Publications
2024
Grand Challenges at the Interface of Engineering and Medicine Journal Article
In: IEEE OPEN JOURNAL OF ENGINEERING IN MEDICINE AND BIOLOGY, vol. 5, pp. 1-13, 2024.
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells Journal Article
In: NATURE METHODS, vol. 21, no. 1, 2024, ISSN: 1548-7091.
A bacterial sensor taxonomy across earth ecosystems for machine learning applications Journal Article
In: MSYSTEMS, vol. 9, no. 1, 2024, ISSN: 2379-5077.
2023
Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting Journal Article
In: CELL SYSTEMS, vol. 14, no. 12, 2023, ISSN: 2405-4712.
Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments Journal Article
In: BIOINFORMATICS, vol. 39, no. 12, 2023, ISSN: 1367-4803.
Predicting the Raman Spectra of Liquid Water with a Monomer-Field Model Journal Article
In: JOURNAL OF PHYSICAL CHEMISTRY LETTERS, vol. 14, no. 51, pp. 11742-11749, 2023, ISSN: 1948-7185.
Force transmission and SUN-KASH higher-order assembly in the LINC complex models Journal Article
In: BIOPHYSICAL JOURNAL, vol. 122, no. 23, pp. 4582-4597, 2023, ISSN: 0006-3495.
Interlayer, gallery-engineered graphene oxide using selective protection of mono-Boc-ethylenediamine as anode for sodium ion batteries Journal Article
In: JOURNAL OF ENERGY STORAGE, vol. 73, no. D, 2023, ISSN: 2352-152X.
Individually tailored spatial-spectral pulsed CEST MRI for ratiometric mapping ofmyocardial energetic species at 3T Journal Article
In: MAGNETIC RESONANCE IN MEDICINE, vol. 90, no. 6, pp. 2321-2333, 2023, ISSN: 0740-3194.
Using machine learning to go beyond potential energy surface benchmarking for chemical reactivity Journal Article
In: NATURE COMPUTATIONAL SCIENCE, 2023.
Enabling AI in synthetic biology through Construction File specification Journal Article
In: PLOS ONE, vol. 18, no. 11, 2023, ISSN: 1932-6203.
ChatGPT Research Group for Optimizing the Crystallinity of MOFs and COFs Journal Article
In: ACS CENTRAL SCIENCE, vol. 9, no. 11, pp. 2161-2170, 2023, ISSN: 2374-7943.
The Energetic Origins of Pi-Pi Contacts in Proteins Journal Article
In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 145, no. 45, pp. 24836-24851, 2023, ISSN: 0002-7863.
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells Journal Article
In: NATURE METHODS, vol. 20, no. 11, 2023, ISSN: 1548-7091.
HIV-1 Remission: Accelerating the Path to Permanent HIV-1 Silencing Journal Article
In: VIRUSES-BASEL, vol. 15, no. 11, 2023.
Virus-Based Pyroelectricity Journal Article
In: ADVANCED MATERIALS, vol. 35, no. 46, 2023, ISSN: 0935-9648.
Microfluidics-free single-cell genomics with templated emulsification Journal Article
In: NATURE BIOTECHNOLOGY, vol. 41, no. 11, pp. 1557+, 2023, ISSN: 1087-0156.
Greater transferability and accuracy of norm-conserving pseudopotentials using nonlinear core corrections Journal Article
In: CHEMICAL SCIENCE, vol. 14, no. 39, pp. 10934-10943, 2023, ISSN: 2041-6520.
Diverse functional polyethylenes by catalytic amination Journal Article
In: SCIENCE, vol. 381, no. 6665, pp. 1433-1440, 2023, ISSN: 0036-8075.
Multiscale computational framework to investigate integrin mechanosensing and cell adhesion Journal Article
In: JOURNAL OF APPLIED PHYSICS, vol. 134, no. 11, 2023, ISSN: 0021-8979.
Chemical Modification of Oxidized Polyethylene Enables Access to Functional Polyethylenes with Greater Reuse Journal Article
In: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 145, no. 39, pp. 21527-21537, 2023, ISSN: 0002-7863.
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells Journal Article
In: NATURE METHODS, 2023, ISSN: 1548-7091.
Lipid Nanoparticles Deliver mRNA to the Brain after an Intracerebral Injection Journal Article
In: BIOCHEMISTRY, vol. 62, no. 24, pp. 3533-3547, 2023, ISSN: 0006-2960.
Fail-tests of DNA methylation clocks, and development of a noise barometer for measuring epigenetic pressure of aging and disease Journal Article
In: AGING-US, vol. 15, no. 17, pp. 8552-8575, 2023, ISSN: 1945-4589.
Intra-cluster Charge Migration upon Hydration of Protonated Formic Acid Revealed by Anharmonic Analysis of Cold Ion Vibrational Spectra Journal Article
In: JOURNAL OF PHYSICAL CHEMISTRY A, vol. 127, no. 36, pp. 7501-7509, 2023, ISSN: 1089-5639.
Hippocampal representation during collective spatial behaviour in bats Journal Article
In: NATURE, vol. 621, no. 7980, pp. 796+, 2023, ISSN: 0028-0836.
Loss of TJP1 disrupts gastrulation patterning and increases differentiation toward the germ cell lineage in human pluripotent stem cells Journal Article
In: DEVELOPMENTAL CELL, vol. 58, no. 16, 2023, ISSN: 1534-5807.
Using Diffusion Maps to Analyze Reaction Dynamics for a Hydrogen Combustion Benchmark Dataset Journal Article
In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 19, no. 17, pp. 5872-5885, 2023, ISSN: 1549-9618.
Single-cell multiomic analysis of thymocyte development reveals drivers of CD4<SUP>+</SUP> T cell and CD8<SUP>+</SUP> T cell lineage commitment Journal Article
In: NATURE IMMUNOLOGY, 2023, ISSN: 1529-2908.
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq Journal Article
In: MOLECULAR METABOLISM, vol. 74, 2023, ISSN: 2212-8778.
How thermal fluctuations influence the function of the FeMo cofactor in nitrogenase enzymes Journal Article
In: CHEM CATALYSIS, vol. 3, no. 7, 2023, ISSN: 2667-1093.
Comparison of Velocity and Reynolds Stress Distributions in a Straight Rectangular Channel with Submerged and Emergent Vegetation Journal Article
In: WATER, vol. 15, no. 13, 2023.
In utero delivery of mRNA to the heart, diaphragm and muscle with lipid nanoparticles Journal Article
In: BIOACTIVE MATERIALS, vol. 25, pp. 387-398, 2023.
Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication Journal Article
In: RSC ADVANCES, vol. 13, no. 26, pp. 17667-17677, 2023.
DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner Journal Article
In: PLOS BIOLOGY, vol. 21, no. 6, 2023, ISSN: 1544-9173.
Turbulence Kinetic Energy and High-Order Moments of Velocity Fluctuations of Flows in the Presence of Submerged Vegetation in Pools Journal Article
In: WATER, vol. 15, no. 12, 2023.
On the interactions of peptides with gold nanoparticles: effects of sequence and size Journal Article
In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2023, ISSN: 0739-1102.
Engineered molecular sensors for quantifying cell surface crowding Journal Article
In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 120, no. 21, 2023, ISSN: 0027-8424.
Learning to evolve structural ensembles of unfolded and disordered proteins using experimental solution data Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 158, no. 17, 2023, ISSN: 0021-9606.
The Good, the Bad, and the Ugly: Pseudopotential Inconsistency Errors in Molecular Applications of Density Functional Theory Journal Article
In: JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 19, no. 10, pp. 2827-2841, 2023, ISSN: 1549-9618.
M-Chem: a modular software package for molecular simulation that spans scientific domains Journal Article
In: MOLECULAR PHYSICS, vol. 121, no. 9-10, SI, 2023, ISSN: 0026-8976.
In: JOURNAL OF CHEMICAL PHYSICS, vol. 158, no. 16, 2023, ISSN: 0021-9606.
A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication Journal Article
In: RSC ADVANCES, vol. 13, no. 16, pp. 10636-10641, 2023.
Towards an active droplet-based microfluidic platform for programmable fluid handling Journal Article
In: LAB ON A CHIP, vol. 23, no. 8, pp. 2029-2038, 2023, ISSN: 1473-0197.
Smartphone-assisted lab-in-a-tube device using gold nanocluster-based aptasensor for detection of MUC1-overexpressed tumor cells Journal Article
In: ANALYTICA CHIMICA ACTA, vol. 1252, 2023, ISSN: 0003-2670.
Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome Journal Article
In: NATURE BIOTECHNOLOGY, vol. 41, no. 4, pp. 488+, 2023, ISSN: 1087-0156.
Checkpoint kinase 1/2 inhibition potentiates anti-tumoral immune response and sensitizes gliomas to immune checkpoint blockade Journal Article
In: NATURE COMMUNICATIONS, vol. 14, no. 1, 2023.
Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose Journal Article
In: ACS APPLIED BIO MATERIALS, vol. 6, no. 3, pp. 1041-1053, 2023, ISSN: 2576-6422.
Droplet-based forward genetic screening of astrocyte-microglia cross-talk Journal Article
In: SCIENCE, vol. 379, no. 6636, pp. 1023-1030, 2023, ISSN: 0036-8075.
On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation Journal Article
In: VIRUS RESEARCH, vol. 326, 2023, ISSN: 0168-1702.