Cynipid wasps systematically reprogram host metabolism and restructure cell walls in developing galls
Markel K, Bowen BP, Tian Y, Chen YC, Sirirungruang S, Zhou A, Louie KB, Northen TR, Eudes A, Scheller HV, Shih PM.
Plant Physiology. (2024), doi: https://doi.org/10.1093/plphys/kiae001
Harnessing plant sugar metabolism for glycoengineering
Tang SN*, Barnum CR*, Szarzanowicz MJ, Sirirungruang S, Shih PM
Biology. (2023), doi: https://doi.org/10.3390/biology12121505
Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals
Brunoir T, Mulligan C Sisitiaga A, Vuu KM, Shih PM, O’Reilly SS, Summons RE, Gold DA
Nature Communications. (2023), doi: https://doi.org/10.1038/s41467-023-43545-z
Deep-branching evolutionary intermediates reveal structural origins of form I rubisco
Liu AK,* Kaeser B*, Chen LX, West-Roberts J, Taylor-Kearney LJ, Lavy A, Günzing D, Li WJ, Hammel M, Nogales E, Banfield JF, Shih PM
Current Biology. (2023), doi: https://doi.org/10.1016/j.cub.2023.10.053
Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials
Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai C-J and Urbanowicz B
Frontiers in Plant Science. (2023), doi: https://doi.org/10.3389/fpls.2023.1288826
Genome edited foods
Tuncel A, Pan C, Sprink T, Wilhelm R, Barrangou R, Li Li, Shih PM, Varshney R, Tripathi L, Van Eck J, Mandadi K, Qi Y
Nature Review Bioengineering. (2023), doi: https://doi.org/10.1038/s44222-023-00115-8
Alternative Identification of Glycosides using MS/MS Matching with an In-Silico Modified Aglycone Mass Spectra Library.
Rodríguez EP, Li Y, Vaniya A, Shih PM, Fiehn O
Analytical Chemistry. (2023), doi: https://doi.org/10.1021/acs.analchem.3c00957
Genome-wide transcription start site architecture in the three main lineages of agrobacteria
Waldburger L, Thompson MG, Weisberg A, Lee N, Chang J, Keasling JD, Shih PM
mSystems. (2023), doi: https://doi.org/10.1128/msystems.00333-23
How to engineer the unknown: Advancing a quantitative and predictive understanding of plant and soil biology to address climate change
Alamos S and Shih PM
PLOS Biology. (2023), doi: https://doi.org/10.1371/journal.pbio.3002190
The trans-regulatory landscape of gene networks in plants
Hummel NFC, Zhou A, Li B, Markel K, Ornelas IJ, Shih PM
Cell Systems, (2023), doi: https://doi.org/10.1016/j.cels.2023.05.002
The pGinger family of expression plasmids
Pearson AN, Thompson MG, Kirkpatrick LD, Ho C, Vuu KM, Waldburger LM, Keasling JD‡, Shih PM‡.
Microbiology Spectrum, (2023), doi: https://doi.org/10.1128/spectrum.00373-23
Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2 through geologic time should be re-evaluated
Wang RZ, Nichols RJ, Liu AK, Flamholz A, Artier J, Banda DM, Savage DF, EilerJ, Shih PM, Fischer WW
Proceedings of the National Academy of Sciences, (2023), doi: https://doi.org/10.1073/pnas.2300466120
A suite of constitutive promoters for tuning gene expression in plants
Zhou A, Kirkpatrick LD, Ornelas IJ, Washington LJ, Hummel NFC, Gee CW, Tang SN, Barnum CR, Scheller HV, Shih PM
ACS Synthetic Biology, (2023), doi: https://doi.org/10.1021/acssynbio.3c00075
A Bacterial Form I’ rubisco has smaller carbon isotope fractionation than its Form I counterpart
Wang RZ, Liu AK, Banda DM. Fischer WW, Shih PM
Biomolecules, (2023), doi: https://doi.org/10.3390/biom13040596
Plant glycosyltransferases for expanding bioactive glycoside diversity
Sirirungruang S, Barnum CR, Tang S, Shih PM
Natural Product Reports, (2023), doi: https://doi.org/10.1039/D2NP00077F
A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize (Zea mays)
Murphy KM, Dowd T, Khalil A, Yang B, Endelman BJ, Shih PM, Topp C, Schmelz E, Zerbe P
Plant Physiology, (2023), doi: https://doi.org/10.1093/plphys/kiad150
Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production
Valencia LE, Incha MR, Schmidt M, Pearson AN, Thompson MG, Roberts JB, Mehling M, Yin K, Sun N, Oka A, Shih PM, Blank LM, Gladden J, Keasling JD
Communications Biology, (2022), doi: https://doi.org/10.1038/s42003-022-04336-2
Expression of Dehydroshikimate Dehydratase in Sorghum Improves Biomass Yield, Accumulation of Protocatechuate, and Biorefinery Economics
Tian Y, Yang M, Lin CY, Park JH, Wu CY, Kakumanu R, De Ben C, Dalton J, Vuu KM, Shih PM, Baidoo EEK, Temple S, Putnam D, Scheller HV, Scown CD, Eudes A
ACS Sustainable Chemistry & Engineering, (2022), doi: https://doi.org/10.1021/acssuschemeng.2c01160
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: https://doi.org/10.1126/sciadv.adc9440
Synthetic gene circuits take root
Alamos S and PM Shih
Science, (2022), doi: https://doi.org/10.1126/science.add6805
Phototrophy and carbon fixation in Chlorobi postdate the rise of oxygen
Ward LM and Shih PM
PLoS ONE, (2022), doi: https://doi.org/10.1371/journal.pone.0270187
Plant-based engineering for production of high-valued natural products
Sirirungruang S, Markel K, Shih PM
Natural Product Reports, (2022), doi: https://doi.org/10.1039/D2NP00017B
Optimization of heterologous glucoraphanin production in planta
Barnum CR*, Endelman BJ*, Ornelas IJ, Pignolet RM, Shih PM
ACS Synthetic Biology, (2022), doi: https://doi.org/10.1021/acssynbio.2c00030
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: https://doi.org/10.1128/aem.02430-21
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: https://doi.org/10.1093/plphys/kiac024
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: https://doi.org/10.1186/s13068-021-02068-9
Utilizing Plant Synthetic Biology to Improve Human Health and Wellness
Barnum CR, Endelman BJ, Shih PM
Frontiers in Plant Sciences, (2021), doi: https://doi.org/10.3389%2Ffpls.2021.691462
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: https://doi.org/10.1371/journal.pgen.1009725
From breeding to genome design: a genomic makeover for potatoes
Markel K and Shih PM
Cell, (2021), doi: https://doi.org/10.1016/j.cell.2021.06.027
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: https://doi.org/10.1038/s41477-021-00953-7
Draft Genome Sequence of Mycobacterium sp. JC1 DSM3803
Thompson MG, Eiben CB, Pearson AN, Shih PM
Microbiology Resource Announcements, (2021), doi: https://doi.org/10.1128/MRA.00150-21
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: https://doi.org/10.1016/j.ymben.2021.04.011
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: https://doi.org/10.1371/journal.pone.0239248
Phanerozoic Radiation of Ammonia Oxidizing Bacteria
Ward LM, Johnston DT, Shih PM
Scientific Reports, (2021), doi: https://doi.org/10.1038/s41598-021-81718-2
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: https://doi.org/10.34133/2020/8051764
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: https://doi.org/10.34133/2020/3686791
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: https://doi.org/10.1038/s41477-020-00762-4
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: https://doi.org/10.1128/AEM.01665-20
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: https://doi.org/10.1186/s12934-020-01423-z
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: https://doi.org/10.1021/acscentsci.0c00241
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: https://doi.org/10.1128/MRA.00506-20
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: https://doi.org/10.1038/s41467-020-16815-3
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: https://doi.org/10.34133/2020/8189219
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: https://doi.org/10.1038/s41589-020-0547-4
Cell biology of photosynthesis over geologic time
Flamholz A and Shih PM
Current Biology, (2020), doi: https://doi.org/10.1016/j.cub.2020.01.076
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: https://doi.org/10.1073/pnas.2000053117
Defining and engineering bioenergy plant feedstock ideotypes
Markel K, Belcher MS, Shih PM
Current Opinion in Biotechnology, (2020), doi: https://doi.org/10.1016/j.copbio.2019.11.014
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: https://doi.org/10.1016/j.freeradbiomed.2019.01.049
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: https://doi.org/10.1021/acssynbio.9b00255
Early cyanobacteria and the innovation of microbial sunscreens
Shih PM
mBio, (2019), doi: https://doi.org/10.1128/MBIO.01262-19
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: https://doi.org/10.1038/s41467-018-08246-y
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: https://doi.org/10.1038/s41559-018-0625-0
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: https://doi.org/10.1186/s13068-018-1196-7
MetaPOAP: Presence or Absence of Metabolic Pathways in Metagenome-Assembled Genomes
Ward LM, Shih PM, Fischer WW
Bioinformatics, (2018), doi: https://doi.org/10.1093/bioinformatics/bty510
Towards a sustainable bio-based economy: Redirecting primary metabolism to new products with plant synthetic biology
Shih PM
Plant Science, (2018), doi: https://doi.org/10.1016/j.plantsci.2018.03.012
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: https://doi.org/10.3389/fmicb.2018.00260
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: https://doi.org/10.1186/s13068-017-1007-6
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: https://doi.org/10.1130/G39829.1
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: https://doi.org/10.1073/pnas.1710798114
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: https://doi.org/10.1111/gbi.12200
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: https://doi.org/10.1038/ncomms13215
Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops
Shih PM*, Liang Y*, Loqué D
The Plant Journal, (2016), doi: https://doi.org/10.1111/tpj.13176
Biochemical characterization of predicted Precambrian RuBisCO
Shih PM‡, Occhialini A, Cameron JC, Andralojc PJ, Parry MAJ, Kerfeld CA‡
Nature Communications, (2016), doi: https://doi.org/10.1038/ncomms10382
Photosynthesis and early Earth
Shih PM
Current Biology, (2015), doi: https://doi.org/10.1016/j.cub.2015.04.046
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: https://doi.org/10.1111/nph.13532
Cyanobacterial Evolution: Fresh Insight into Ancient Questions
Shih PM
Current Biology, (2015), doi: https://doi.org/10.1016/j.cub.2014.12.046
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: https://doi.org/10.1074/jbc.C113.543132
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: https://doi.org/10.1371/journal.pone.0085103
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: https://doi.org/10.1073/pnas.1305813110
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, (2013), doi: https://doi.org/10.1073/pnas.1217107110
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: https://doi.org/10.1038/ismej.2013.83
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: https://doi.org/10.1016/j.bbabio.2010.08.013
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: https://doi.org/10.1371/journal.pone.0011688
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: https://doi.org/10.1371/journal.ppat.1000192
* Authors contributed equally
‡ Co-corresponding authorship