* denote co-first authorship, # denote co-corresponding/co-senior authorship.


Chen SP, Wang HH. An Engineered Cas-Transposon System for Programmable and Precise DNA Transpositions. BioRxiv doi: 10.1101/654996 (2019).

Huang Y*, Sheth RU*, Kaufman AM, Wang HH. Scalable and cost-effective ribonuclease-based rRNA depletion for bacterial transcriptomics. BioRxiv doi: 10.1101/645895 (2019).

Munck C*, Sheth RU*, Freedberg DE, Wang HH. Real-time capture of horizontal gene transfers from gut microbiota by engineered CRISPR-Cas acquisition. BioRxiv doi: 10.1101/492751 (2018).

Yim SS*, Johns NI*, Park J, Gomes ALC, McBee RM, Richardson M, Ronda C, Chen SP, Garenne D, Noireaux V, Wang HH. Multiplex transcriptional characterizations across diverse and hybrid bacterial cell-free expression systems. BioRxiv doi: 10.1101/427559 (2018).

Konate M,  Plata G, Park J, Wang HH, Vitkup D. Molecular function limits divergent protein evolution on planetary timescales. BioRxiv doi: 10.1101/198663 (2018).


Ji BW*, Sheth RU*, Dixit PD, Huang Y, Kaufman A, Wang HH#, Dennis Vitkup#. Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling. Nature Methods doi: 10.1038/s41592-019-0467-y (2019). [pdf]

Ronda C*, Chen SP*, Cabral V*, Yaung SJ, Wang HH. Metagenomic engineering of the mammalian gut microbiome in situ. Nature Methods 16:167–170 (2019). [pdf]

Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E , Wang HH, Cho BK , Yang C , Palsson BO, Church GM, Lewis NE. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proc Natl Acad Sci USA 115(43):11096–11101 (2018). [pdf]

Sheth R, Wang HH. DNA-based memory devices for recording cellular events. Nature Reviews Genetics 19:718–732 (2018). [pdf]

Johns NI*, Gomes ALC*, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nature Methods 15:323–329 (2018). [pdf]

Park J, Wang HH. Systematic and synthetic approaches to rewire regulatory networksCurr Opin Syst Biol 8:90–96 (2018). [pdf]

Sheth RU, Yim SS, Wu FL, Wang HH. Multiplex recording of cellular events over time on CRISPR biological tape. Science 358:1457–1461 (2017). [pdf]

Kelsic ED*, Chung H*, Cohen N, Park J, Wang HH#, Kishony R#. RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Systems 3(6):563–571 (2016). [pdf]

Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH. A high-throughput strategy for dissecting mammalian genetic interactions. PLoS One 11(12):e0167617 (2016) [pdf]

Boeke JD, Church GM, Hessel A, Kelly NJ, et al. The genome project-write. Science 353:126-127 (2016).  [pdf]

Gomes ALC, Wang HH. The role of genome accessibility in transcription factor binding in bacteria. PLoS Comput Biol 12(4):e1004891 (2016). [pdf]

Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang HH, Armenta-Medina D, Feist AM, Palsson BO. Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution. Cell Systems 2:260-271 (2016). [pdf

Johns NI, Blazejewski T, Gomes ALC, Wang HH. Principles for designing synthetic microbial communities. Curr Opin Microbiol 31:146–153 (2016). [pdf]

Widder S., Allen RJ , Pfeiffer T, Curtis TP, et al. Challenges in microbial ecology: building predictive understanding of community function and dynamicsThe ISME Journal 10(11):2557-2568 (2016). [pdf]

Sheth RU, Cabral V, Chen SP, Wang HH. Manipulating bacterial communities by in situ microbiome engineering. Trends in Genetics 32:189-200 (2016). [pdf]

Freedberg DE, Toussaint NC, Chen SP, Ratner AJ, Susan Whittier S, Wang TC, Wang HH#, Abrams JA#. Proton Pump Inhibitors Alter Specific Taxa in the Human Fecal Microbiome: Results of a Crossover TrialGastroenterology 149:883–5 (2015). [pdf]

Tasoff J, Mee MT, Wang HH. An Economic Framework of Microbial Trade. PLoS One doi: 10.1371/journal.pone.0132907 (2015). [pdf]

Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang HH#, Gerber GK#. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomicsMol Syst Biol 11:788 (2015). [pdf] Also see MSB news & views commentary [here].

Munck C, Gumpert HK, Wallin AIN, Wang HH, Sommer MOA. Prediction of resistance development against drug combinations by collateral responses to component drugsScience Transl Med 262(6):262ra156 (2014). [pdf]

Orena Y, Smith MB, Johns NI, Zeevia MK, Birand D, Rond EZ, Coranderf J, Wang HH, Alm EJ, Pupko T. Transfer of noncoding DNA drives regulatory rewiring in bacteriaProc Natl Acad Sci USA doi: 10.1073/pnas.1413272111 (2014). [pdf]

Mee MT, Collins JJ, Church GM#, Wang HH#. Syntrophic Exchange in Synthetic Microbial CommunitiesProc Natl Acad Sci USA 111:E2149–E2156 (2014). [pdf]

Bonde MT, Klausen MS, Anderson MV, Wallin AIN, Wang HH#, Sommer MOA#. MODEST: A Web-based Design Tool for Oligonucleotide-mediated Genome Engineering and Recombineering. Nucleic Acids Res doi: 10.1093/nar/gku428 (2014). [pdf]

Bonde MT*, Kosuri S*, Genee HJ, Sarup-Lytzen K, Church GM#, Sommer MOA#, Wang HH#. Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides. ACS Synth Biol doi: 10.1021/sb5001565 (2014). [pdf]

Yaung S, Church G, Wang HH. Recent Progress in Engineering Human-Associated Microbiomes. Method Mol Bio 1151:3-25 (2014). [pdf]

DiCarlo JE, Conley AJ, Penttilä M, Jäntti J, Wang HH#, Church GM#. Yeast Oligo-mediated Genome Engineering (YOGE)ACS Synth Biol 342: 357-360 (2013). [pdf]

Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD, Kuznetsov G, Mercer JA,Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG, Jacobson JM, Rinehart J, Church GM, Isaacs FJ. Genomically recoded organisms expand biological functions. Science 342: 357-360 (2013). [pdf]

Esvelt KM#, Wang HH#. Genome-Scale Engineering for Systems and Synthetic Biology. Mol Syst Biol 9:641 (2013). [pdf]

Wang HH, Mee MT, Church GM. Applications of Engineered Synthetic Ecosystems in Synthetic Biology: Tools and Applications, Editor: Huimin Zhao, Elsevier, (2013). [pdf]


Mee M, Wang HH. Engineering ecosystems and synthetic ecologiesMol BioSys 8:2470-2483, (2012). [pdf]

Wang HH*, Kim HB*, Cong L, Jeong JH, Bang D, Church GM. Genome-scale Promoter Engineering by Co-Selection MAGENature Methods 9: 591-593 (2012). [pdf]

Wang HH*, Huang P*, Xu G, Marbelstone A, Li J, Forster T, Jewett MC, Church GM. Multipliexed in vivo tagging of enzyme ensembles with MAGE for in vitro single-pot multi-enzyme catalysisACS Synth Biol 1:43-52 (2012). [pdf]

Carr PA*, Wang HH*, Sterling B*, Isaacs FJ, Xu G, Kraal L, Bang D, Jacobson J, Church GM. Enhanced Multiplex Genome Engineering through Cooperative Oligonucleotide Co-selectionNucleic Acids Res doi: 10.1093/nar/gks455 (2012). [pdf]

Mosberg JA, Gregg CJ, Lajoie MJ, Wang HH, Church GM. Improving Lambda Red Genome Engineering via Rational Removal of Endogenous NucleasesPLoS ONE 7(9): e44638. doi:10.1371/journal.pone.0044638 (2012). [pdf]

Wang HH, Church GM. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineeringMethods Enzymol 498:409-26 (2011). [pdf]

Isaacs FJ*, Carr PA*, Wang HH*, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333: 348-53 (2011). [pdf]

Wang HH, Xu G, Vonner AJ, Church G. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res 39(16): 7336-47 (2011). [pdf]

Wang HH. Synthetic Genomes for Synthetic BiologyJ Mol Cell Biol 2(4): 178-179 (2010). [pdf]

Wang HH*, Isaacs FJ*, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM. Programming cells by multiplex genome engineering and accelerated evolutionNature 460:894-8 (2009). [pdf]

Wang HH, Menezes NM, Zhu MW, Ay H, Koroshetz WJ, Aronen HJ, Karonen JO, Liu Y, Nuutinen J, Wald LL, Sorensen AG. Physiological noise in MR images: an indicator of the tissue response to ischemia? J Magn Reson Imaging 27(4): 866-71 (2008). [pdf]

Wang HH, Wang XF. "Analytical methods of atherosclerosis research." in Current Development in Atherosclerosis Research, 33-66, Nova Science Publishing, NY (2006).

Wang HH, Wang XF. "Modeling atherosclerosis." in Trends in Atherosclerosis Research, 279-311, Nova Science Publishing, NY, (2004).

Wang HH. Analytical models of atherosclerosisAtherosclerosis 159: 1-7 (2001).  [pdf]