Structural plasticity enables evolution and innovation of rubisco assemblies
Liu AK, Pereira JH*, Kehl AJ*, Rosenberg DJ*, Orr DJ*, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM
Science Advances, (2022), doi:

Synthetic gene circuits take root
Alamos S and PM Shih
Science, (2022), doi:

Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen
Ward LM and Shih PM
PLoS ONE, (2022), doi:

Plant-based engineering for production of high-valued natural products
Sirirungruang S, Markel K, Shih PM
Natural Product Reports, (2022), doi:

Optimization of heterologous glucoraphanin production in planta
Barnum CR*, Endelman BJ*, Ornelas IJ, Pignolet RM, Shih PM
ACS Synthetic Biology, (2022), doi:

Nitrogen metabolism in Pseudomonas putida: functional analysis using random barcode transposon sequencing
Schmidt M, Pearson AN, Incha MR, Thompson MG, Baidoo EEK, Kakumanu R, Mukhopadhyay A, Shih PM, Deutschbauer AM, Blank LM, Keasling JD
Applied and Environmental Microbiology, (2022), doi:

Heinz resistant tomato cultivars show a lignin-based resistance to Cuscuta campestris parasitism
Jhu MY, Farhi M, Wang L, Philbrook RN, Belcher MS, Nakayama H, Zumstein KS, Rowland SD, Ron M, Shih PM, Sinha NR
Plant Physiology, (2021), doi:

Overexpression of the rice BAHD acyltransferase AT10 increases xylan-bound p-coumarate and reduces lignin in Sorghum bicolor
Tian Y, Lin CY, Park JH, Wu CY, Kakumanu R, Pidatala V, Vuu KM, Rodriguez A, Shih PM, Baidoo EEK, Temple S, Simmons BA, Gladden JM, Scheller HV, Eudes A
Biotechnology for Biofuels, (2022), doi:

Utilizing Plant Synthetic Biology to Improve Human Health and Wellness
Barnum CR, Endelman BJ, Shih PM
Frontiers in Plant Sciences, (2021), doi:

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii
Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK
PLoS Genetics, (2021), doi:

From breeding to genome design: a genomic makeover for potatoes
Markel K and Shih PM
Cell, (2021), doi:

CRISPR-Act3.0 for highly efficient multiplexed gene activation in plants
Pan C, Wu X, Markel K, Malzahn AA, Kundagrami N, Sretenovic S, Zhang Y, Cheng Y, Shih PM, Qi Y
Nature Plants, (2021), doi:

Draft Genome Sequence of Mycobacterium sp. JC1 DSM3803
Thompson MG, Eiben CB, Pearson AN, Shih PM
Microbiology Resource Announcements, (2021), doi:

In-planta production of the biodegradable polyester precursor 2-pyrone-4,6-dicarboxylic acid (PDC): Stacking reduced biomass recalcitrance with value-added co-product
Lin CY, Vuu KM, Amer B, Shih PM, Baidoo EEK, Scheller HV, Eudes A
Metabolic Engineering, (2021), doi:

Granick Revisited: Synthesizing Evolutionary and Ecological Evidence for the Late Origin of Bacteriochlorophyll via Ghost Lineages and Horizontal Gene Transfer
Ward LM and Shih PM
PLoS ONE, (2021), doi:

Phanerozoic Radiation of Ammonia Oxidizing Bacteria
Ward LM, Johnston DT, Shih PM
Scientific Reports, (2021), doi:

Plant Biosystems Design Research Roadmap 1.0
Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham P, Chen JG, Weston D, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee J, Cottingham RW, Martin S, Lu M, Tschaplinski TK, Yuan G, Lu H, Ranjan P, Mitchell J, Wullschleger SD, Tuskan GA.
BioDesign Research, (2020), doi:

Biosystems Design to Accelerate C3-to-CAM Progression
Yuan G, Hassan MM, Liu D, Lim SD, Yim WC, Cushman JC, Markel K, Shih PM, Lu H, Weston DJ, Chen JG, Tschaplinski TJ, Tuskan GA, Yang X.
BioDesign Research, (2020), doi:

Novel bacterial clade reveals origin of Form I Rubisco
Banda DM, Pereira JH*, Liu AK*, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E., Adams PD, Banfield JF‡, and Shih PM‡
Nature Plants, (2020), doi:

Functional analysis of the fatty acid and alcohol metabolism of Pseudomonas putida using RB-TnSeq
Thompson MG*, Incha MR*, Pearson AN*, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, Deutschbauer AM, Shih PM‡, Keasling JD‡.
Applied and Environmental Microbiology, (2020), doi:

Investigation of Bar-seq as a method to study population dynamics of Saccharomyces cerevisiae deletion library during bioreactor cultivation.
Wehrs M*, Thompson MG*, Banerjee D*, Prahl JP, Barcelos CA, Moon J, Morella N, Costello Z, Keasling JD, Shih PM, Tanjore D, Mukhopadhyay A
Microbial Cell Factories, (2020), doi:

Engineering Plant Synthetic Pathways for the Biosynthesis of Novel Antifungals
Calgaro-Kozina A, Vuu KM, Keasling JD, Loque D, Sattely ES‡, Shih PM‡. 
ACS Central Science, (2020), doi:

Draft Genome Sequence of Agrobacterium fabrum ARqua1
Thompson MG , Cruz-Morales P, Moore WB, Pearson AN, Keasling JD, Scheller HV, Shih PM. 
Microbiology Resource Announcements​, (2020), doi:

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism
Thompson MG, Blake-Hedges JM, Pereira JH, Hangasky JA, Belcher MS, Moore WM, Barajas JF, Cruz-Morales, Washington LJ, Haushalter RW, Eiben CB, Liu Y, Skyrud W, Benites VT, Barnum TP, Baidoo E, Scheller HV, Marletta MA, Shih PM, Adams PD, Keasling JD. 
Nature Communications, (2020), doi:

Agrobacterium tumefaciens: A Bacterium Primed for Synthetic Biology
Thompson MG, Moore WM, Hummel NFC, Pearson AN, Barnum CR, Scheller HV, Shih PM
BioDesign Research, (2020), doi:

Design of orthogonal regulatory systems for modulating gene expression in plants
Belcher MS, Vuu K, Zhou A, Mansoori N, Agosto Ramos A, Thompson MG, Scheller HV, Loque D, Shih PM
Nature Chemical Biology, (2020), doi:

Cell biology of photosynthesis over geologic time​
Flamholz A and Shih PM
Current Biology, (2020), doi:​

Accumulation of high-value bioproducts in planta can improve the economics of advanced biofuels
Yang M, Baral NR, Simmons BA, Mortimer JC, Shih PM‡, Scown CD‡
Proceedings of the National Academy of Sciences, (2020), doi:

Defining and engineering bioenergy plant feedstock ideotypes
Markel K, Belcher MS, Shih PM
Current Opinion in Biotechnology, (2020), doi:

The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time​
Ward LM​‡ and Shih PM​‡
Free Radical Biology and Medicine, (2019), doi:

Robust characterization of two distinct glutarate sensing transcription factors of Pseudomonas putida L-lysine metabolism
Thompson MG, Costello Z, Hummel NFC, Cruz-Morales Pablo, Blake-Hedges JM, Krishna RN, Skyrud W, Incha MR, Shih PM, Garcia Martin H, Keasling JD 
ACS Synthetic Biology, 8:2385-2396 (2019), doi:

Early cyanobacteria and the innovation of microbial sunscreens
Shih PM
mBio, (2019), doi:

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria​
Carnevali PBM, Schulz F, Castelle CJ, Kantor RS, Shih PM, Sharon I, Santini JM, Olm MR, Amano Y, Thomas BC, Anantharaman K, Burstein D, Becraft ED, Stepanauskas R, Woyke T, Banfield JF
Nature Communications, (2019), doi:

Bacterial diversity and diversification through geological time
Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M
Nature Ecology and Evolution, (2018), doi:

Increased drought tolerance in plants engineered for low lignin and low xylan content
Yan J, Aznar A, Chalvin C, Birdseye DS, Baidoo EEK, Eudes A, Shih PM, Loqué D, Zhang A, Scheller HV
Biotechnology for Biofuels, (2018), doi:

MetaPOAP: Presence or Absence of Metabolic Pathways in Metagenome-Assembled Genomes
Ward LM, Shih PM, Fischer WW
Bioinformatics, (2018), doi:

Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology
Shih PM
Plant Science, (2018), doi:

Evolution of phototrophy in the Chloroflexi phylum driven by horizontal gene transfer
Ward LM, Hemp J, Shih PM, McGlynn SE, Fischer WW
Frontiers in Microbiology, (2018), doi:

Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass
Aznar A, Chalvin C, Shih PM, Maimann M, Ebert B, Birdseye DS, Loqué D, Scheller HV
Biotechnology for Biofuels, (2018), doi:

Precise age of Bangiomorpha pubescens dates the origin of eukaryotic photosynthesis
Gibson TM, Shih PM, Cumming VM, Fischer WW, Crockford PW, Hodgskiss MSW, Wörndle S, Creaser RA, Rainbird RH, Skulski TM, Halverson GP.
Geology, (2017), doi:

Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi
Shih PM​‡, Ward LM, Fischer WW​‡
Proceedings of the National Academy of Sciences, (2017), doi:

Plant synthetic biology – A brief history and outlook on plant engineering
Shih PM
Chemical Engineering Progress, (2017), pdf

Crown group Oxyphotobacteia postdate the rise of oxygen
Shih PM​‡, Hemp J, Ward LM, Matzke NJ, Fischer WW​‡
Geobiology, (2017), doi:

A robust gene stacking method utilizing yeast assembly for plant synthetic biology
Shih PM, Vuu K, Mansoori N, Ayad L, Louie K, Bowen BP, Northen TR, Loqué D
Nature Communications, (2016), doi:

Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops
Shih PM*, Liang Y*, Loqué D
The Plant Journal, (2016), doi:

Biochemical characterization of predicted Precambrian RuBisCO
Shih PM​‡, Occhialini A, Cameron JC, Andralojc PJ, Parry MAJ, Kerfeld CA​‡
Nature Communications, (2016), doi:

Photosynthesis and early Earth
Shih PM
Current Biology, (2015), doi:

Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts
Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb A, Ocke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JDG, Kuhn H, Robatzek S, Van Esse HP, Oldroyd G, Martin C, Field R, O’Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux P, Loque D, Granell A, Tissier A, Shih P, Brutnell TP, Quick P, Rischer H, Fraser PD, Aharoni A, Raines C, South P, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JAH, Osbourn A, Haseloff J
New Phytologist, (2015), doi:

Cyanobacterial Evolution: Fresh Insight into Ancient Questions
Shih PM
Current Biology, (2015), doi:

Introduction of a synthetic CO2-fixing photorespiratory bypass into a cyanobacterium
Shih PM, Zarzycki J, Niyogi KK​, Kerfeld CA
Journal of Biological Chemistry, (2014), doi:

Bayesian analysis of core genes in Prochlorococcus and Synechococcus and implications on horizontal gene transfer
Matzke NJ*, Shih PM*, Kerfeld CA
PLoS ONE, (2014), doi:

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins
Shih PM*​‡ and Matzke NM*​‡
Proceedings of the National Academy of Sciences, (2013), doi:

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing
Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA
Proceedings of the National Academy of Sciences 110, (2013), doi:

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust
Rajeev L*, Nunes da Rocha U*, Klitgord NJ*, Luning EG, Fortney J, Axen SP, Shih PM, Bouskill NJ, Bowen B, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A
The ISME Journal, (2013), doi:​

Excited-state properties of the 16 kDa red carotenoid protein from Arthrospira maxima
Chabera P, Burchan M, Shih PM, Kerfeld CA, Polivka T
Biochimica et Biophysica Acta, (2010), doi:

Arabidopsis thaliana PGR7 Encodes a Conserved Chloroplast Protein That Is Necessary for Efficient Photosynthetic Electron Transport
Jung HS, Okegawa Y, Shih PM, Kellogg E, Abdel-Ghany SE, Pilon M, Sjölander K, Shikanai T, Niyogi KK
PLoS ONE, (2010), doi:

Direct Identification of the Meloidogyne incognita Secretome Reveals Proteins with Host Cell Reprogramming Potential
Bellafiore S, Shen Z, Rosso M-N, Abad P, Shih P, Briggs SP
PLoS Pathogens, (2008), doi:

* Authors contributed equally
​‡ Co-corresponding authorship