Publications

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

Preprints

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

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

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

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

Published

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
Mol Syst Biol 15:e8875 (2019) [pdf]

Synthetic sequence entanglement augments stability and containment of genetic information in cells
Blazejewski T*, Ho HI*, Wang HH.
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
Ji BW*, Sheth RU*, Dixit PD, Huang Y, Kaufman A, Wang HH#, Dennis Vitkup#
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
Stockman VB, Ghamsari L, Lasso G, Honig B, Shapira SD, Wang HH 
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 
PLoS Comput Biol 12(4):e1004891 (2016). [pdf]

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]

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

Proton Pump Inhibitors Alter Specific Taxa in the Human Fecal Microbiome: Results of a Crossover Trial 
Freedberg DE, Toussaint NC, Chen SP, Ratner AJ, Susan Whittier S, Wang TC, Wang HH#, Abrams JA#
Gastroenterology 149:883–5 (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#
Mol Syst Biol 11:788 (2015) [pdf] Also see MSB news & views commentary [here].

Prediction of resistance development against drug combinations by collateral responses to component drugs
Munck C, Gumpert HK, Wallin AIN, Wang HH, Sommer MOA 
Science Transl Med 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 
Bonde MT, Klausen MS, Anderson MV, Wallin AIN, Wang HH#, Sommer MOA# 
Nucleic Acids Res 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 Synth Biol 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 Synth Biol 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# 
Mol Syst Biol 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]

Pre-2013

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

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

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

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

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

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

Precise manipulation of chromosomes in vivo enables genome-wide codon replacement 
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
Science 333: 348-53 (2011) [pdf]

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

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

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

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

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

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

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