2024
An explainable deep learning
platform for molecular discovery. Nature Protocols: published online (2024).
Accurate RNA 3D structure prediction using
a language model-based deep learning
approach. Nature Methods: published online (2024).
Catalase activity deficiency sensitizes
multidrug-resistant Mycobacterium
tuberculosis to the ATP synthase inhibitor
bedaquiline. Nature Communications 15 : 9792 (2024).
Deep generative design of RNA aptamers
using structural predictions. Nature Computational Science 4 : 829–839 (2024).
Customizable gene sensing and response
without altering endogenous coding
sequences. Nature Chemical Biology: published online (2024).
Rapid discovery and evolution of nanosensors containing fluorogenic amino acids. Nature Communications 15 : 7531 (2024).
A high-throughput synthetic biology approach
for studying combinatorial chromatin-based
transcriptional regulation. Molecular Cell 84 : 2382–2396 (2024).
Discovery of antibiotics that selectively
kill metabolically dormant bacteria. Cell Chemical Biology 31 : 712-728 (2024).
Rapid, multiplexed, and enzyme-free nucleic acid detection using programmable aptamer-based RNA switches. Chem 10 : 2220-2244 (2024).
Machine learning for antimicrobial
peptide identification and design. Nature Reviews Bioengineering 2 : 392-407 (2024).
Discovery of a structural class of antibiotics
with explainable deep learning. Nature 626 : 177-185 (2024).
2023
Synthetic genetic circuits to uncover the OCT4
trajectories of successful reprogramming of human
fibroblasts. Science Advances 9 : eadg8495 (2023).
Engineering microbial division of labor for plastic upcycling. Nature Communications 14 : 5712 (2023).
Leveraging artificial intelligence in the fight
against infectious diseases. Science 381 : 164-170 (2023).
BioAutoMATED: An end-to-end automated
machine learning tool for explanation
and design of biological sequences. Cell Systems 14 : 525–542 (2023).
Controlled continuous evolution of enzymatic activity screened at ultrahigh throughput using drop-based microfluidics. Angewandte Chemie 62 : e202303112 (2023).
Gaming bacterial metabolism. Nature Microbiology 8 : 1004-1005 (2023).
Deep learning-guided discovery of
an antibiotic targeting Acinetobacter baumannii. Nature Chemical Biology 19 : 1342-1350 (2023).
Detection of viral RNAs at ambient
temperature via reporter proteins
produced through the target-splinted
ligation of DNA probes. Nature Biomedical Engineering 7 : 1571-1582 (2023).
Discovering small-molecule senolytics with
deep neural networks. Nature Aging 3 : 734-750 (2023).
A self-propagating, barcoded transposon system for
the dynamic rewiring of genomic networks. Molecular Systems Biology 19 : e11398 (2023).
Harnessing synthetic biology to enhance
ocean health. Trends in Biotechnology 41 : 860-874 (2023).
Autocatalytic base editing for RNA-responsive translational control. Nature Communications 14 : 1339 (2023).
Lateral flow test engineering and
lessons learned from COVID-19. Nature Reviews Bioengineering 1 : 13-31 (2023).
2022
The sound of silence: Transgene silencing
in mammalian cell engineering. Cell Systems 13 : 950-973 (2022).
Multiplexed rapid antigen tests developed using multicolored nanoparticles and cross-reactive antibody pairs: Implications for pandemic preparedness. Nano Today 47 : e101669 (2022).
Enhancing nutritional niche and host defenses by
modifying the gut microbiome. Molecular Systems Biology 18 : e9933 (2022).
End-to-end design of wearable sensors. Nature Reviews Materials 7 : 887–907 (2022).
Nanozyme-catalysed CRISPR assay for
preamplification-free detection of non-coding RNAs. Nature Nanotechnology 17 : 1120–1126 (2022).
Reactive metabolic byproducts contribute to
antibiotic lethality under anaerobic conditions. Molecular Cell 82 : 3499-3512 (2022).
Benchmarking AlphaFold-enabled molecular docking predictions for antibiotic discovery. Molecular Systems Biology 18 : e11081 (2022).
Primary screen dataset available here here.
A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma. Nature Biomedical Engineering 6 : 968–978 (2022).
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Research 50 : 7326–7349 (2022).
An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis. Nature Biomedical Engineering 6 : 910-921 (2022).
Modulating the evolutionary trajectory of tolerance using antibiotics with different metabolic dependencies. Nature Communications 13 : 2525 (2022).
CellComm infers cellular crosstalk that drives haematopoietic stem and progenitor cell development. Nature Cell Biology 24 : 579-589 (2022).
RNA-responsive elements for eukaryotic translational control. Nature Biotechnology 40 : 539-545 (2022).
Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples. Nature Biomedical Engineering 6 : 246-256 (2022).
Increased energy demand from anabolic-catabolic processes drives beta-lactam antibiotic lethality. Cell Chemical Biology 29 : 276-286 (2022).
2021
Engineering living therapeutics with synthetic biology. Nature Reviews Drug Discovery 20 : 941-960 (2021).
Deep learning identifies synergistic drug combinations for treating COVID-19. Proceedings of the National Academy of Sciences USA 118 : e2105070118 (2021).
Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Science Advances 7 : eabh2944 (2021).
CRISPR-based diagnostics. Nature Biomedical Engineering 5 : 643-656 (2021).
Wearable materials with embedded synthetic
biology sensors for biomolecule detection. Nature Biotechnology 39: 1366–1374 (2021).
Designing biological circuits: synthetic biology within the operon model and beyond. Annual Review of Biochemistry 90 : 221-244 (2021).
Cytoplasmic condensation induced by membrane damage is associated with antibiotic lethality. Nature Communications 12 : 2321 (2021).
Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 184 : 881-898 (2021).
Clinically relevant mutations in core metabolic genes confer antibiotic resistance. Science 371 : eaba0862 (2021).
Using deep learning for dermatologist-level detection of suspicious pigmented skin lesions from wide-field images. Science Translational Medicine 13 : eabb3652 (2021).
Engineering advanced logic and distributed computing in human CAR immune cells. Nature Communications 12 : 792 (2021).
Anomalous COVID-19 tests hinder researchers. Science 371 : 244-245 (2021).
Deep-learning resources for studying glycan-mediated host-microbe interactions. Cell Host & Microbe 29 : 132-144 (2021).
2020
Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria. Proceedings of the National Academy of Sciences USA 117 : 25722-25731 (2020).
Cell-free biosensors for rapid detection of water
contaminants. Nature Biotechnology 38 : 1451–1459 (2020).
Evidence that coronavirus superspreading is fat-tailed. Proceedings of the National Academy of Sciences USA 117 : 29416-29418 (2020).
A deep learning approach to programmable RNA switches. Nature Communications 11 : 5057 (2020).
Sequence-to-function deep learning frameworks for engineered riboregulators. Nature Communications 11 : 5058 (2020).
Eradicating bacterial persisters with combinations of strongly and weakly metabolism-dependent antibiotics. Cell Chemical Biology 27 : 1544-1552 (2020).
Creating CRISPR-responsive smart materials for diagnostics and programmable cargo release. Nature Protocols 15 : 3030-3063 (2020).
Continuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway. Nature Communications 11 : 4202 (2020).
Predictive biology: modelling, understanding and harnessing microbial complexity. Nature Reviews Microbiology 18 : 507-520 (2020).
A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection. Nature Biomedical Engineering 4 : 601-609 (2020).
Point-of-care devices to detect Zika and other emerging viruses. Annual Reviews in Biomedical Engineering 22 : 371-386 (2020).
Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing. Science Advances 6 : eaba1190 (2020).
Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility. Genome Research 30 : 1027-1039 (2020).
A deep learning approach to antibiotic discovery. Cell 180 : 688-702 (2020). Primary screen dataset available here.
2019
A systems biology pipeline identifies regulatory
networks for stem cell engineering. Nature Biotechnology 37 : 810-818 (2019).
De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nature Chemical Biology 15 : 1173-1182 (2019).
Engineering microbial peer pressure. Science 365 : 986-987 (2019).
Programmable CRISPR-responsive smart materials. Science 365 : 780-785 (2019).
Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science 364 : 593-597 (2019).
Bacterial metabolic state more accurately predicts antibiotic lethality than growth rate. Nature Microbiology 4 : 2109-2117 (2019).
Bacterial metabolism and antibiotic efficacy. Cell Metabolism 30 : 251-259 (2019).
Definitions and guidelines for research on antibiotic persistence. Nature Reviews Microbiology 17 : 441-448 (2019).
Complex host-microbe-antibiotic interactions. Cell Host & Microbe 26 : 8 (2019).
A white-box machine learning approach for revealing antibiotic mechanisms of action. Cell 177 : 1649-1661 (2019).
Altered metabolic states. Cell Metabolism 29 : 509 (2019).
A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria. Nature Methods 16 : 303-306 (2019).
2018
Designing microbial consortia with defined social interactions. Nature Chemical Biology 14 : 821-829 (2018).
An enhanced CRISPR repressor for targeted mammalian gene regulation. Nature Methods 15 : 611-616 (2018).
A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers. Nature Communications 9 : 3347 (2018).
BioBits Explorer: A modular synthetic biology education kit. Science Advances 4 : eaat5105 (2018).
BioBits Bright: A fluorescent synthetic biology education kit. Science Advances 4 : eaat5107 (2018).
Next-generation machine learning for biological networks. Cell 173 : 1581-1592 (2018).
Probiotic strains detect and suppress cholera in mice. Science Translational Medicine 10 : eaao2586 (2018).
High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nature Biotechnology 36 : 540-549 (2018).
Universal chimeric antigen receptors for multiplexed and logical control of T cell responses. Cell 173 : 1426-1438 (2018).
Understanding biological regulation through synthetic biology. Annual Review of Biophysics 47 : 399-423 (2018).
Next-generation biocontainment systems for engineered organisms. Nature Chemical Biology 14 : 530-537 (2018).
CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nature Reviews Microbiology 16 : 333-339 (2018).
Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science 360 : 439-444 (2018).
Precise Cas9 targeting enables genomic mutation prevention. Proceedings of the National Academy of Sciences USA 115 : 3669-3673 (2018).
A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology 2 : 73-82 (2018).
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. BMC Biology 16 : 62 (2018).
Targeting antibiotic tolerance, pathogen by pathogen. Cell 172 : 1228-1238 (2018).
Reconstruction of complex single-cell trajectories using CellRouter. Nature Communications 9 : 892 (2018).
2017
Using engineered bacteria to characterize infection dynamics and antibiotic effects in vivo. Cell Host & Microbe 22 : 263-268 (2017).
Complex cellular logic computation using ribocomputing devices. Nature 548 : 117-121 (2017).
Biophysical constraints arising from compositional context in synthetic gene networks. Cell Systems 5 : 11-24, e1-e12 (2017).
Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356 : 438-442 (2017).
A blueprint for a synthetic genetic feedback controller to reprogram cell fate. Cell Systems 4 : 109-120 (2017).
Understanding and sensitizing density-dependent persistence to quinolone antibiotics. Molecular Cell 68 : 1019-1021 (2017).
Antibiotic-induced changes to the host metabolic environment inhibit drug efficacy and alter immune function. Cell Host & Microbe 22 : 757-765 (2017).
Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling. Cell Reports 21 : 2965-2977 (2017).
Antibiotic efficacy - context matters. Current Opinion in Microbiology 39 : 73-80 (2017).
ZSCAN10 expression corrects the genomic instability of iPSCs from aged donors. Nature Cell Biology 19 : 1037-1048 (2017).
Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality. Proceedings of the National Academy of Sciences USA 114 : 9164-9169 (2017).
Carbon sources tune antibiotic susceptibility in Pseudomonas aeruginosa via tricarboxylic acid cycle control. Cell Chemical Biology 24 : 195-206 (2017).
Engineering models to scale. Cell 165 : 516-517 (2017).
2016
Portable, on-demand biomolecular manufacturing. Cell 167 : 248-259 (2016).
Creating single-copy genetic circuits. Molecular Cell 63 : 329-336 (2016).
Comparison of Cas9 activators in multiple species. Nature Methods 13 : 563-567 (2016).
Synthetic biology platform technologies for antimicrobial applications. Advanced Drug Delivery Reviews 105 : 35-43 (2016).
Targeted erythropoietin selectively stimulates blood cell expansion in vivo. Proceedings of the National Academy of Sciences USA 113 : 5245-5250 (2016).
Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell 165 : 1255-1266 (2016).
'Deadman' and 'Passcode' microbial kill switches for bacterial containment. Nature Chemical Biology 12 : 82-86 (2016).
Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip. Proceedings of the National Academy of Sciences USA 113 : 7-15 (2016).
Multiple mechanisms disrupt the let-7 microRNA family in neuroblastoma. Nature 535 : 246-251 (2016).
LIN28 regulates stem cell metabolism and conversion to primed pluripotency. Cell Stem Cell 19 : 66-80 (2016).
RNAi reveals phase-specific global regulators of human somatic cell reprogramming. Cell Reports 15 : 2597-2607 (2016).
Chemogenomics and orthology-based design of antibiotic combination therapies. Molecular Systems Biology 12 : 1-12 (2016).
A role for the bacterial GATC methylome in antibiotic stress survival. Nature Genetics 48 : 581-586 (2016).
2015
Synthetic biology devices for in vitro and in vivo diagnostics. Proceedings of the National Academy of Sciences USA 112 : 14429-14435 (2015).
DNA sense-and-respond protein modules for mammalian cells. Nature Methods 12 : 1085-1090 (2015).
Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods 12 : 1051-1054 (2015).
Engineered phagemids for nonlytic, targeted antibacterial therapies. Nano Letters 15 : 4808-4813 (2015).
Highly efficient Cas9-mediated transcriptional programming. Nature Methods 12 : 326-328 (2015).
Chromatin regulation at the frontier of synthetic biology. Nature Reviews Genetics 16 : 159-171 (2015).
Bactericidal antibiotics induce toxic metabolic perturbations that lead to cellular damage. Cell Reports 13 : 968-980 (2015).
Systematic identification of factors for provirus silencing in embryonic stem cells. Cell 163 : 230-245 (2015).
Antibiotic efficacy is linked to bacterial cellular respiration. Proceedings of the National Academy of Sciences USA 112 : 8173-8180 (2015).
Boosting bacterial metabolism to combat antibiotic resistance. Cell Metabolism 21 : 154-155 (2015).
Unraveling the physiological complexities of antibiotic lethality. Annual Review of Pharmacology and Toxicology 55 : 313-312 (2015).
2014
Tunable protein degradation in bacteria. Nature Biotechnology 32 : 1276-1281 (2014).
Paper-based synthetic gene networks. Cell 159 : 940-954 (2014).
Toehold switches: de-novo-designed regulators of gene expression. Cell 159 : 925-939 (2014).
Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158 : 110-120 (2014).
Bone marrow-on-a-chip replicates hematopoietic niche physiology in vitro. Nature Methods 11 : 663-669 (2014).
Syntrophic exchange in synthetic microbial communities. Proceedings of the National Academy of Sciences USA 111 : E2149-E2156 (2014).
Synthetic biology: How best to build a cell. Nature 509 : 155-157 (2014).
A brief history of synthetic biology. Nature Reviews Microbiology 12 : 381-390 (2014).
Programmable bacteria detect and record an environmental signal in the mammalian gut. Proceedings of the National Academy of Sciences USA 111 : 4838-4843 (2014).
Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 157 : 151-161 (2014).
Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516 : 56-61 (2014).
A community effort to assess and improve drug sensitivity prediction algorithms. Nature Biotechnology 32 : 1202-1212 (2014).
Defining cellular identity through network biology. Cell Cycle 13 : 3313-3314 (2014).
Editorial overview: Antimicrobials: Grappling with the complexities of antibiotics and resistance. Current Opinion in Microbiology 21 : v-vi (2014).
Antibiotics and the gut microbiota. Journal of Clinical Investigation 124 : 4212-4218 (2014).
A Parkinson's disease gene regulatory network identifies the signaling protein RGS2 as a modulator of LRRK2 activity and neuronal toxicity. Human Molecular Genetics 23 : 4887-4905 (2014).
Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes. PLOS Computational Biology 10 : e1003734 (2014).
CellNet: network biology applied to stem cell engineering. Cell 158 : 903-915 (2014).
Dissecting engineered cell types and enhancing cell fate conversion via CellNet. Cell 158 : 889-902 (2014).
Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 15 : 92-101 (2014).
Antibiotics induce redox-related physiological alterations as part of their lethality. Proceedings of the National Academy of Sciences USA 111 : E2100-E2109 (2014).
The distribution of genomic variations in human iPSCs is related to replication-timing reorganization during reprogramming. Cell Reports 7 : 70-78 (2014).
Central role for RNase YbeY in Hfq-dependent and Hfq-independent small-RNA regulation in bacteria. BMC Genomics 15 : 121 (2014).
Zfp322a regulates mouse ES cell pluripotency and enhances reprogramming efficiency. PLOS Genetics 10 : e1004038 (2014).
Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice. Science Translational Medicine 6 : 217ra2 (2014).
2013
Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell 13 : 459-470 (2013).
Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports 1 : 266-280 (2013).
Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance.Proceedings of the National Academy of Sciences USA 110 : 14420-14425 (2013).
Differential splicing across immune system lineages. Proceedings of the National Academy of Sciences USA 110 : 14324-14329 (2013).
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499 : 219-222 (2013).
Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in mammalian cells. Science Translational Medicine 5 : 192ra85 (2013).
Silver enhances antibiotic activity against Gram-negative bacteria. Science Translational Medicine 5 : 190ra81 (2013).
Introduction to Focus Issue: Quantitative approaches to genetic networks. Chaos 23 : 25001 (2013).
Microbial persistence and the road to drug resistance. Cell Host & Microbe 13 : 632-642 (2013).
Fungicidal drugs induce a common oxidative-damage cellular death pathway. Cell Reports 3 : 350-358 (2013).
Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nature Biotechnology 31 : 160-165 (2013).
2012
Insulating gene circuits from context by RNA processing. Nature Biotechnology 30 : 1061-1062 (2012).
Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nature Methods 9 : 1077-1080 (2012).
A synthetic biology framework for programming eukaryotic transcription functions. Cell 150 : 647-658 (2012).
Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences USA 109 : 5850-5855 (2012).
Synthetic biology: bits and pieces come to life. Nature 483 : S8-S10 (2012).109 : 5850-5855 (2012).
The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell 11 : 701-714 (2012).
A multiply redundant genetic switch "locks in" the transcriptional signature of regulatory T cells. Nature Immunology 13 : 972-980 (2012).
Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma. Nature Medicine 18 : 1503-1510 (2012).
microRNA regulatory network inference identifies miR-34a as a novel regulator of TFG-ß signaling in glioblastoma. Cancer Discovery 2 : 736-749 (2012).
Wisdom of crowds for robust gene network inference. Nature Methods 9 : 796-804 (2012).
Making a noisy gene: HDACs turn up the static. Molecular Cell 47 : 151-153 (2012).
Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Molecular Cell 46 : 561-572 (2012).
Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science 336 : 315-319 (2012).
Signaling-mediated bacterial persister formation. Nature Chemical Biology 8 : 431-433 (2012).
Cellular signal processing: out of one, many. Molecular Cell 45 : 143-144 (2012).
Microbial environments confound antibiotic efficacy. Nature Chemical Biology 8 : 6-9 (2012).
2011
Synthetic biology moving into the clinic. Science 333 : 1248-1252 (2011).
Tunable signal processing in synthetic MAP kinase cascades. Cell 144 : 119-131 (2011).
Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nature Biotechnology 29 : 1117-1119 (2011).
Antioxidant strategies to tolerate antibiotics. Science 334 : 915-916 (2011).
Heterogeneous bacterial persisters and engineering approaches to eliminate them. Current Opinion in Microbiology 14 : 593-598 (2011).
Genomic approaches to deconstruct pluripotency. Annual Review of Genomics and Human Genetics 12 : 165-185 (2011).
Functional characterization of bacterial sRNAs using a network biology approach. Proceedings of the National Academy of Sciences USA 108 : 15522-15527 (2011).
Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature 473 : 216-220 (2011).
Cellular decision making and biological noise: from microbes to mammals. Cell 144 : 910-925 (2011).
Bacteria as control engineers. Molecular Cell 41 : 4-5 (2011).
2010
Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7 : 618-630 (2010).
Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences USA 107 : 15898-15903 (2010).
Synthetic biology: applications come of age. Nature Reviews Genetics 11 : 367-379 (2010).
Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Research 38 :2712-2726 (2010).
Bacterial charity work leads to population-wide resistance. Nature 467 : 82-86 (2010).
Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli . Proceedings of the National Academy of Sciences USA 107 : 15517-15522 (2010).
Reprogramming of T cells from human peripheral blood. Cell Stem Cell 7 : 15-19 (2010).
How antibiotics kill bacteria: from targets to networks. Nature Reviews Microbiology 8 : 423-435 (2010).
Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Molecular Cell 37 : 311-320 (2010).
2009
Next-generation synthetic gene networks. Nature Biotechnology 27 :1139-1150 (2009).
Synthetic gene networks that count. Science 324 : 1199-1202 (2009).
Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nature Biotechnology 27 : 465-471 (2009).
Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proceedings of the National Academy of Sciences USA 106 : 4629-4634 (2009).
Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli . Molecular Cell 36 : 845-860 (2009).
Role of reactive oxygen species in antibiotic action and resistance. Current Opinion in Microbiology 12 ; 482-489 (2009).
Systems biology makes it personal. Molecular Cell 34 : 137-138 (2009).
Systems biology strikes gold. Cell 137 : 24-26 (2009).
MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proceedings of the National Academy of Sciences USA 106 : 2319-2324 (2009).
A network biology approach to aging in yeast. Proceedings of the National Academy of Sciences USA 106 : 1145-1150 (2009).
2008
Rewiring bacteria, two components at a time. Cell 133 : 947-948 (2008).
Networking opportunities for bacteria. Cell 135 : 1153-1156 (2008).
Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 135 : 679-690 (2008).
The Immunological Genome Project: networks of gene expression in immune cells. Nature Immunology 9 : 1091-1094 (2008).
Gene regulation: hacking the network on a sugar high. Molecular Cell 30 : 1-2 (2008).
2007
A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophysical Journal 93 : L55-L57 (2007).
A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130 : 363-372 (2007).
Combinatorial promoter design for engineering noisy gene expression. Proceedings of the National Academy of Sciences USA 104 : 12726-12731 (2007).
Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences USA 104 : 11197-11202 (2007).
Taking the inventory inside single cells. Nature Chemical Biology 3: 141-142 (2007).
A common mechanism of cellular death induced by bactericidal antibiotics. Cell 130 : 797-810 (2007).
Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli . Molecular Systems Biology 3 : 91 (2007).
A network biology approach to prostate cancer. Molecular Systems Biology 3: 82 (2007).
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLOS Biology 5 (1) : e8 (2007).
Size matters: network inference tackles the genome scale. Molecular Systems Biology 3: 77 (2007).
2006
Phenotypic consequences of promoter-mediated transcriptional noise. Molecular Cell 24 : 853-865 (2006).
Engineering life: building a FAB for biology. Scientific American 294: 44-51 (2006).
RNA synthetic biology. Nature Biotechnology 24: 545-554 (2006).
A bottom-up approach to gene regulation. Nature 439: 856-860 (2006).
2005
And the noise played on: stochastic gene expression and HIV-1 infection. Cell 122 : 147-155 (2005).
Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6: 451-464 (2005).
Signal processing in single cells. Science 307: 1886-1888 (2005).
Plug-and-play with RNA. Nature Biotechnology 23 : 306-307 (2005).
Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology 23: 377-383 (2005).
2004
Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology 22 : 841-847 (2004).
Programmable cells: Interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences USA 101 : 8414-8419 (2004).
Evolving complex dynamics in electronic models of genetic networks. Chaos 14: 707-715 (2004).
Inferring microbial genetic networks. ASM News 70: 121-126 (2004).
