Sara Molinari. Synthetic pluripotent bacterial stem cells. BioRxiv 2019
George Britton. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm. BioRxiv 2019
Sapna Chhabra. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. BioRxiv 2019
Josh T. Atkinson. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat. Chem. Biol. 2019; 15(2): 189-195
Dongya Jia and Shubham Tripathi. Testing the gene expression classification of the EMT spectrum. 2019 Physical Biology; 16(20): 025002
Qian Mei. Bacteria-to-human protein networks reveal origins of endogenous DNA damage. Cell 2019; 176(1-2):127-143
Qian Mei. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microb Cell 2019; 6(1):1-64
Qian Mei. Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells. DNA Repair 2018; 72:86-92
Jinny X. Zhang. Predicting DNA hybridization kinetics from sequence. Nature Chemistry 2018; 10:91-98
David M. Zong. Predicting transcriptional output of synthetic multi-input promoters. ACS Synth Biol. 2018; 7(8):1834-1843.
Josh T. Atkinson. Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis. Nucleic Acids Res. 2018; 46(13):e76.
Dongya Jia. RACIPE: a computational tool for modeling gene regulatory circuits using randomization. BMC Syst Biol. 2018; 12(1):74.
Timothy H. Davis. Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity. Exp Physiol. 2018; 103(4):456-460.
Ilenne Del Valle. Ratiometric gas reporting: a nondisruptive approach to monitor gene expression in soils. ACS Synth Biol. 2018; 7(3):903-911.
Dongya Jia. Elucidating the metabolic plasticity of cancer: mitochondrial reprogramming and hybrid metabolic states. Cells. 2018; 7(3). pii: E21.
Dongya Jia. Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma. Oncotarget. 2018; 9(19):15015-15026.
Shubham Tripathi. Analysis of hierarchical organization in gene expression networks reveals underlying principles of collective tumor cell dissemination and metastatic aggressiveness of inflammatory breast cancer. Front Oncol. 2018; 8: 244.
Shubham Tripathi. The standard genetic code facilitates exploration of the space of functional nucleotide sequences. J. Mol. Evol. 2018; 86(6):325–339.
Sapna Chhabra. Morphogen dynamics control patterning in a stem cell model of the human embryo. BioRxiv 2017
Carlos Bueno. Resolving the NFκB heterodimer binding paradox: strain and frustration guide the binding of dimeric transcription factors. J Am Chem Soc. 2017; 139(51): 18558–18566.
Dongya Jia. The GRHL2/ZEB feedback loop-a key axis in the regulation of EMT in breast cancer. J Cell Biochem. 2017; 118(9):2559-2570.
Timothy H. Davis. CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies. Blood. 2017; 130(3):285-296.
Dongya Jia. Phenotypic plasticity and cell fate decisions in cancer: insights from dynamical systems theory. Cancers (Basel). 2017;9(7). pii: E70.
Robert T. McLaughlin. The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks. Biol Open. 2017 Jun 15;6(6):785-799.
Dongya Jia. Operating principles of tristable circuits regulating cellular differentiation. Phys Biol. 2017; 14(3):035007.
Dongya Jia. Modeling the genetic regulation of cancer metabolism: interplay between glycolysis and oxidative phosphorylation. Cancer Res. 2017; 77(7):1564-1574.
Dongya Jia. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017; 13(3):e1005456.
Dongya Jia. Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity. Proc Natl Acad Sci USA. 2017; 114(13):E2644-E2653.
Dongya Jia. Distinguishing mechanisms underlying emt tristability. Cancer Convergence 2017; 1:2.
Timothy H. Davis. Design and validation of CRISPR/Cas9 systems for targeted gene modification in induced pluripotent stem cells. Methods Mol Biol. 2017; 1498:3-21.
Juexiao S. Wang and Helen Y. Yan. Modular probes for enriching and detecting complex nucleic acid sequences. Nature Chemistry 2017; 9:1222-1229
Josh T. Atkinson. PERMutation Using Transposase Engineering (PERMUTE): a simple approach for constructing circularly permuted protein libraries. Methods Mol Biol. 2017; 1498:295-308.
Josh T. Atkinson. Cellular assays for ferredoxins: a strategy for understanding electron flow through protein carriers that link metabolic pathways. Biochem. 2016; 55(51):7047-7064.
Qian Mei. Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase. Sci Adv. 2016; 2(11):e1601605.
Felix Ekness. An open-hardware platform for optogenetics and photobiology. Sci Rep. 2016; 6:35363.
Dongya Jia. Modeling delayed processes in biological systems. Phys Rev E. 2016; 94(3-1):032408.
Brianna E. Kuypers. Tolerance of a knotted near-infrared fluorescent protein to random circular permutation. Biochem. 2016; 55(27):3763-73.
Josh T. Atkinson. The structure of a thermophilic kinase shapes fitness upon random circular permutation. ACS Synth Biol. 2016; 5(5):415-25.
Dongya Jia. Stability of the hybrid epithelial/mesenchymal phenotype. Oncotarget. 2016 May 10;7(19):27067-84.
Dongya Jia. Tumor Budding: The Name is EMT. Partial EMT. J Clin Med. 2016; 5(5). pii: E51.
Robert T. McLaughlin. Collective dynamics of processive cytoskeletal motors. Soft Matter. 2016; 12(1):14-21.
Ilenne Del Valle. Charcoal disrupts soil microbial communication through a combination of signal sorption and hydrolysis. ACS Omega, 2016; 1(2), pp 226–233.
Juexiao S. Wang. Continuously tunable nucleic acid hybridization probes. Nat Methods. 2015; 12(12):1191-6.
Dongya Jia. Coupling the modules of EMT and stemness: A tunable 'stemness window' model. Oncotarget. 2015 Sep 22;6(28):25161-74.
Dongya Jia. Implications of the hybrid epithelial/mesenchymal phenotype in metastasis. Front Oncol. 2015; 5:155.
Juexiao S. Wang. Simulation-guided DNA probe design for consistently ultraspecific hybridization. Nat Chem. 2015 Jul;7(7):545-53.
Dongya Jia. OVOL guides the epithelial-hybrid-mesenchymal transition. Oncotarget. 2015; 6(17):15436-48.
Shubham Tripathi S. Hierarchy in gene expression is predictive of risk, progression, and outcome in adult acute myeloid leukemia. Phys Biol. 2015; 12(1):016016.
Brianna E. Kuypers. Synthetic virology: engineering viruses for gene delivery. Wiley Interdiscip Rev Nanomed Nanobiotechnol. 2014; 6(6):548-58.