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Bioinformatics 40(7):btae380 (2024) [pdf]
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Nature Microbiology 9:561-575 (2024) [pdf]
Bacterial genome engineering using CRISPR-associated transposases
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Nature Methods 20:841-848 (2023) [pdf][protocol]
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Nature Biotechnology 41:1424-1433 (2023) [pdf]
Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants
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Cell doi: 10.1016/j.cell.2022.12.018 (2022) [pdf]
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Engineering living and regenerative fungal–bacterial biocomposite structures
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Cell Reports 36(8):109590 (2021) [pdf]
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ACS Synthetic Biology 10(8):1859-1873 (2021) [pdf]
Fusobacterium nucleatum secretes amyloid-likeFadA to enhance pathogenicity
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Robust direct digital-to-biological data storage in living cells
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Nature Chemical Biology 17:246-253 (2021) [pdf]
CRISPR RNA-guided integrases for high-efficiency and multiplexed bacterial genome engineering
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Nature Biotechnology 39:480-489 (2020) [pdf]
Protecting Linear DNA Templates in Cell-Free Expression Systems from Diverse Bacteria
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ACS Synthetic Biology 9(10):2851-2855 (2020) [pdf]
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Molecular Systems Biology 16:e9427 (2020) [pdf]
The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study
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Freedberg DE, Messina M, Lynch E, Tess M, Miracle E, Chong DH, Wahab R, Abrams JA, Wang HH, Munck C.
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Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform
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Nature Communications 11:95 (2020) [pdf]
Scalable and cost-effective ribonuclease-based rRNA depletion for bacterial transcriptomics
Huang Y*, Sheth RU*, Kaufman AM, Wang HH
Nucleic Acids Research 48(4):e20 (2019) [pdf]
An engineered Cas-Transposon system for programmable and site-directed DNA transpositions
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The CRISPR Journal doi: 10.1089/crispr.2019.0030 (2019) [pdf]
Molecular function limits divergent protein evolution on planetary timescales
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Elife 8:e39705 (2019) [pdf]
Multiplex transcriptional characterizations across diverse bacterial species using cell‐free systems
Yim SS*, Johns NI*, Park J, Gomes ALC, McBee RM, Richardson M, Ronda C, Chen SP, Garenne D, Noireaux V, Wang HH
Molecular Systems Biology 15:e8875 (2019) [pdf]
Synthetic sequence entanglement augments stability and containment of genetic information in cells
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Science 365:595-598 (2019) [pdf]
Spatial metagenomic characterization of microbial biogeography in the gut
Sheth RU, Li M, Jiang W, Sims PA, Leong KW, Wang HH.
Nature Biotechnology 37:877-883 (2019) [pdf]
Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling
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Nature Methods 16:731-736 (2019) [pdf]
Metagenomic engineering of the mammalian gut microbiome in situ
Ronda C*, Chen SP*, Cabral V*, Yaung SJ, Wang HH
Nature Methods 16:167-170 (2019) [pdf]
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
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
Proc Natl Acad Sci USA 115(43):11096-11101 (2018) [pdf]
DNA-based memory devices for recording cellular events
Sheth R, Wang HH
Nature Reviews Genetics 19:718–732 (2018) [pdf]
Metagenomic mining of regulatory elements enables programmable species-selective gene expression
Johns NI*, Gomes ALC*, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH
Nature Methods 15:323-329 (2018) [pdf]
Systematic and synthetic approaches to rewire regulatory networks
Park J, Wang HH
Curr Opin Syst Biol 8:90-96 (2018) [pdf]
Multiplex recording of cellular events over time on CRISPR biological tape
Sheth RU, Yim SS, Wu FL, Wang HH
Science 358:1457-1461 (2017) [pdf]
RNA structural determinants of optimal codons revealed by MAGE-Seq
Kelsic ED*, Chung H*, Cohen N, Park J, Wang HH#, Kishony R#
Cell Systems 3(6):563-571 (2016) [pdf]
A high-throughput strategy for dissecting mammalian genetic interactions
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PLoS One 11(12):e0167617 (2016) [pdf]
The genome project-write
Boeke JD, Church GM, Hessel A, Kelly NJ, et al.
Science 353:126-127 (2016) [pdf]
The role of genome accessibility in transcription factor binding in bacteria
Gomes ALC, Wang HH
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Global rebalancing of cellular resources by pleiotropic point mutations illustrates a multi-scale mechanism of adaptive evolution
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang HH, Armenta-Medina D, Feist AM, Palsson BO
Cell Systems 2:260-271 (2016) [pdf]
Principles for designing synthetic microbial communities
Johns NI, Blazejewski T, Gomes ALC, Wang HH
Curr Opin Microbiol 31:146-153 (2016) [pdf]
Manipulating bacterial communities by in situ microbiome engineering
Sheth RU, Cabral V, Chen SP, Wang HH
Trends in Genetics 32:189-200 (2016) [pdf]
Challenges in microbial ecology: building predictive understanding of community function and dynamics
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The ISME Journal 10(11):2557-2568 (2016) [pdf]
Proton pump inhibitors alter specific taxa in the human fecal microbiome: results of a crossover trial
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Gastroenterology 149:883-885 (2015) [pdf]
An economic framework of microbial trade
Tasoff J, Mee MT, Wang HH
PLoS One 10(7):e0132907 (2015) [pdf]
Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics
Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang HH#, Gerber GK#
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Prediction of resistance development against drug combinations by collateral responses to component drugs
Munck C, Gumpert HK, Wallin AIN, Wang HH, Sommer MOA
Science Translational Medicine 262(6):262ra156 (2014) [pdf]
Transfer of noncoding DNA drives regulatory rewiring in bacteria
Orena Y, Smith MB, Johns NI, Zeevia MK, Birand D, Rond EZ, Coranderf J, Wang HH, Alm EJ, Pupko T
Proc Natl Acad Sci USA 111(45): 16112-16117 (2014) [pdf]
Syntrophic exchange in synthetic microbial communities
Mee MT, Collins JJ, Church GM#, Wang HH#
Proc Natl Acad Sci USA 111:E2149-E2156 (2014) [pdf]
MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering
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Nucleic Acids Research 42(W1):W408-W415 (2014) [pdf]
Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides
Bonde MT*, Kosuri S*, Genee HJ, Sarup-Lytzen K, Church GM#, Sommer MOA#, Wang HH#
ACS Synthetic Biology doi: 10.1021/sb5001565 (2014) [pdf]
Recent progress in engineering human-associated microbiomes
Yaung S, Church G, Wang HH
Method Mol Bio 1151:3-25 (2014) [pdf]
Yeast Oligo-mediated Genome Engineering (YOGE)
DiCarlo JE, Conley AJ, Penttilä M, Jäntti J, Wang HH#, Church GM#
ACS Synthetic Biology 342: 357-360 (2013) [pdf]
Genomically recoded organisms expand biological functions
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
Science 342: 357-360 (2013) [pdf]
Genome-scale engineering for systems and synthetic Biology
Esvelt KM#, Wang HH#
Molecular Systems Biology 9:641 (2013) [pdf]
Applications of engineered synthetic ecosystems
Wang HH, Mee MT, Church GM
Synthetic Biology: Tools and Applications, Editor: Huimin Zhao, Elsevier, (2013) [pdf]