Student Publications

The following is a list of publications our graduate students have co-authored while in the SSPB program.
Note: references are annotated to only highlight SSPB student authors.

2023
  • Prashant Kalvapalle. Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections. Water Res. 2023, 231: 119648. [link]
2022
  • Zhuo Chen. Bacillus subtilis Histidine Kinase KinC Activates Biofilm Formation by Controlling Heterogeneity of Single-Cell Responses. Microb. Gen. 2022, (13)1: e01694-21. [link]
  • Jeannette Ingabire. Evaluation of Aerosol Particle Leak and Standard Surgical Mask Fit With 3 Elastomeric Harness Designs. JAMA Netw. Open. 2022;5(1):e214581. [link]
  • Jihwan Lee. Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell. 2022, 185(18): 3408-3425.e29. [link]
  • Jihwan Lee. A blueprint for glow tag engineering. Nat. Rev. Chem. 2022, 6, 7-8. [link]
  • Baiyang Liu. RNA Compensation: A Positive Feedback Insulation Strategy for RNA-Based Transcription Networks. ACS Synth. Biol. 2022, 11, 3, 1240–1250. [link]
  • Shubham Tripathi. A mechanistic modeling framework reveals the key principles underlying tumor metabolism. PLOS Comput. Biol. 2022, 18(2): e1009841. [link]
  • Shubham Tripathi. DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases. Nucleic Acids Res. 2022, 50(3): 1269-1279. [link]
2021
  • Dreycey Albin and Qi Wang. SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome Res. 2021, 31(4): 635–644. [link]
  • Kathryn Brink. Insights into the impact of inflammatory acidification on the mucosa. FASEB J. 2021, 35(S1). [link]
  • Kathryn Brink. Mucosal acidosis elicits a unique molecular signature in epithelia and intestinal tissue mediated by GPR31-induced CREB phosphorylation. PNAS 2021, 118(20): e2023871118. [link]
  • George Britton and Sapna Chhabra. Fate-Patterning of 2D Gastruloids and Ectodermal Colonies Using Micropatterned Human Pluripotent Stem Cells. Methods Mol. Biol. 2021, 2258: 119-130. [link]
  • Carlos Bueno. OpenAWSEM with Open3SPN2: A fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations. PLOS Comput. Biol. 2021, 17(2): e1008308. [link]
  • Carlos Bueno and Kiara Reyes-Gamas. Frustration and Direct-Coupling Analyses to Predict Formation and Function of Adeno-Associated Virus. Biophys. J. 2021, 120(3): 489-503. [link]
  • Yujie Chen. Genomic trajectory in leukemogenesis of myeloproliferative neoplasms: a case report. BMC Med. Genomics. 2021, 14: 137. [link]
  • Ilenne Del Valle, Emily M. Fulk, and Prashant Kalvapalle. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front. Microbiol. 2021, 11:618373. [link]
  • Esteban Dodero-Rojas. The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Res. 2021, 49(D1): D172–D182. [link]
  • Esteban Dodero-Rojas. Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain. PNAS 2021, 118(30): e2105739118. [link]
  • Nicolas E. Grandel and Kiara Reyes Gamas. Control of synthetic microbial consortia in time, space, and composition. Trends Microbiol. 2021. [link]
  • Rosa S. Guerra-Resendez. Reversing Post-Infectious Epigenetic-Mediated Immune Suppression. Front. Immunol. 2021, 12: 2093. [link]
  • Brianna Jayanthi. A platform for post-translational spatiotemporal control of cellular proteins. Synth. Biol. 2021, 6(1): ysab002. [link]
  • Dongya Jia and Shubham Tripathi. Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer. Br. J. Cancer. 2021, 124: 1902-1911. [link]
  • Prashant Kalvapalle and Kiara Reyes Gamas. Evaluating recovery, cost, and throughput of different concentration methods for SARS-CoV-2 wastewater-based epidemiology. Water Res. 2021, 197, 117043. [link]
  • Biki Bapi Kundu. Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Nat. Commun. 2021,12: 4158. [link]
  • Jihwan Lee. A synthetic circuit for buffering gene dosage variation between individual mammalian cells. Nat. Commun. 2021, 12, 4132. [link]
  • Jiaming Li and Jinny X. Zhang. Highly multiplexed rapid DNA detection with single-nucleotide specificity via convective PCR in a portable device. Nat. Biomed. Eng. 2021, 5: 702-712. [link]
  • Kareem Mehrabiani. Expanding Direct Coupling Analysis to Identify Heterodimeric Interfaces from Limited Protein Sequence Data. J. Phys. Chem. B 2021, 125(41): 11408-11417. [link]
  • Yidan Pan. The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells. Nat. Commun. 2021, 12: 472. [link]
  • Robert F. Tesoriero Jr. Engineering High-Yield Biopolymer Secretion Creates an Extracellular Protein Matrix for Living Materials. mSystems 2021, 6(2): e00902-20. [link]
  • Robert F. Tesoriero Jr. Bottom Up Approaches to Living Materials: Challenges and Future Directions. Matter, 2021, in press.
  • Shubham Tripathi. Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing. PNAS 2021, 118(19): e2102050118. [link]
  • Shubham Tripathi. Mathematical Modeling of Plasticity and Heterogeneity in EMT. Methods Mol. Biol. 2021, 179: 385-413. [link]
  • Qi Wang. PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment. Nat. Commun. 2021, 12: 1167. [link]
  • Yan Helen Yan. Selective multiplexed enrichment for the detection and quantitation of low-fraction DNA variants via low-depth sequencing. Nat. Biomed. Eng. 2021, 5: 690-701. [link]
  • Xiaoyu Yang. Living fabrication of functional semi-interpenetrating polymeric materials. Nat. Commun. 2021, 12: 3422. [link]
  • Jinny X. Zhang and Jiaming Li. A deep learning model for predicting next-generation sequencing depth from DNA sequence. Nat. Commun. 2021, 12: 4387. [link]
2020
  • Dreycey Albin. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine. F1000Research 2020, 9:1141. [link]
  • Shyam Bhakta and David Zong. Synthetic biology open language visual (SBOL visual) version 2.2. J. Integr. Bioinform. 2020, 17(2-3); 20200014. [link]
  • Carlos Bueno. Metallochaperones are needed for mycobacterium tuberculosis and Escherichia coli Nicotinamidase-Pyrazinamidase activity. J.Bacteriol. 2020; 202(2): 1-16. [link]
  • Carlos Bueno. Protein structure prediction in CASP13 using AWSEM-Suite. J. Chem. Theory Comput. 2020; 16(6): 3977-88. [link]
  • Carlos Bueno. AWSEM-Suite: A protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes. Nucleic Acids Res. 2020; 48(W1): W25-30. [link]
  • 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. [link]
  • Sapna Chhabra. Mesenchymal-epithelial transition regulates initiation of pluripotency exit before gastrulation. Development 2020, 147(3): dev184960. [link]
  • Esteban Dodero-Rojas. On twin peak quasi-periodic oscillations resulting from the interaction between discoseismic modes and turbulence in accretion discs around black holes. MNRAS 2020, 492(2): 1755-1760. [link]
  • Esteban Dodero-Rojas. Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. PLoS ONE 2020, 15(1): e0222900. [link]
  • Emily M. Fulk. A Split Methyl Halide Transferase AND Gate That Reports by Synthesizing an Indicator Gas. ACS Synth. Biol. 2020, 9(11): 3104-3113. [link]
  • Kiara Gamas Reyes. An essential N-terminal serine-rich motif in the AAV VP1 and VP2 subunits that may play a role in viral transcription. Virology 2020, 546: 127-132. [link]
  • Jihwan Lee and Xiaoyu Lu. Versatile phenotype-activated cell sorting. Sci. Adv. 2020, 6(43): eabb7438. [link]
  • R. Tyler McLaughlin. Membrane and Actin Tethering Transitions Help IQGAP1 Coordinate GTPase and Lipid Messenger Signaling. Biophys. J. 2020, 118(3): 586-599. [link]
  • Elena Musteata and Lauren Gambill. Optogenetic control of gut bacterial metabolism to promote longevity. eLife 2020, 9:e56849. [link]
  • Yidan Pan. Fine-mapping within eQTL credible intervals by expression CROP-seq. Biol. Methods Protoc. 2020, 5(1): bpaa008. [link]
  • Yidan Pan. Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-Map Regulatory Intervals. Genes 2020, 11(5): 504. [link]
  • Yidan Pan. Tools for experimental and computational analyses of off-target editing by programmable nucleases. Nat Protoc. 2020, 16: 10-26. [link]
  • Shubham Tripathi. Biological networks regulating cell fate choice are minimally frustrated. Phys. Rev. Lett. 2020; 125(8), 088101. [link]
  • Shubham Tripathi. The physics of cellular decision making during epithelial–mesenchymal transition. Annu. Rev. Biophys. 2020, 49, 1-18. [link]
  • Shubham Tripathi. A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells. PLoS Comput. Biol. 2020, 16(2), e1007619. [link]
  • Shubham Tripathi. Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum. Front. Bioeng. Biotechnol. 2020, 8, 220. [link]
  • Shubham Tripathi. Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT. Oncotarget 2020, 11(27): 2611-2624. [link]
  • Qi Wang. To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics. Nucleic Acids Res. 2020, 48(10): 5217-5134. [link]
  • Yan Helen Yan. Encoding multiple digital DNA signals in a single analog channel. Nucleic Acids Res. 2020, 48(11): e65. [link]
  • Xiaoyu Yang. Mammalian signaling circuits from bacterial parts. Nat. Chem. Biol. 2020, 16: 110-111. [link]
2019
  • Josh T. Atkinson. Metalloprotein switches that display chemical-dependent electron transfer in cells. Nat. Chem. Biol. 2019, 15(2): 189-195. [link]
  • Josh T. Atkinson. Combinatorial design of chemical-dependent protein switches for controlling intracellular electron transfer. AICHE Journal 2019, 66(3): e16796. [link]
  • Josh T Atkinson. Life simplified: recompiling a bacterial genome for synonymous codon compression. Synthetic Biol. 2019; 4(1), ysz017. [link]
  • Josh T Atkinson. Overcoming component limitations in synthetic biology through transposon-mediated protein engineering. Methods Enzymol. 2019, 621, 191-212. [link]
  • Joshua T. Atkinson. Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts. Protein Eng. Des. Sel. 2019, 32(11): 489-501. [link]
  • Shyam Bhakta. Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. J. Integr. Bioinform. 2019, 16(2): 20180101. [link]
  • Shyam Bhakta. Communicating Structure and Function in Synthetic Biology Diagrams. ACS Synth. Biol. 2019, 8(8): 1818-1825. [link]
  • George Britton. A novel self-organizing embryonic stem cell system reveals signaling logic underlying the patterning of human ectoderm. Development. 2019, 146(20): dev179093. [link]
  • 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. [link]
  • Sapna Chhabra. Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids. PLoS Biol. 2019, 17(10): e3000498. [link]
  • Sapna Chhabra. Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells. Elife 2019, 8: e40526. [link]
  • Felix Ekness and Kathryn Brink. Rewiring bacterial two-component systems by modular DNA-binding domain swapping. Nat. Chem. Biol. 2019; 15(7): 690-698. [link]
  • Lauren Gambill and Baiyang Liu. Brave new ‘RNA’ world—advances in RNA tools and their application for understanding and engineering biological systems. Curr. Opin. Syst. Biol. 2019; 14: 32-40. [link]
  • Brianna Jayanthi. Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems. Meth. Enzymol. 2019, 622: 1-27. [link]
  • Dongya Jia. Testing the gene expression classification of the EMT spectrum. Phys. Biol. 2019, 16(20): 025002. [link]
  • Dongya Jia. Elucidating cancer metabolic plasticity by coupling gene regulation with metabolic pathways. PNAS 2019, 116(9): 3909-3918. [link]
  • Dongya Jia and Shubham Tripathi. Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response. J. Clin. Med. 2019. 8(5): 725. [link]
  • Qian Mei. Bacteria-to-human protein networks reveal origins of endogenous DNA damage. Cell 2019, 176(1-2): 127-143. [link]
  • Qian Mei. Tools To Live By: Bacterial DNA Structures Illuminate Cancer. 2019 Trends Genet. 2019, 35(5): 383-395. [link]
  • Qian Mei. Gamblers: An Antibiotic-Induced Evolvable Cell Subpopulation Differentiated by Reactive-Oxygen-Induced General Stress Response. Mol. Cell 2019, 74(4): 785-800. [link]
  • Qian Mei. Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways. Microb. Cell 2019, 6(1):1-64. [link]
  • Sara Molinari and Shyam Bhakta. A synthetic system for asymmetric cell division in Escherichia coli. Nat. Chem. Biol. 2019; 15(9):917-924. [link]
2018
  • Josh T. Atkinson. Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis. Nucleic Acids Res. 2018, 46(13): e76. [link]
  • 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. [link]
  • Ilenne Del Valle. Ratiometric gas reporting: a nondisruptive approach to monitor gene expression in soils. ACS Synth. Biol. 2018, 7(3):903-911. [link]
  • Dongya Jia. Elucidating the metabolic plasticity of cancer: mitochondrial reprogramming and hybrid metabolic states. Cells. 2018, 7(3): 21. [link]
  • Dongya Jia. Modularity of the metabolic gene network as a prognostic biomarker for hepatocellular carcinoma. Oncotarget 2018, 9(19): 15015-15026. [link]
  • Dongya Jia. Interconnected feedback loops among ESRP1, HAS2, and CD44 regulate epithelial-mesenchymal plasticity in cancer. APL Bioeng. 2018, 2(3): 031908. [link]
  • Dongya Jia. RACIPE: a computational tool for modeling gene regulatory circuits using randomization. BMC Syst. Biol. 2018, 12(1): 74. [link]
  • Qian Mei. Fluorescent fusions of the N protein of phage Mu label DNA damage in living cells. DNA Repair 2018, 72:86-92. [link]
  • 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. [link]
  • Shubham Tripathi. The standard genetic code facilitates exploration of the space of functional nucleotide sequences. J. Mol. Evol. 2018; 86(6): 325-339. [link]
  • Jinny X. Zhang. Predicting DNA hybridization kinetics from sequence. Nat. Chem. 2018, 10: 91-98. [link]
  • David M. Zong. Predicting transcriptional output of synthetic multi-input promoters. ACS Synth. Biol. 2018; 7(8): 1834-1843. [link]
2017
  • Josh T. Atkinson. PERMutation Using Transposase Engineering (PERMUTE): a simple approach for constructing circularly permuted protein libraries. Methods Mol Biol. 2017; 1498:295-308. [link]
  • 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. [link]
  • 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. [link]
  • 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. [link]
  • Dongya Jia. Phenotypic plasticity and cell fate decisions in cancer: insights from dynamical systems theory. Cancers 2017, 9(7): 70. [link]
  • 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. [link]
  • Dongya Jia. Operating principles of tristable circuits regulating cellular differentiation. Phys. Biol. 2017, 14(3): 035007. [link]
  • Dongya Jia. Modeling the genetic regulation of cancer metabolism: interplay between glycolysis and oxidative phosphorylation. Cancer Res. 2017; 77(7):1564-1574. [link]
  • Dongya Jia. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017, 13(3): e1005456. [link]
  • Dongya Jia. Phosphorylation-induced conformational dynamics in an intrinsically disordered protein and potential role in phenotypic heterogeneity. PNAS 2017, 114(13): E2644-E2653. [link]
  • Dongya Jia. Distinguishing mechanisms underlying EMT tristability. Cancer Converg. 2017, 1: 2. [link]
  • Prashant Kalvapalle. Using cellular fitness to map the structure and function of a major facilitator superfamily effluxes. Mol. Sys. Biol. 2017; 13(12): 964. [link]
  • R. Tyler McLaughlin. The coordinating role of IQGAP1 in the regulation of local, endosome-specific actin networks. Biol Open. 2017, 6(6): 785-799. [link]
  • Juexiao Sherry Wang and Yan Helen Yan. Modular probes for enriching and detecting complex nucleic acid sequences. Nat. Chem. 2017, 9:1222-1229. [link]
2016
  • 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. [link]
  • Josh T. Atkinson. The structure of a thermophilic kinase shapes fitness upon random circular permutation. ACS Synth. Biol. 2016, 5(5): 415-425. [link]
  • Ilenne Del Valle. Charcoal disrupts soil microbial communication through a combination of signal sorption and hydrolysis. ACS Omega, 2016 1(2): 226–233. [link]
  • Felix Ekness. An open-hardware platform for optogenetics and photobiology. Sci Rep. 2016; 6: 35363. [link]
  • Dongya Jia. Modeling delayed processes in biological systems. Phys. Rev. E. 2016; 94: 032408. [link]
  • Dongya Jia. Stability of the hybrid epithelial/mesenchymal phenotype. Oncotarget 2016, 7(19): 27067-27084. [link]
  • Dongya Jia. Tumor Budding: The Name is EMT. Partial EMT. J. Clin. Med. 2016; 5(5): 51. [link]
  • Brianna E. Kuypers. Tolerance of a knotted near-infrared fluorescent protein to random circular permutation. Biochem. 2016, 55(27): 3763-3773. [link]
  • R. Tyler McLaughlin. Collective dynamics of processive cytoskeletal motors. Soft Matter 2016, 12(1): 14-21. [link]
  • Qian Mei. Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase. Sci Adv. 2016, 2(11): e1601605. [link]
  • Yidan Pan. Prediction of influenza B vaccine effectiveness from sequence data. Vaccine 2016, 34(38): 4610-4617. [link]
2015
  • Felix Ekness. A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization. ACS Synth. Biol. 2015, 4(1): 32-38. [link]
  • Dongya Jia. OVOL guides the epithelial-hybrid-mesenchymal transition. Oncotarget 2015; 6(17):15436-15448. [link]
  • Dongya Jia. Coupling the modules of EMT and stemness: A tunable 'stemness window' model. Oncotarget 2015, 6(28): 25161-25174. [link]
  • Dongya Jia. Implications of the hybrid epithelial/mesenchymal phenotype in metastasis. Front Oncol. 2015; 5:155. [link]
  • Juexiao Sherry Wang. Continuously tunable nucleic acid hybridization probes. Nat Methods. 2015, 12(12): 1191-1196. [link]
  • Juexiao Sherry Wang. Simulation-guided DNA probe design for consistently ultraspecific hybridization. Nat. Chem. 2015,7(7): 545-553. [link]
2014
  • Brianna E. Kuypers. Efficiency of Protease-Activatable Virus Nanonodes Tuned Through Incorporation of Wild-Type Capsid Subunits. Cell. Mol. Bioeng. 2014, 7: 334-343. [link]
  • Brianna E. Kuypers. Synthetic virology: engineering viruses for gene delivery. Wiley Interdiscip. Rev Nanomed. Nanobiotechnol. 2014; 6(6): 548-558. [link]