication type:

Article

On the design of clone-based haplotyping

Published in:

Genome Biology, 2013, v. 14, n. 9, p. R100, doi. 10.1186/gb-2013-14-9-r100

By:

Lo, Christine;
Liu, Rui;
Lee, Jehyuk;
Robasky, Kimberly;
Byrne, Susan;
Lucchesi, Carolina;
Aach, John;
Church, George;
Bafna, Vineet;
Kun Zhang

Publication type:

Article

Automated modelling of signal transduction networks.

Published in:

BMC Bioinformatics, 2002, v. 3, p. 34, doi. 10.1186/1471-2105-3-34

By:

Steffen, Martin;
Petti, Allegra;
Aach, John;
D'haeseleer, Patrik;
Church, George

Publication type:

Article

A haplotype-aware de novo assembly of related individuals using pedigree sequence graph.

Published in:

Bioinformatics, 2020, v. 36, n. 8, p. 2385, doi. 10.1093/bioinformatics/btz942

By:

Garg, Shilpa;
Aach, John;
Li, Heng;
Sebenius, Isaac;
Durbin, Richard;
Church, George

Publication type:

Article

Optimizing complex phenotypes through model-guided multiplex genome engineering.

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1217-z

By:

Kuznetsov, Gleb;
Goodman, Daniel B.;
Filsinger, Gabriel T.;
Landon, Matthieu;
Rohland, Nadin;
Aach, John;
Lajoie, Marc J.;
Church, George M.

Publication type:

Article

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

Published in:

Nature Protocols, 2015, v. 10, n. 3, p. 442, doi. 10.1038/nprot.2014.191

By:

Je Hyuk Lee;
Daugharthy, Evan R.;
Scheiman, Jonathan;
Kalhor, Reza;
Ferrante, Thomas C.;
Terry, Richard;
Turczyk, Brian M.;
Yang, Joyce L.;
Ho Suk Lee;
Aach, John;
Kun Zhang;
Church, George M.

Publication type:

Article

Multiplex single-molecule interaction profiling of DNA-barcoded proteins.

Published in:

Nature, 2014, v. 515, n. 7528, p. 554, doi. 10.1038/nature13761

By:

Gu, Liangcai;
Aach, John;
Li, Chao;
Hill, David E.;
Vidal, Marc;
Church, George M.

Publication type:

Article

Addressing the ethical issues raised by synthetic human entities with embryo-like features.

Published in:

eLife, 2017, p. 1, doi. 10.7554/eLife.20674

By:

Aach, John;
Lunshof, Jeantine;
Iyer, Eswar;
Church, George M.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2015, v. 43, n. 3, p. e21, doi. 10.1093/nar/gku1246

By:

Byrne, Susan M.;
Ortiz, Luis;
Mali, Prashant;
Aach, John;
Church, George M.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2014, v. 42, n. 7, p. 4779, doi. 10.1093/nar/gkt1374

By:

Gregg, Christopher J.;
Lajoie, Marc J.;
Napolitano, Michael G.;
Mosberg, Joshua A.;
Goodman, Daniel B.;
Aach, John;
Isaacs, Farren J.;
Church, George M.

Publication type:

Article

Optimization of scarless human stem cell genome editing.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 19, p. 9049, doi. 10.1093/nar/gkt555

By:

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

Publication type:

Article

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 7, p. 4336, doi. 10.1093/nar/gkt135

By:

DiCarlo, James E.;
Norville, Julie E.;
Mali, Prashant;
Rios, Xavier;
Aach, John;
Church, George M.

Publication type:

Article

Chromosome-scale, haplotype-resolved assembly of human genomes.

Published in:

Nature Biotechnology, 2021, v. 39, n. 3, p. 309, doi. 10.1038/s41587-020-0711-0

By:

Garg, Shilpa;
Fungtammasan, Arkarachai;
Carroll, Andrew;
Chou, Mike;
Schmitt, Anthony;
Zhou, Xiang;
Mac, Stephen;
Peluso, Paul;
Hatas, Emily;
Ghurye, Jay;
Maguire, Jared;
Mahmoud, Medhat;
Cheng, Haoyu;
Heller, David;
Zook, Justin M.;
Moemke, Tobias;
Marschall, Tobias;
Sedlazeck, Fritz J.;
Aach, John;
Chin, Chen-Shan

Publication type:

Article

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

Published in:

Nature Biotechnology, 2013, v. 31, n. 9, p. 833, doi. 10.1038/nbt.2675

By:

Mali, Prashant;
Aach, John;
Stranges, P Benjamin;
Esvelt, Kevin M;
Moosburner, Mark;
Kosuri, Sriram;
Yang, Luhan;
Church, George M

Publication type:

Article

Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.

Published in:

Nature Biotechnology, 2013, v. 31, n. 8, p. 688, doi. 10.1038/nbt.2654

By:

Li, Jian-Feng;
Norville, Julie E;
Aach, John;
McCormack, Matthew;
Zhang, Dandan;
Bush, Jenifer;
Church, George M;
Sheen, Jen

Publication type:

Article