Research record
Publications
Papers, preprints, chapters, commentaries, and conference contributions spanning computational biology, systems biology, genomics, and diagnostics.
27 records
Deep Profiling of EV Long RNAs Reveals Biofluid-Specific Transcriptomes and Splicing Landscapes
Preprint · 10.1101/2025.08.05.668716
Salivary Extracellular Vesicle RNA Profiling Reveals Biomarkers for Sjögren’s
Preprint · 10.1101/2025.08.05.668729
Extracellular Vesicle Gene Expression Enables Sensitive Detection of Colorectal Neoplasia
Preprint · 10.1101/2025.08.14.670394
Stratification of patients with prostate cancer using a urine exosome gene expression signature
Journal of Clinical Oncology · 10.1200/jco.2024.42.16_suppl.e17095
Signatures of antibiotic tolerance and persistence in response to divergent stresses
Preprint · 10.1101/2023.02.05.527212
Overlapping stimulons arising in response to divergent stresses inEscherichia coli
Preprint · 10.1101/2021.12.17.473201
Tasting the Terroir with Tsr
Biophysical Journal · 10.1016/j.bpj.2019.09.049
A novel metric reveals previously unrecognized distortion in the analysis of scRNA-seq data
Preprint · 10.1101/689851
Diversity in lac Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness
mBio · 10.1128/mbio.02232-19
Lineage space and the propensity of bacterial cells to undergo growth transitions
PLOS Computational Biology · 10.1371/journal.pcbi.1006380
Computation by natural systems
Interface Focus · 10.1098/rsfs.2018.0058
Intergenerational Cellular Signal Transfer and Erasure
The Energetics of Computing in Life and Machines · 10.37911/9781947864078.05
Dynamical predictors of an imminent phenotypic switch in bacteria
Physical Biology · 10.1088/1478-3975/aa7870
Survival of Phenotypic Information during Cellular Growth Transitions.
ACS synthetic biology · 10.1021/acssynbio.5b00229
Cellular Growth Arrest and Persistence from Enzyme Saturation.
PLoS computational biology · 10.1371/journal.pcbi.1004825
Stress-response balance drives the evolution of a network module and its host genome.
Molecular systems biology · 10.15252/msb.20156185
Amino acid positions subject to multiple coevolutionary constraints can be robustly identified by their eigenvector network centrality scores.
Proteins · 10.1002/prot.24948
Adaptive evolution of the lactose utilization network in experimentally evolved populations of Escherichia coli.
PLoS genetics · 10.1371/journal.pgen.1002444
Interplay of gene expression noise and ultrasensitive dynamics affects bacterial operon organization.
PLoS computational biology · 10.1371/journal.pcbi.1002672
Bistable responses in bacterial genetic networks: designs and dynamical consequences.
Mathematical biosciences · 10.1016/j.mbs.2011.03.004
Non-transcriptional regulatory processes shape transcriptional network dynamics.
Nature reviews. Microbiology · 10.1038/nrmicro2667
Adaptable functionality of transcriptional feedback in bacterial two-component systems.
PLoS computational biology · 10.1371/journal.pcbi.1000676
Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection.
Journal of immunology (Baltimore, Md. : 1950) · 10.4049/jimmunol.0802297
The timing of TNF and IFN-gamma signaling affects macrophage activation strategies during Mycobacterium tuberculosis infection.
Journal of theoretical biology · 10.1016/j.jtbi.2008.01.010
A methodology for performing global uncertainty and sensitivity analysis in systems biology.
Journal of theoretical biology · 10.1016/j.jtbi.2008.04.011
Requirement for multiple activation signals by anti-inflammatory feedback in macrophages.
Journal of theoretical biology · 10.1016/j.jtbi.2005.11.037
The effect of phospholipids and mucin on bacterial internalization in an enterocyte-cell culture model.
Pediatric surgery international · 10.1007/s003830050543
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