Photo of George M. Church, PhD

George M. Church, PhD

Harvard Medical School

Harvard Medical School
Phone: (617) 432-7562
Fax: (617) 432-7266

Photo of George M. Church, PhD

Harvard Medical School
Phone: (617) 432-7562
Fax: (617) 432-7266

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George M. Church, PhD

Harvard Medical School

EDUCATIONAL TITLES

  • Robert Winthrop Professor of Genetics, Genetics, Harvard Medical School

DF/HCC PROGRAM AFFILIATION

Research Abstract

We use genomic systems biology to model

regulatory and enzymatic networks in mammalian and microbial cells. We develop technologies based on DNA-arrays, mass-spectrometry, automated microfluidics, polonies, and homologous recombination genome engineering. We have used these to discover genes affectng cell proliferation, alternative RNA splicing, and new regulatory sites involved in cell-cycle control and stress responses. We have developed integrated gene expression and functional genomics databases. For additional information see arep.med.harvard.edu.

Publications from Harvard Catalyst Profiles

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  • Garruss AS, Collins KM, Church GM. Deep representation learning improves prediction of LacI-mediated transcriptional repression. Proc Natl Acad Sci U S A 2021. PubMed
  • Norman M, Ter-Ovanesyan D, Trieu W, Lazarovits R, Kowal EJK, Lee JH, Chen-Plotkin AS, Regev A, Church GM, Walt DR. L1CAM is not associated with extracellular vesicles in human cerebrospinal fluid or plasma. Nat Methods 2021; 18:631-634. PubMed
  • Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, Pawlowski AC, Jindal K, Tam JM, Mifflin L, Alon S, Sinha A, Wassie AT, Chen F, Cheng A, Willocq V, Meyer K, Ling KH, Camplisson CK, Kohman RE, Aach J, Lee JH, Yankner BA, Boyden ES, Church GM. Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. Nucleic Acids Res 2021. PubMed
  • Bryant DH, Bashir A, Sinai S, Jain NK, Ogden PJ, Riley PF, Church GM, Colwell LJ, Kelsic ED. Deep diversification of an AAV capsid protein by machine learning. Nat Biotechnol 2021. PubMed
  • Chan YK, Wang SK, Chu CJ, Copland DA, Letizia AJ, Costa Verdera H, Chiang JJ, Sethi M, Wang MK, Neidermyer WJ, Chan Y, Lim ET, Graveline AR, Sanchez M, Boyd RF, Vihtelic TS, Inciong RGCO, Slain JM, Alphonse PJ, Xue Y, Robinson-McCarthy LR, Tam JM, Jabbar MH, Sahu B, Adeniran JF, Muhuri M, Tai PWL, Xie J, Krause TB, Vernet A, Pezone M, Xiao R, Liu T, Wang W, Kaplan HJ, Gao G, Dick AD, Mingozzi F, McCall MA, Cepko CL, Church GM. Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses. Sci Transl Med 2021. PubMed
  • Sun B, Yang X, Hou F, Yu X, Wang Q, Oh HS, Raja P, Pesola JM, Vanni EAH, McCarron S, Morris-Love J, Ng AHM, Church GM, Knipe DM, Coen DM, Pan D. Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency. Nat Microbiol 2021. PubMed
  • Filsinger GT, Wannier TM, Pedersen FB, Lutz ID, Zhang J, Stork DA, Debnath A, Gozzi K, Kuchwara H, Volf V, Wang S, Rios X, Gregg CJ, Lajoie MJ, Shipman SL, Aach J, Laub MT, Church GM. Characterizing the portability of phage-encoded homologous recombination proteins. Nat Chem Biol 2021. PubMed
  • Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F. In situ genome sequencing resolves DNA sequence and structure in intact biological samples. Science 2021. PubMed
  • Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, , Church GM, Marblestone AH, Boyden ES. Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Science 2021. PubMed
  • Palla M, Punthambaker S, Stranges B, Vigneault F, Nivala J, Wiegand D, Ayer A, Craig T, Gremyachinskiy D, Franklin H, Sun S, Pollard J, Trans A, Arnold C, Schwab C, Mcgaw C, Sarvabhowman P, Dalal D, Thai E, Amato E, Lederman I, Taing M, Kelley S, Qwan A, Fuller CW, Roever S, Church GM. Multiplex Single-Molecule Kinetics of Nanopore-Coupled Polymerases. ACS Nano 2021; 15:489-502. PubMed
  • Jung S, Appleton E, Ali M, Church GM, Del Sol A. A computer-guided design tool to increase the efficiency of cellular conversions. Nat Commun 2021; 12:1659. PubMed
  • Leeper K, Kalhor K, Vernet A, Graveline A, Church GM, Mali P, Kalhor R. Lineage barcoding in mice with homing CRISPR. Nat Protoc 2021; 16:2088-2108. PubMed
  • Xiang X, Corsi GI, Anthon C, Qu K, Pan X, Liang X, Han P, Dong Z, Liu L, Zhong J, Ma T, Wang J, Zhang X, Jiang H, Xu F, Liu X, Xu X, Wang J, Yang H, Bolund L, Church GM, Lin L, Gorodkin J, Luo Y. Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning. Nat Commun 2021; 12:3238. PubMed
  • Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, Moemke T, Marschall T, Sedlazeck FJ, Aach J, Chin CS, Church GM, Li H. Chromosome-scale, haplotype-resolved assembly of human genomes. Nat Biotechnol 2020. PubMed
  • Ng AHM, Khoshakhlagh P, Rojo Arias JE, Pasquini G, Wang K, Swiersy A, Shipman SL, Appleton E, Kiaee K, Kohman RE, Vernet A, Dysart M, Leeper K, Saylor W, Huang JY, Graveline A, Taipale J, Hill DE, Vidal M, Melero-Martin JM, Busskamp V, Church GM. A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol 2020. PubMed
  • Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, Beliveau BJ, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT. 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. Nat Methods 2020; 17:822-832. PubMed
  • Wang K, Lin RZ, Hong X, Ng AH, Lee CN, Neumeyer J, Wang G, Wang X, Ma M, Pu WT, Church GM, Melero-Martin JM. Robust differentiation of human pluripotent stem cells into endothelial cells via temporal modulation of ETV2 with modified mRNA. Sci Adv 2020; 6:eaba7606. PubMed
  • Smith CJ, Castanon O, Said K, Volf V, Khoshakhlagh P, Hornick A, Ferreira R, Wu CT, Güell M, Garg S, Ng AHM, Myllykallio H, Church GM. Enabling large-scale genome editing at repetitive elements by reducing DNA nicking. Nucleic Acids Res 2020; 48:5183-5195. PubMed
  • Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, Vera DL, Zeng Q, Yu D, Bonkowski MS, Yang JH, Zhou S, Hoffmann EM, Karg MM, Schultz MB, Kane AE, Davidsohn N, Korobkina E, Chwalek K, Rajman LA, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Levine ME, Gregory-Ksander MS, Ksander BR, He Z, Sinclair DA. Reprogramming to recover youthful epigenetic information and restore vision. Nature 2020; 588:124-129. PubMed
  • Zhang L, Tian L, Dai X, Yu H, Wang J, Lei A, Zhu M, Xu J, Zhao W, Zhu Y, Sun Z, Zhang H, Hu Y, Wang Y, Xu Y, Church GM, Huang H, Weng Q, Zhang J. Pluripotent stem cell-derived CAR-macrophage cells with antigen-dependent anti-cancer cell functions. J Hematol Oncol 2020; 13:153. PubMed
  • Lee H, Wiegand DJ, Griswold K, Punthambaker S, Chun H, Kohman RE, Church GM. Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage. Nat Commun 2020; 11:5246. PubMed
  • Garg S, Aach J, Li H, Durbin R, Church G. A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. Bioinformatics 2019. PubMed
  • Minev D, Guerra R, Kishi JY, Smith C, Krieg E, Said K, Hornick A, Sasaki HM, Filsinger G, Beliveau BJ, Yin P, Church GM, Shih WM. Rapid in vitro production of single-stranded DNA. Nucleic Acids Res 2019; 47:11956-11962. PubMed
  • Kalhor K, Church GM. Single-Cell CRISPR-Based Lineage Tracing in Mice. Biochemistry 2019; 58:4775-4776. PubMed
  • Alley EC, Khimulya G, Biswas S, AlQuraishi M, Church GM. Unified rational protein engineering with sequence-based deep representation learning. Nat Methods 2019; 16:1315-1322. PubMed
  • Zhang H, Schaefer A, Wang Y, Hodge RG, Blake DR, Diehl JN, Papageorge AG, Stachler MD, Liao J, Zhou J, Wu Z, Akarca FG, de Klerk LK, Derks S, Pierobon M, Hoadley KA, Wang TC, Church G, Wong KK, Petricoin EF, Cox AD, Lowy DR, Der CJ, Bass AJ. Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer. 2019. PubMed
  • Ostrov N, Beal J, Ellis T, Gordon DB, Karas BJ, Lee HH, Lenaghan SC, Schloss JA, Stracquadanio G, Trefzer A, Bader JS, Church GM, Coelho CM, Efcavitch JW, Güell M, Mitchell LA, Nielsen AAK, Peck B, Smith AC, Stewart CN, Tekotte H. Technological challenges and milestones for writing genomes. Science 2019; 366:310-312. PubMed
  • Grishin D, Obbad K, Church GM. Data privacy in the age of personal genomics. Nat Biotechnol 2019; 37:1115-1117. PubMed
  • Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P. Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. Nat Biotechnol 2019; 37:1080-1090. PubMed
  • Xiao Y, Muhuri M, Li S, Qin W, Xu G, Luo L, Li J, Letizia AJ, Wang SK, Chan YK, Wang C, Fuchs SP, Wang D, Su Q, Nahid MA, Church GM, Farzan M, Yang L, Wei Y, Desrosiers RC, Mueller C, Tai PW, Gao G. Circumventing cellular immunity by miR142-mediated regulation sufficiently supports rAAV-delivered OVA expression without activating humoral immunity. JCI Insight 2019. PubMed
  • Lee HH, Ostrov N, Wong BG, Gold MA, Khalil AS, Church GM. Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi. Nat Microbiol 2019. PubMed
  • Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. PubMed
  • Noble C, Min J, Olejarz J, Buchthal J, Chavez A, Smidler AL, DeBenedictis EA, Church GM, Nowak MA, Esvelt KM. Daisy-chain gene drives for the alteration of local populations. Proc Natl Acad Sci U S A 2019. PubMed
  • Wiegand DJ, Lee HH, Ostrov N, Church GM. Cell-free Protein Expression Using the Rapidly Growing Bacterium Vibrio natriegens. 2019. PubMed
  • Kaminski Strauss S, Schirman D, Jona G, Brooks AN, Kunjapur AM, Nguyen Ba AN, Flint A, Solt A, Mershin A, Dixit A, Yona AH, Csörgő B, Busby BP, Hennig BP, Pál C, Schraivogel D, Schultz D, Wernick DG, Agashe D, Levi D, Zabezhinsky D, Russ D, Sass E, Tamar E, Herz E, Levy ED, Church GM, Yelin I, Nachman I, Gerst JE, Georgeson JM, Adamala KP, Steinmetz LM, Rübsam M, Ralser M, Klutstein M, Desai MM, Walunjkar N, Yin N, Aharon Hefetz N, Jakimo N, Snitser O, Adini O, Kumar P, Soo Hoo Smith R, Zeidan R, Hazan R, Rak R, Kishony R, Johnson S, Nouriel S, Vonesch SC, Foster S, Dagan T, Wein T, Karydis T, Wannier TM, Stiles T, Olin-Sandoval V, Mueller WF, Bar-On YM, Dahan O, Pilpel Y. Evolthon: A community endeavor to evolve lab evolution. PLoS Biol. 2019; 17:e3000182. PubMed
  • Caldwell BJ, Zakharova E, Filsinger GT, Wannier TM, Hempfling JP, Chun-Der L, Pei D, Church GM, Bell CE. Crystal structure of the Redβ C-terminal domain in complex with λ Exonuclease reveals an unexpected homology with λ Orf and an interaction with Escherichia coli single stranded DNA binding protein. Nucleic Acids Res 2019; 47:1950-1963. PubMed
  • Lee HH, Kalhor R, Goela N, Bolot J, Church GM. Terminator-free template-independent enzymatic DNA synthesis for digital information storage. Nat Commun 2019; 10:2383. PubMed
  • Ogden PJ, Kelsic ED, Sinai S, Church GM. Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design. Science 2019; 366:1139-1143. PubMed
  • Zoltick ES, Linderman MD, McGinniss MA, Ramos E, Ball MP, Church GM, Leonard DGB, Pereira S, McGuire AL, Caskey CT, Sanderson SC, Schadt EE, Nielsen DE, Crawford SD, Green RC, . Predispositional genome sequencing in healthy adults: design, participant characteristics, and early outcomes of the PeopleSeq Consortium. Genome Med 2019; 11:10. PubMed
  • Zullo JM, Drake D, Aron L, O'Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA. Regulation of lifespan by neural excitation and REST. Nature 2019; 574:359-364. PubMed
  • Møller HD, Lin L, Xiang X, Petersen TS, Huang J, Yang L, Kjeldsen E, Jensen UB, Zhang X, Liu X, Xu X, Wang J, Yang H, Church GM, Bolund L, Regenberg B, Luo Y. CRISPR-C: circularization of genes and chromosome by CRISPR in human cells. Nucleic Acids Res 2018; 46:e131. PubMed
  • Wiegand DJ, Lee HH, Ostrov N, Church GM. Establishing a Cell-Free Vibrio natriegens Expression System. ACS Synth Biol 2018. PubMed
  • Juárez JF, Lecube-Azpeitia B, Brown SL, Johnston CD, Church GM. Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators. Nat Commun 2018; 9:3101. PubMed
  • Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods 2018; 15:611-616. PubMed
  • Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M. Inter-homologue repair in fertilized human eggs? Nature 2018; 560:E5-E7. PubMed
  • Clarke R, Heler R, MacDougall MS, Yeo NC, Chavez A, Regan M, Hanakahi L, Church GM, Marraffini LA, Merrill BJ. Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks. Mol Cell 2018; 71:42-55.e8. PubMed
  • Guo X, Chavez A, Tung A, Chan Y, Kaas C, Yin Y, Cecchi R, Garnier SL, Kelsic ED, Schubert M, DiCarlo JE, Collins JJ, Church GM. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nat Biotechnol 2018; 36:540-546. PubMed
  • Musah S, Dimitrakakis N, Camacho DM, Church GM, Ingber DE. Directed differentiation of human induced pluripotent stem cells into mature kidney podocytes and establishment of a Glomerulus Chip. Nat Protoc 2018; 13:1662-1685. PubMed
  • Noble C, Adlam B, Church GM, Esvelt KM, Nowak MA. Current CRISPR gene drive systems are likely to be highly invasive in wild populations. Elife 2018. PubMed
  • Lubner JM, Balsbaugh JL, Church GM, Chou MF, Schwartz D. Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach. Curr Protoc Chem Biol 2018; 10:e38. PubMed
  • Frumkin I, Lajoie MJ, Gregg CJ, Hornung G, Church GM, Pilpel Y. Codon usage of highly expressed genes affects proteome-wide translation efficiency. Proc Natl Acad Sci U S A 2018; 115:E4940-E4949. PubMed
  • Henikoff S, Church GM. Simultaneous Discovery of Cell-Free DNA and the Nucleosome Ladder. Genetics 2018; 209:27-29. PubMed
  • de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ. High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. Nucleic Acids Res 2018. PubMed
  • Bester AC, Lee JD, Chavez A, Lee YR, Nachmani D, Vora S, Victor J, Sauvageau M, Monteleone E, Rinn JL, Provero P, Church GM, Clohessy JG, Pandolfi PP. An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell 2018; 173:649-664.e20. PubMed
  • Chan Y, Chan YK, Goodman DB, Guo X, Chavez A, Lim ET, Church GM. Enabling multiplexed testing of pooled donor cells through whole-genome sequencing. Genome Med 2018; 10:31. PubMed
  • Chavez A, Pruitt BW, Tuttle M, Shapiro RS, Cecchi RJ, Winston J, Turczyk BM, Tung M, Collins JJ, Church GM. Precise Cas9 targeting enables genomic mutation prevention. Proc Natl Acad Sci U S A 2018; 115:3669-3673. PubMed
  • Wannier TM, Kunjapur AM, Rice DP, McDonald MJ, Desai MM, Church GM. Adaptive evolution of genomically recoded. Proc Natl Acad Sci U S A 2018; 115:3090-3095. PubMed
  • Nivala J, Shipman SL, Church GM. Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. Nat Microbiol 2018; 3:310-318. PubMed
  • Kunjapur AM, Stork DA, Kuru E, Vargas-Rodriguez O, Landon M, Söll D, Church GM. Engineering posttranslational proofreading to discriminate nonstandard amino acids. Proc Natl Acad Sci U S A 2018. PubMed
  • Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM. Developmental barcoding of whole mouse via homing CRISPR. Science 2018. PubMed
  • Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM. The Future of Multiplexed Eukaryotic Genome Engineering. ACS Chem Biol 2017. PubMed
  • Chen X, Sun YC, Church GM, Lee JH, Zador AM. Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res 2017. PubMed
  • Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature 2017; 550:345-353. PubMed
  • Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P. Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. Nano Lett 2017. PubMed
  • Lubock NB, Zhang D, Sidore AM, Church GM, Kosuri S. A systematic comparison of error correction enzymes by next-generation sequencing. Nucleic Acids Res 2017; 45:9206-9217. PubMed
  • Chari R, Church GM. Beyond editing to writing large genomes. Nat Rev Genet 2017. PubMed
  • Shipman SL, Nivala J, Macklis JD, Church GM. CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 2017; 547:345-349. PubMed
  • Giwa S, Lewis JK, Alvarez L, Langer R, Roth AE, Church GM, Markmann JF, Sachs DH, Chandraker A, Wertheim JA, Rothblatt M, Boyden ES, Eidbo E, Lee WPA, Pomahac B, Brandacher G, Weinstock DM, Elliott G, Nelson D, Acker JP, Uygun K, Schmalz B, Weegman BP, Tocchio A, Fahy GM, Storey KB, Rubinsky B, Bischof J, Elliott JAW, Woodruff TK, Morris GJ, Demirci U, Brockbank KGM, Woods EJ, Ben RN, Baust JG, Gao D, Fuller B, Rabin Y, Kravitz DC, Taylor MJ, Toner M. The promise of organ and tissue preservation to transform medicine. Nat Biotechnol 2017; 35:530-542. PubMed
  • Goodman DB, Kuznetsov G, Lajoie MJ, Ahern BW, Napolitano MG, Chen KY, Chen C, Church GM. Millstone: software for multiplex microbial genome analysis and engineering. Genome Biol 2017; 18:101. PubMed
  • Kuznetsov G, Goodman DB, Filsinger GT, Landon M, Rohland N, Aach J, Lajoie MJ, Church GM. Optimizing complex phenotypes through model-guided multiplex genome engineering. Genome Biol 2017; 18:100. PubMed
  • Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP. Nucleotide-time alignment for molecular recorders. PLoS Comput. Biol. 2017; 13:e1005483. PubMed
  • Noble C, Olejarz J, Esvelt KM, Church GM, Nowak MA. Evolutionary dynamics of CRISPR gene drives. Sci Adv 2017; 3:e1601964. PubMed
  • Li J, Haas W, Jackson K, Kuru E, Jewett MC, Fan ZH, Gygi S, Church GM. Cogenerating Synthetic Parts toward a Self-Replicating System. ACS Synth Biol 2017. PubMed
  • Aach J, Lunshof J, Iyer E, Church GM. Addressing the ethical issues raised by synthetic human entities with embryo-like features. Elife 2017. PubMed
  • Chari R, Yeo NC, Chavez A, Church GM. sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity. ACS Synth Biol 2017. PubMed
  • Lubner JM, Dodge-Kafka KL, Carlson CR, Church GM, Chou MF, Schwartz D. Cushing's syndrome mutant PKA(L)(205R) exhibits altered substrate specificity. FEBS Lett 2017. PubMed
  • Ter-Ovanesyan D, Kowal EJK, Regev A, Church GM, Cocucci E. Imaging of Isolated Extracellular Vesicles Using Fluorescence Microscopy. Methods Mol Biol 2017; 1660:233-241. PubMed
  • Kowal EJK, Ter-Ovanesyan D, Regev A, Church GM. Extracellular Vesicle Isolation and Analysis by Western Blotting. Methods Mol Biol 2017; 1660:143-152. PubMed
  • Li J, Zhang C, Huang P, Kuru E, Forster-Benson ETC, Li T, Church GM. Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system. Translation (Austin) 2017; 5:e1327006. PubMed
  • Wang G, Yang L, Grishin D, Rios X, Ye LY, Hu Y, Li K, Zhang D, Church GM, Pu WT. Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies. Nat Protoc 2017; 12:88-103. PubMed
  • Kalhor R, Mali P, Church GM. Rapidly evolving homing CRISPR barcodes. Nat Methods 2016. PubMed
  • Cho YS, Kim H, Kim HM, Jho S, Jun J, Lee YJ, Chae KS, Kim CG, Kim S, Eriksson A, Edwards JS, Lee S, Kim BC, Manica A, Oh TK, Church GM, Bhak J. An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes. Nat Commun 2016; 7:13637. PubMed
  • Mao Q, Ciotlos S, Zhang RY, Ball MP, Chin R, Carnevali P, Barua N, Nguyen S, Agarwal MR, Clegg T, Connelly A, Vandewege W, Zaranek AW, Estep PW, Church GM, Drmanac R, Peters BA. The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes. Gigascience 2016; 5:42. PubMed
  • Chew WL, Tabebordbar M, Cheng JK, Mali P, Wu EY, Ng AH, Zhu K, Wagers AJ, Church GM. A multifunctional AAV-CRISPR-Cas9 and its host response. Nat Methods 2016; 13:868-74. PubMed
  • Vasiliou SK, Diamandis EP, Church GM, Greely HT, Baylis F, Thompson C, Schmitt-Ulms G. CRISPR-Cas9 System: Opportunities and Concerns. Clin Chem 2016; 62:1304-11. PubMed
  • Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L, Mosberg JA, Kuznetsov G, Goodman DB, Vargas-Rodriguez O, Isaacs FJ, Söll D, Church GM. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli. Proc Natl Acad Sci U S A 2016; 113:E5588-97. PubMed
  • Ostrov N, Landon M, Guell M, Kuznetsov G, Teramoto J, Cervantes N, Zhou M, Singh K, Napolitano MG, Moosburner M, Shrock E, Pruitt BW, Conway N, Goodman DB, Gardner CL, Tyree G, Gonzales A, Wanner BL, Norville JE, Lajoie MJ, Church GM. Design, synthesis, and testing toward a 57-codon genome. Science 2016; 353:819-22. PubMed
  • Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES. Nanoscale imaging of RNA with expansion microscopy. Nat Methods 2016. PubMed
  • Chavez A, Tuttle M, Pruitt BW, Ewen-Campen B, Chari R, Ter-Ovanesyan D, Haque SJ, Cecchi RJ, Kowal EJ, Buchthal J, Housden BE, Perrimon N, Collins JJ, Church G. Comparison of Cas9 activators in multiple species. Nat Methods 2016; 13:563-7. PubMed
  • Shipman SL, Nivala J, Macklis JD, Church GM. Molecular recordings by directed CRISPR spacer acquisition. Science 2016. PubMed
  • Biteen JS, Blainey PC, Cardon ZG, Chun M, Church GM, Dorrestein PC, Fraser SE, Gilbert JA, Jansson JK, Knight R, Miller JF, Ozcan A, Prather KA, Quake SR, Ruby EG, Silver PA, Taha S, van den Engh G, Weiss PS, Wong GC, Wright AT, Young TD. Tools for the Microbiome: Nano and Beyond. ACS Nano 2016; 10:6-37. PubMed
  • Rogers JK, Church GM. Multiplexed Engineering in Biology. Trends Biotechnol 2016. PubMed
  • Braff JL, Yaung SJ, Esvelt KM, Church GM. Characterizing Cas9 Protospacer-Adjacent Motifs with High-Throughput Sequencing of Library Depletion Experiments. Cold Spring Harb Protoc 2016; 2016:pdb.prot090183. PubMed
  • Braff JL, Yaung SJ, Esvelt KM, Church GM. Characterization of Cas9-Guide RNA Orthologs. Cold Spring Harb Protoc 2016; 2016:pdb.top086793. PubMed
  • Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehár J, Sommer MO. Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis. PLoS ONE 2016; 11:e0147651. PubMed
  • DiCarlo JE, Chavez A, Dietz SL, Esvelt KM, Church GM. Safeguarding CRISPR-Cas9 gene drives in yeast. Nat Biotechnol 2015; 33:1250-1255. PubMed
  • Ho JM, Reynolds NM, Rivera K, Connolly M, Guo LT, Ling J, Pappin DJ, Church GM, Söll D. Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli. ACS Synth Biol 2015. PubMed
  • Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods 2015. PubMed
  • Akbari OS, Bellen HJ, Bier E, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, James AA, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O'Connor-Giles KM, Parks AL, Perrimon N, Port F, Russell S, Ueda R, Wildonger J. BIOSAFETY. Safeguarding gene drive experiments in the laboratory. Science 2015; 349:927-9. PubMed
  • Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M, P R Iyer E, Lin S, Kiani S, Guzman CD, Wiegand DJ, Ter-Ovanesyan D, Braff JL, Davidsohn N, Housden BE, Perrimon N, Weiss R, Aach J, Collins JJ, Church GM. Highly efficient Cas9-mediated transcriptional programming. Nat Methods 2015; 12:326-8. PubMed
  • Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc 2015; 10:442-58. PubMed
  • Byrne SM, Ortiz L, Mali P, Aach J, Church GM. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells. Nucleic Acids Res 2015; 43:e21. PubMed
  • Bonde MT, Kosuri S, Genee HJ, Sarup-Lytzen K, Church GM, Sommer MO, Wang HH. Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides. ACS Synth Biol 2015. PubMed
  • Drmanac R, Peters BA, Church GM, Reid CA, Xu X. Accurate whole genome sequencing as the ultimate genetic test. Clin Chem 2015; 61:305-6. PubMed
  • Keane M, Craig T, Alföldi J, Berlin AM, Johnson J, Seluanov A, Gorbunova V, Di Palma F, Lindblad-Toh K, Church GM, de Magalhães JP. The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations. Bioinformatics 2014. PubMed
  • Gu L, Li C, Aach J, Hill DE, Vidal M, Church GM. Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature 2014. PubMed
  • Güell M, Yang L, Church GM. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics 2014; 30:2968-70. PubMed
  • Esvelt KM, Smidler AL, Catteruccia F, Church GM. Concerning RNA-guided gene drives for the alteration of wild populations. Elife 2014. PubMed
  • Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM. High-resolution antibody dynamics of vaccine-induced immune responses. Proc Natl Acad Sci U S A 2014; 111:4928-33. PubMed
  • Church GM, Elowitz MB, Smolke CD, Voigt CA, Weiss R. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 2014; 15:289-94. PubMed
  • Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science 2014; 343:1360-3. PubMed
  • Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH. Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences. J Immunol 2014; 192:867-74. PubMed
  • Umbarger MA, Kennedy CJ, Saunders P, Breton B, Chennagiri N, Emhoff J, Greger V, Hallam S, Maganzini D, Micale C, Nizzari MM, Towne CF, Church GM, Porreca GJ. Next-generation carrier screening. Genet Med 2014; 16:132-40. PubMed
  • Yaung SJ, Esvelt KM, Church GM. CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4. PLoS ONE 2014; 9:e98811. PubMed
  • Ball MP, Bobe JR, Chou MF, Clegg T, Estep PW, Lunshof JE, Vandewege W, Zaranek A, Church GM. Harvard Personal Genome Project: lessons from participatory public research. Genome Med 2014; 6:10. PubMed
  • Robasky K, Lewis NE, Church GM. The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet 2014; 15:56-62. PubMed
  • Li J, Gu L, Aach J, Church GM. Improved cell-free RNA and protein synthesis system. PLoS ONE 2014; 9:e106232. PubMed
  • Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM. Rapid neurogenesis through transcriptional activation in human stem cells. Mol Syst Biol 2014; 10:760. PubMed
  • Hoehe MR, Church GM, Lehrach H, Kroslak T, Palczewski S, Nowick K, Schulz S, Suk EK, Huebsch T. Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat Commun 2014; 5:5569. PubMed
  • Yang L, Yang JL, Byrne S, Pan J, Church GM. CRISPR/Cas9-Directed Genome Editing of Cultured Cells. Curr Protoc Mol Biol 2014; 107:31.1.1-31.1.17. PubMed
  • O'Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D. pLogo: a probabilistic approach to visualizing sequence motifs. Nat Methods 2013; 10:1211-2. PubMed
  • Tzur YB, Friedland AE, Nadarajan S, Church GM, Calarco JA, Colaiácovo MP. Heritable custom genomic modifications in Caenorhabditis elegans via a CRISPR-Cas9 system. Genetics 2013; 195:1181-5. PubMed
  • Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 2013; 10:1116-21. PubMed
  • Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 2013; 31:833-8. PubMed
  • Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F. Optical control of mammalian endogenous transcription and epigenetic states. Nature 2013; 500:472-6. PubMed
  • Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM, Calarco JA. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods 2013; 10:741-3. PubMed
  • Eminaga S, Christodoulou DC, Vigneault F, Church GM, Seidman JG. Quantification of microRNA expression with next-generation sequencing. Curr Protoc Mol Biol 2013; Chapter 4:Unit 4.17. PubMed
  • Larman HB, Laserson U, Querol L, Verhaeghen K, Solimini NL, Xu GJ, Klarenbeek PL, Church GM, Hafler DA, Plenge RM, Nigrovic PA, De Jager PL, Weets I, Martens GA, O'Connor KC, Elledge SJ. PhIP-Seq characterization of autoantibodies from patients with multiple sclerosis, type 1 diabetes and rheumatoid arthritis. J Autoimmun 2013. PubMed
  • Mali P, Aach J, Lee JH, Levner D, Nip L, Church GM. Barcoding cells using cell-surface programmable DNA-binding domains. Nat Methods 2013. PubMed
  • DiCarlo JE, Norville JE, Mali P, Rios X, Aach J, Church GM. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 2013; 41:4336-43. PubMed
  • Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science 2013; 339:823-6. PubMed
  • Eroshenko N, Church GM. Mutants of Cre recombinase with improved accuracy. Nat Commun 2013; 4:2509. PubMed
  • Plank M, Hu G, Silva AS, Wood SH, Hesketh EE, Janssens G, Macedo A, de Magalhães JP, Church GM. An analysis and validation pipeline for large-scale RNAi-based screens. Sci Rep 2013; 3:1076. PubMed
  • Rockwell G, Guido NJ, Church GM. Redirector: designing cell factories by reconstructing the metabolic objective. PLoS Comput. Biol. 2013; 9:e1002882. PubMed
  • Church GM, Gao Y, Kosuri S. Next-generation digital information storage in DNA. Science 2012; 337:1628. PubMed
  • Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res 2012; 40:e132. PubMed
  • Alon S, Mor E, Vigneault F, Church GM, Locatelli F, Galeano F, Gallo A, Shomron N, Eisenberg E. Systematic identification of edited microRNAs in the human brain. Genome Res 2012; 22:1533-40. PubMed
  • Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A 2012; 109:11920-7. PubMed
  • Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 2012; 487:190-5. PubMed
  • Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nat Methods 2012; 9:591-3. PubMed
  • Wang HH, Huang PY, Xu G, Haas W, Marblestone A, Li J, Gygi SP, Forster AC, Jewett MC, Church GM. Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synth Biol 2012; 1:43-52. PubMed
  • Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF. How accurate can genetic predictions be? BMC Genomics 2012; 13:340. PubMed
  • Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM. Improving lambda red genome engineering in Escherichia coli via rational removal of endogenous nucleases. PLoS ONE 2012; 7:e44638. PubMed
  • Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 2011; 29:149-53. PubMed
  • Matzas M, Stähler PF, Kefer N, Siebelt N, Boisguérin V, Leonard JT, Keller A, Stähler CF, Häberle P, Gharizadeh B, Babrzadeh F, Church GM. High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat Biotechnol 2010; 28:1291-4. PubMed
  • Kosuri S, Eroshenko N, Leproust EM, Super M, Way J, Li JB, Church GM. Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat Biotechnol 2010; 28:1295-9. PubMed
  • Mosberg JA, Lajoie MJ, Church GM. Lambda Red Recombination in Escherichia coli Occurs Through a Fully Single-Stranded Intermediate. Genetics 2010; 186:791-9. PubMed
  • Loh YH, Hartung O, Li H, Guo C, Sahalie JM, Manos PD, Urbach A, Heffner GC, Grskovic M, Vigneault F, Lensch MW, Park IH, Agarwal S, Church GM, Collins JJ, Irion S, Daley GQ. Reprogramming of T cells from human peripheral blood. Cell Stem Cell 2010; 7:15-9. PubMed
  • Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D, Neff NF, Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB. Clinical assessment incorporating a personal genome. Lancet 2010; 375:1525-35. PubMed
  • Schwartz D, Church GM. Collection and motif-based prediction of phosphorylation sites in human viruses. Sci Signal 2010; 3:rs2. PubMed
  • Lunshof JE, Bobe J, Aach J, Angrist M, Thakuria JV, Vorhaus DB, Hoehe MR, Church GM. Personal genomes in progress: from the human genome project to the personal genome project. Dialogues Clin Neurosci 2010; 12:47-60. PubMed
  • Zaranek AW, Levanon EY, Zecharia T, Clegg T, Church GM. A survey of genomic traces reveals a common sequencing error, RNA editing, and DNA editing. PLoS Genet. 2010; 6:e1000954. PubMed
  • Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross JA, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I. Generation of functional human hepatic endoderm from human induced pluripotent stem cells. Hepatology 2010; 51:329-35. PubMed
  • Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 2010; 327:78-81. PubMed
  • Carr PA, Church GM. Genome engineering. Nat Biotechnol 2009; 27:1151-62. PubMed
  • Fuller CW, Middendorf LR, Benner SA, Church GM, Harris T, Huang X, Jovanovich SB, Nelson JR, Schloss JA, Schwartz DC, Vezenov DV. The challenges of sequencing by synthesis. Nat Biotechnol 2009; 27:1013-23. PubMed
  • Barak M, Levanon EY, Eisenberg E, Paz N, Rechavi G, Church GM, Mehr R. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Res 2009; 37:6905-15. PubMed
  • Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 2009; 5:e1000718. PubMed
  • Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res 2009; 19:1606-15. PubMed
  • Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 2009; 325:1128-31. PubMed
  • Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS. A highly annotated whole-genome sequence of a Korean individual. Nature 2009; 460:1011-5. PubMed
  • Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009; 460:894-8. PubMed
  • Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res 2009; 37:5001-6. PubMed
  • Zhang K, Li JB, Gao Y, Egli D, Xie B, Deng J, Li Z, Lee JH, Aach J, Leproust EM, Eggan K, Church GM. Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods 2009; 6:613-8. PubMed
  • Khoury MJ, McBride CM, Schully SD, Ioannidis JP, Feero WG, Janssens AC, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, Duross A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SL, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts JS, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J, . The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop. Genet Med 2009; 11:559-67. PubMed
  • Li JB,Levanon EY,Yoon JK,Aach J,Xie B,Leproust E,Zhang K,Gao Y,Church GM. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 2009; 324:1210-3. PubMed
  • de Magalhaes JP,Curado J,Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 2009; 25:875-81. PubMed
  • Ball MP,Li JB,Gao Y,Lee JH,LeProust EM,Park IH,Xie B,Daley GQ,Church GM. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 2009; 27:361-8. PubMed
  • Schwartz D,Chou MF,Church GM. Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics 2009; 8:365-79. PubMed
  • de Magalhaes JP,Budovsky A,Lehmann G,Costa J,Li Y,Fraifeld V,Church GM. The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell 2009; 8:65-72. PubMed
  • Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM. Large-scale identification of genetic design strategies using local search. Mol Syst Biol 2009; 5:296. PubMed
  • Vigneault F,Sismour AM,Church GM. Efficient microRNA capture and bar-coding via enzymatic oligonucleotide adenylation. Nat Methods 2008; 5:777-9. PubMed
  • Dantas G, Sommer MO, Oluwasegun RD, Church GM. Bacteria subsisting on antibiotics. Science 2008; 320:100-3. PubMed
  • Snitkin ES,Dudley AM,Janse DM,Wong K,Church GM,Segre D. Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biol 2008; 9:R140. PubMed
  • Lunshof JE,Chadwick R,Church GM. Hippocrates revisited? Old ideals and new realities. Genomic Med 2008; 2:1-3. PubMed
  • Bang D, Church GM. Gene synthesis by circular assembly amplification. Nat Methods 2008; 5:37-9. PubMed
  • Kettler GC, Martiny AC, Huang K, Zucker J, Coleman ML, Rodrigue S, Chen F, Lapidus A, Ferriera S, Johnson J, Steglich C, Church GM, Richardson P, Chisholm SW. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet 2007; 3:e231. 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 2007; 4:931-6. 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 2007; 103:1228-36. PubMed
  • Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 2007; 449:83-6. PubMed
  • Bakal C, Aach J, Church G, Perrimon N. Quantitative morphological signatures define local signaling networks regulating cell morphology. Science 2007; 316:1753-6. PubMed
  • Wright MA, Kharchenko P, Church GM, Segre D. Chromosomal periodicity of evolutionarily conserved gene pairs. Proc Natl Acad Sci U S A 2007; 104:10559-64. 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 2007; 316:1481-4. PubMed
  • Bugl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, Endy D. DNA synthesis and biological security. Nat Biotechnol 2007; 25:627-9. PubMed
  • de Magalhaes JP, Sedivy JM, Finch CE, Austad SN, Church GM. A proposal to sequence genomes of unique interest for research on aging. J Gerontol A Biol Sci Med Sci 2007; 62:583-4. PubMed
  • de Magalhães JP, Costa J, Church GM. An analysis of the relationship between metabolism, developmental schedules, and longevity using phylogenetic independent contrasts. J Gerontol A Biol Sci Med Sci 2007; 62:149-60. PubMed
  • Forster AC, Church GM. Synthetic biology projects in vitro. Genome Res 2007; 17:1-6. PubMed
  • Reppas NB, Wade JT, Church GM, Struhl K. The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 2006; 24:747-57. PubMed
  • Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell 2006; 24:593-602. PubMed
  • Derti A, Roth FP, Church GM, Wu CT. Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat Genet 2006; 38:1216-20. PubMed
  • Jaffe JD, Mani DR, Leptos KC, Church GM, Gillette MA, Carr SA. PEPPeR: A platform for experimental proteomic pattern recognition. Mol Cell Proteomics 2006; 5:1927-41. 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 2006; 103:14062-7. PubMed
  • Kuo WP, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple ME, Maysuria M, Serikawa K, Lee SY, McCrann D, Kang J, Shearstone JR, Burke J, Park DJ, Wang X, Rector TL, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim JH, Short GF 3rd, Freeman MW, Seed B, Jensen R, Church GM, Hovig E, Cepko CL, Park P, Ohno-Machado L, Jenssen TK. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat Biotechnol 2006; 24:832-840. 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 2006; 24:680-6. PubMed
  • Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM. MapQuant: open-source software for large-scale protein quantification. Proteomics 2006; 6:1770-82. 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 2006; 38:382-7. PubMed
  • Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, Busser BW, Halfon MS, Church GM, Michelson AM. An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet 2006; 2:e16. PubMed
  • Tolonen AC, Aach J, Lindell D, Johnson ZI, Rector T, Steen R, Church GM, Chisholm SW. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol Syst Biol 2006; 2:53. PubMed
  • Forster AC, Church GM. Towards synthesis of a minimal cell. Mol Syst Biol 2006; 2:45. PubMed
  • Church GM. Genomes for all. Sci Am 2006; 294:46-54. PubMed
  • Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 2006; 7:177. PubMed
  • Church GM. From systems biology to synthetic biology. Mol Syst Biol 2005; 1:2005.0032. PubMed
  • Church GM. The personal genome project. Mol Syst Biol 2005; 1:2005.0030. PubMed
  • Dudley AM, Janse DM, Tanay A, Shamir R, Church GM. A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol 2005; 1:2005.0001. PubMed
  • Kharchenko P, Church GM, Vitkup D. Expression dynamics of a cellular metabolic network. Mol Syst Biol 2005; 1:2005.0016. PubMed
  • Weber G, Shendure J, Tanenbaum DM, Church GM, Meyerson M. Identification of foreign gene sequences by transcript filtering against the human genome. Nat Genet 2002; 30:141-2. PubMed
  • de Magalhães JP, Church GM. Analyses of human-chimpanzee orthologous gene pairs to explore evolutionary hypotheses of aging. Mech Ageing Dev ; 128:355-64. PubMed
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DF/HCC members that share similar concepts* with George M. Church, PhD but have yet to coauthor a publication with this researcher.

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