Student Publications


Shubham Tripathi. Biological networks regulating cell fate choice are minimally frustrated. Physical Review Letters 2020; 125(8), 088101.

Carlos Bueno. Metallochaperones are needed for mycobacterium tuberculosis and Escherichia coli Nicotinamidase-Pyrazinamidase activity. Journal of Bacteriology 2020; 202(2): 1-16.

Carlos Bueno. Protein structure prediction in CASP13 using AWSEM-Suite. Journal of Chemical Theory and Computation 2020; 16(6): 3977-88.

Shubham Tripathi. The physics of cellular decision making during epithelial–mesenchymal transition. Annual Review of Biophysics 2020, 49, 1-18.

Carlos Bueno. AWSEM-Suite: A protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Research 2020; 48(W1): W25-30.

Shubham Tripathi. A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. PLOS Computational Biology 2020, 16(2), e1007619.

Carlos Bueno. The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks. PNAS 2020; 117(20):10825-31.

Shubham Tripathi. Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum. Frontiers in Bioengineering and Biotechnology 2020, 8, 220.

Lauren Gambill. Brave new 'RNA' world - Advances in RNA tools and their application for understanding and engineering biological systems. Current Opinion in Systems Biology 2019; 14: 32-40.

Sara Molinari and Shyam Bhatka. A synthetic system for asymmetric cell division in Escherichia coli. Nat. Chem. Biol. 2019; 15(9):917-924, doi: 10.1038/s41589-019-0339-x

Felix Eckness and Kathryn Brink. Rewiring bacterial two-component systems by modular DNA-binding domain swapping. Nat Chem Biol. 2019; 15(7):690-698.

Sapna Chhabra. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. Elife 2019;8. pii: e40526.

Josh T. Atkinson. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat. Chem. Biol. 2019; 15(2): 189-195.

Qian Mei. Bacteria-to-human protein networks reveal origins of endogenous DNA damage. Cell 2019; 176(1-2):127-143.

Carlos Bueno. Assemblies of calcium/calmodulin-dependent kinase II with actin and their dynamic regulation by calmodulin in dendritic spines. PNAS 2019; 116(38); 18937-18942.

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.

Shubham Tripathi. Mathematical Modeling of Plasticity and Heterogeneity in EMT. BioRxiv 2019.

Dongya Jia and Shubham Tripathi. Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response. J Clin Med. 2019;8(5). pii: E725.

George Britton. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm. Development. 2019, in press.

Josh T. Atkinson. Combinatorial design of chemical-dependent protein switches for controlling intracellular electron transfer. AICHE Journal 2019; in press.

Lauren Gambill and Baiyang Liu. Brave new ‘RNA’ world—advances in RNA tools and their application for understanding and engineering biological systems. Current Opinion in Systems Biology 2019; 14: 32-40.

Qian Mei. Tools To Live By: Bacterial DNA Structures Illuminate Cancer. 2019 Trends Genet. 2019;35(5):383-395.

Shyam Bhakta. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. Journal of Integrative Bioinformatics 2019; 16, doi: 10.1515/jib-2018-0101.

Qian Mei. Gamblers: An Antibiotic-Induced Evolvable Cell Subpopulation Differentiated by Reactive-Oxygen-Induced General Stress Response. Mol Cell. 2019;74(4):785-800.

Josh T Atkinson. Life simplified: recompiling a bacterial genome for synonymous codon compression. Synthetic Biology 2019; 4 (1), ysz017.

Dongya Jia. Testing the gene expression classification of the EMT spectrum. 2019 Physical Biology; 16(20): 025002.

Brianna Jayanthi. Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems. Methods in Enzymology 2019; 622, 1-27.

Josh T Atkinson. Overcoming component limitations in synthetic biology through transposon-mediated protein engineering. Methods in Enzymology 2019; 621, 191-212.

Qian Mei. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microb Cell 2019; 6(1):1-64.

Shyam Bhakta. Communicating Structure and Function in Synthetic Biology Diagrams. ACS Synth Biol 2019, doi: 10.1021/acssynbio.9b00139.

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. Interconnected feedback loops among ESRP1, HAS2, and CD44 regulate epithelial-mesenchymal plasticity in cancer. APL Bioeng. 2018;2(3):031908.

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.

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.

Prashant B. Kalvapalle. Using cellular fitness to map the structure and function of a major facilitator superfamily effluxes. Molecular Systems Biology 2017; 13(12): 964.

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), 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. 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.