Expanding the HP1a-binding consensus and molecular grammar for heterochromatin assembly
The recruitment of Heterochromatin Protein 1 (HP1) partners is essential for heterochromatin assembly and function, yet our knowledge regarding their organiz...
Journal articles
By topic
Cell & Nuclear Biomechanics
Emerging mechanomedicines informed by mechanotransduction along the integrin–cytoskeleton–nucleus axis
Mechanical forces are fundamental to the formation of normal biological tissues and the maintenance of physiological health. These forces are transmitted fro...
Role of pore dilation in molecular transport through the nuclear pore complex: Insights from polymer scaling theory
The nuclear pore complex (NPC), a channel within the nuclear envelope filled with intrinsically disordered proteins, regulates the transport of macromolecule...
Multiscale Kinematic Growth Coupled With Mechanosensitive Systems Biology in Open-Source Software
Multiscale coupling between cell-scale biology and tissue-scale mechanics is a promising approach for modeling disease growth. In such models, tissue-level g...
Nanoscale in silico and in vitro modeling of lipid bilayers for curvature induction and sensing
Cellular functions like motility, differentiation, or protein trafficking often require a change in membrane curvature and protein distribution. Defects asso...
Regulating transport efficiency through the nuclear pore complex: The role of binding affinity with FG-Nups
Macromolecules are transported through the nuclear pore complex (NPC) via a series of transient binding and unbinding events with FG-Nups, which are intrinsi...
Mechanistic understanding of enhancing bioactivity via bio-ionic liquid functionalization of biomaterials
• The role of bio-ionic liquids (BILs) as cell adhesion molecules for enhancing the bioactivity of bio-inert biomaterials has been investigated. • A bio-iner...
Deciphering the intrinsically disordered characteristics of the FG-Nups through the lens of polymer physics
Perspective article connecting polymer physics and intrinsically disordered FG-Nups in the nuclear pore complex.
Multiscale computational framework to investigate integrin mechanosensing and cell adhesion
Integrin mechanosensing plays an instrumental role in cell behavior, phenotype, and fate by transmitting mechanical signals that trigger downstream molecular...
On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation
Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibit...
A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication
Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has...
Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication
The papain-like protease (PLpro) plays a critical role in SARS-CoV-2 (SCoV-2) pathogenesis and is essential for viral replication and for allowing the virus ...
Effects of Ionic Liquids on the Stabilization Process of Gold Nanoparticles
Improving the stability of the gold nanoparticles (AuNPs) is an important challenge in nanoscience, given that the activity and ubiquitous application of the...
Design of a flexing organ-chip to model in situ loading of the intervertebral disc
The leading cause of disability of all ages worldwide is severe lower back pain. To address this untreated epidemic, further investigation is needed into the...
On modeling the multiscale mechanobiology of soft tissues: Challenges and progress
Tissues grow and remodel in response to mechanical cues, extracellular and intracellular signals experienced through various biological events, from the deve...
Decoding the Effect of Hydrostatic Pressure on TRPV1 Lower-Gate Conformation by Molecular-Dynamics Simulation
In response to hydrostatic pressure, the cation channel transient receptor potential vanilloid 1 (TRPV1) is essential in signaling pathways linked to glaucom...
Acid-Sensitive Surfactants Enhance the Delivery of Nucleic Acids
The development of endosomal disruptive agents is a major challenge in the field of drug delivery and pharmaceutical chemistry. Current endosomal disruptive ...
Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex
Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitate...
A Coupled Multiscale Approach to Modeling Aortic Valve Mechanics in Health and Disease
Mechano-biological processes in the aortic valve span multiple length scales ranging from the molecular and cell to tissue and organ levels. The valvular int...
Molecular models of LINC complex assembly at the nuclear envelope
Large protein complexes assemble at the nuclear envelope to transmit mechanical signals between the cytoskeleton and nucleoskeleton. These protein complexes ...
[Retracted] Atomic Scale Interactions between RNA and DNA Aptamers with the TNF‐α Protein
Interest in the design and manufacture of RNA and DNA aptamers as apta-biosensors for the early diagnosis of blood infections and other inflammatory conditio...
Drug delivery and adhesion of magnetic nanoparticles coated nanoliposomes and microbubbles to atherosclerotic plaques under magnetic and ultrasound fields
The use of external fields such as magnet and ultrasound to enhance the targeted drug delivery (TDD) by nano-microcarriers could be a potential method. In th...
A splice acceptor variant in HLA‐DRA affects the conformation and cellular localization of the class II DR alpha‐chain
Class II human leucocyte antigen (HLA) proteins are involved in the immune response by presenting pathogen-derived peptides to CD4+ T lymphocytes. At the mol...
Nanoscale integrin cluster dynamics controls cellular mechanosensing via FAKY397 phosphorylation
Transduction of extracellular matrix mechanics affects cell migration, proliferation, and differentiation. While this mechanotransduction is known to depend ...
Strain-stiffening and strain-softening responses in random viscoelastic fibrous networks: interplay between fiber orientation and viscoelastic softening
Collagen networks are usually modeled as an inelastic material that accentuates the role of bond dynamics in their viscoelastic response. However, permanent ...
Role of KASH domain lengths in the regulation of LINC complexes
The linker of the nucleoskeleton and cytoskeleton (LINC) complex is formed by the conserved interactions between Sad-1 and UNC-84 (SUN) and Klarsicht, ANC-1,...
Mechanobiology of the Nuclear Pore Complex Machinery
Cite This Article R., M. (2019). Mechanobiology of the Nuclear Pore Complex Machinery. Molecular & Cellular Biomechanics, 16(Suppl.2), 19–20.
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples
The author wishes to inform readers that the affiliations for the authors were incorrect in the original paper. They appear correctly above. The paper has be...
Agent‐Based Modeling in Molecular Systems Biology
Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spa...
Quality control of mRNAs at the entry of the nuclear pore: Cooperation in a complex molecular system
Despite extensive research on how mRNAs are quality controlled prior to export into the cytoplasm, the exact underlying mechanisms are still under debate. Sp...
The “Stressful” Life of Cell Adhesion Molecules: On the Mechanosensitivity of Integrin Adhesome
Cells have evolved into complex sensory machines that communicate with their microenvironment via mechanochemical signaling. Extracellular mechanical cues tr...
Multiscale Systems Biology Model of Calcific Aortic Valve Disease Progression
Calcific aortic valve disease is a common cause of aortic stenosis, a life threatening condition. In this study, a mathematical model is developed to simulat...
Looking “Under the Hood” of Cellular Mechanotransduction with Computational Tools: A Systems Biomechanics Approach across Multiple Scales
Signal modulation has been developed in living cells throughout evolution to promote utilizing the same machinery for multiple cellular functions. Chemical a...
Gelatin/chondroitin sulfate nanofibrous scaffolds for stimulation of wound healing: In‐vitro and in‐vivo study
In this research, fabrication of gelatin/chondroitin sulfate (GAG) nanofibrous scaffolds using electrospinning technique for skin tissue engineering was stud...
Differential Collective- and Single-Cell Behaviors on Silicon Micropillar Arrays
Three-dimensional vertically aligned nano- and micropillars have emerged as promising tools for a variety of biological applications. Despite their increasin...
Enhanced intracellular delivery of small molecules and drugs via non-covalent ternary dispersions of single-wall carbon nanotubes
Albumins are used biologically and pharmacologically as transport proteins to deliver molecules to cells. Albumins also efficiently coat single-wall carbon n...
Cooperation within von Willebrand factors enhances adsorption mechanism
von Willebrand factor (VWF) is a naturally collapsed protein that participates in primary haemostasis and coagulation events. The clotting process is trigger...
The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
Molecular traffic between the nucleus and the cytoplasm is regulated by the nuclear pore complex (NPC), which acts as a highly selective channel perforating ...
Directional migration and differentiation of neural stem cells within three-dimensional microenvironments
Harnessing neural stem cells to repair neuronal damage is a promising potential treatment for neuronal diseases. To enable future therapeutic efficacy, the s...
Mechanisms of integrin and filamin binding and their interplay with talin during early focal adhesion formation
Filamin plays a key role in cellular biomechanics as an actin cross-linker and as a versatile focal adhesion binding partner. It binds directly to integrins,...
An agent-based model for mRNA export through the nuclear pore complex
mRNA export from the nucleus is an essential step in the expression of every protein- coding gene in eukaryotes, but many aspects of this process remain poor...
The Interaction of CRM1 and the Nuclear Pore Protein Tpr
While much has been devoted to the study of transport mechanisms through the nuclear pore complex (NPC), the specifics of interactions and binding between ex...
Actin Reorganization through Dynamic Interactions with Single-Wall Carbon Nanotubes
Single-wall carbon nanotubes (SWCNTs) have been widely used for biological applications in recent years, and thus, it is critical to understand how these ine...
Higher Nucleoporin-Importinβ Affinity at the Nuclear Basket Increases Nucleocytoplasmic Import
Several in vitro studies have shown the presence of an affinity gradient in nuclear pore complex proteins for the import receptor Importinβ, at least partial...
The Interaction of Vinculin with Actin
Vinculin can interact with F-actin both in recruitment of actin filaments to the growing focal adhesions and also in capping of actin filaments to regulate a...
Altered Cell Mechanics from the Inside: Dispersed Single Wall Carbon Nanotubes Integrate with and Restructure Actin
With a range of desirable mechanical and optical properties, single wall carbon nanotubes (SWCNTs) are a promising material for nanobiotechnologies. SWCNTs a...
On the Significance of Microtubule Flexural Behavior in Cytoskeletal Mechanics
Quantitative description of cell mechanics has challenged biological scientists for the past two decades. Various structural models have been attempted to an...
Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion
Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and su...
Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex
The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the...
MEMS-based dynamic cell-to-cell culture platforms using electrochemical surface modifications
MEMS-based biological platforms with the capability of both spatial placements and time releases of living cells for cell-to-cell culture experiments have be...
Viscoelastic characterization of the retracting cytoskeleton using subcellular detachment
Characterization of the cytoskeleton’s viscoelastic properties is essential for understanding cellular dynamics in many biological functions of the cell, esp...
A biological breadboard platform for cell adhesion and detachment studies
The dynamic nature of cell adhesion and detachment, which plays a critical role in a variety of physiological and pathological phenomena, still remains uncle...
A Sub-Cellular Viscoelastic Model for Cell Population Mechanics
Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form unique...
Liver-Assist Device With a Microfluidics-Based Vascular Bed in an Animal Model
This device is the first to incorporate a microfluidics network in the systemic circulatory system. The microvascular network supported viability and functio...
Analysis of Circular PDMS Microballoons With Ultralarge Deflection for MEMS Design
This paper presents the simplified analytical and numerical analyses of the ultralarge deflection of circular polydimethylsiloxane (PDMS) microballoons (MBs)...
Averaged implicit hydrodynamic model of semiflexible filaments
We introduce a method to incorporate hydrodynamic interaction in a model of semiflexible filament dynamics. Hydrodynamic screening and other hydrodynamic int...
Mechanotransduction: a major regulator of homeostasis and development
In nearly all aspects of biology, forces are a relevant regulator of life's form and function. More recently, science has established that cells are exquisit...
Hemodynamic Environments from Opposing Sides of Human Aortic Valve Leaflets Evoke Distinct Endothelial Phenotypes In Vitro
The regulation of valvular endothelial phenotypes by the hemodynamic environments of the human aortic valve is poorly understood. The nodular lesions of calc...
On the multiscale modeling of heart valve biomechanics in health and disease
Theoretical models of the human heart valves are useful tools for understanding and characterizing the dynamics of healthy and diseased valves. Enabled by ad...
MEMS-based biological platform for dynamic cell-to-cell interaction characterization
MEMS-based biological platforms with the capability of spatiotemporal control of living cells have been demonstrated. The space control is accomplished by mi...
Pulmonary Tissue Engineering using Dual-Compartment Polymer Scaffolds with Integrated Vascular Tree
We conclude that functional hybrid microsystems mimicking the basic building plan of alveolar tissue can be engineered in vitro.
A Computational Model of Aging and Calcification in the Aortic Heart Valve
The aortic heart valve undergoes geometric and mechanical changes over time. The cusps of a normal, healthy valve thicken and become less extensible over tim...
Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
alpha-Actinin is an actin crosslinking molecule that can serve as a scaffold and maintain dynamic actin filament networks. As a crosslinker in the stressed c...
Band-like Stress Fiber Propagation in a Continuum and Implications for Myosin Contractile Stresses
Stress fibers are band-like features that form with sarcomere-like actin and myosin arrangement between cell regions, resisting myosin contractility. We cons...
Rods-on-string idealization captures semiflexible filament dynamics
We present an approach to modeling the two-dimensional Brownian dynamics of semiflexible filaments in the worm-model description as uniform, isotropic, and c...
Rheology of the Cytoskeleton
The cytoskeleton is the primary internal structure of the cell, providing its structural integrity. The rheology and mechanics of the cytoskeleton, therefore...
Concept and Computational Design for a Bioartificial Nephron-On-A-Chip
A MEMS-based, (Micro Electro Mechanical System) bioartificial device is proposed for replicating the function of a single nephron. Consistent with the anatom...
Endothelialized Microvasculature Based on a Biodegradable Elastomer
Vital organs maintain dense microvasculature to sustain the proper function of their cells. For tissue- engineered organs to function properly, artificial ca...
Force-induced focal adhesion translocation: effects of force amplitude and frequency
Vascular endothelial cells rapidly transduce local mechanical forces into biological signals through numerous processes including the activation of focal adh...
Living three-dimensional micro fabricated constructs for the replacement of vital organ function
We report the first demonstration of high-resolution three-dimensional constructs of living tissue suitable for transplantation for vital organ replacement d...
Vascularized tissue engineering of vital organs: design, modeling and functional testing
We report engineering of vascularized tissue constructs for the replacement of vital organ function. A computational algorithm for simulation of blood flow a...
Single cell micromanipulation using magnetic beads: a computational model
A computational finite element model (FEM) model is developed for cell micromanipulation by magnetocytometry. The model provides a robust tool for analysis o...
Dynamic Rotational Seeding and Cell Culture System for Vascular Tube Formation
Optimization of cell seeding and culturing is an important step for the successful tissue engineering of vascular conduits. We evaluated the effectiveness of...
Stress-Induced Mechanotransduction: Some Preliminaries
Mechanical stimuli affect nearly every aspect of cellular function, yet the underlying mechanisms of transduction of force into biochemical signals are not c...
A microfabricated array bioreactor for perfused 3D liver culture
We describe the design, fabrication, and performance of a bioreactor that enables both morphogenesis of 3D tissue structures under continuous perfusion and r...
Atherosclerotic human carotid bifurcations: mechanical and histological factors
3D finite element analyses were conducted of the diseased carotid bifurcation using reconstructed models based on in vivo MRI geometries and ultrasound veloc...
Oxygen Mass Transfer in a Stenosis: Effects of Blood-Wall Coupling
Abstract Motivation: Arterial transport of blood-borne materials is essential for maintenance of normal arterial wall physiology. Disturbed transport of such...
Microbiome & Bacterial Community Biomechanics
SIMBA-GNN: mechanistic graph learning for microbiome prediction
Predicting how gut microbial communities assemble and change requires models that capture the underlying mechanisms driving interspecies interactions, not ju...
Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities
Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states...
Unravelling the Glycan Code: Molecular Dynamics and Quantum Chemistry Reveal How O‐Glycan Functional Groups Govern OgpA Selectivity in Mucin Degradation by Akkermansia muciniphila
Mucins, heavily O-glycosylated glycoproteins, are a key component of mucus, and certain gut microbiota, including Akkermansia muciniphila, can utilise mucin ...
Antimicrobial peptide interactions with bacterial cell membranes
Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of vir...
Adsorption Process of Various Antimicrobial Peptides on Different Surfaces of Cellulose
Current antimicrobial challenges in hospitals, pharmaceutical production units, and food packaging have motivated the development of antimicrobial agents, am...
Gut-on-a-chip models for dissecting the gut microbiology and physiology
Microfluidic technologies have been extensively investigated in recent years for developing organ-on-a-chip-devices as robust in vitro models aiming to recap...
Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases
The human gut microbiota and its associated perturbations are implicated in a variety of cardiovascular diseases (CVDs). There is evidence that the structure...
Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen
Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. I...
Bacterial Networks on Hydrophobic Micropillars
Bacteria have evolved as intelligent microorganisms that can colonize and form highly structured and cooperative multicellular communities with sophisticated...
Adhesion characteristics ofStaphylococcus aureusbacterial cells on funnel-shaped palladium–cobalt alloy nanostructures
The adhesion properties of Staphylococcus aureus on palladium–cobalt (Pd–Co) alloy nanostructures with various cross-sectional geometries have been character...
Trapping polystyrene and latex nanospheres inside hollow nanostructures usingStaphylococcus aureuscells
A new methodology was developed to trap polystyrene or latex nanospheres in nanocrystalline nickel columnar nanostructures with various cross-sectional geome...
Statistical Learning & Biological Language Processing
Semi-supervised Retrieval of Functional Residues Through the Integration of Protein Language Models and Gene Ontology Data
Abstract Motivation Experimental studies of protein function often focus on mechanistic descriptions, characterizing how specific sites and residues contribu...
Computational drug design in the artificial intelligence era: A systematic review of molecular representations, generative architectures, and performance assessment
Generative drug design has emerged as a transformative approach in pharmaceutical research, leveraging deep learning models to create novel molecules with ta...
Block ratio optimized cationic polyacrylamides for enhanced nitrate rejection under applied potential
Nitrate contamination in water sources is a growing environmental concern, threatening both human health and ecosystems. However, its combination with sodium...
Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function
Chromatin loop formation plays a crucial role in 3D genome interactions, with misfolding potentially leading to irregular gene expression and various disease...
Correction: Identification of acrylamide-based covalent inhibitors of SARS-CoV-2 (SCoV-2) Nsp15 using high-throughput screening and machine learning
[This corrects the article DOI: 10.1039/D4RA06955B.].
Identification of acrylamide-based covalent inhibitors of SARS-CoV-2 (SCoV-2) Nsp15 using high-throughput screening and machine learning
Non-structural protein 15 (Nsp15) is a SARS-CoV-2 (SCoV-2) endoribonuclease and is a promising target for drug development because of its essential role in e...
Fine-tuning protein embeddings for functional similarity evaluation
github.com/mofradlab/go_metric.
HGTDR: Advancing drug repurposing with heterogeneous graph transformers
The source code and data are available at https://github.com/bcb-sut/HGTDR and http://git.dml.ir/BCB/HGTDR.
Deep Learning for Perfusion Cerebral Blood Flow (CBF) and Volume (CBV) Predictions and Diagnostics
Dynamic susceptibility contrast magnetic resonance perfusion (DSC-MRP) is a non-invasive imaging technique for hemodynamic measurements. Various perfusion pa...
Enhanced HP1α homodimer interaction via force-induced salt bridge formation: implications for chromatin crosslinking and phase separation
Unlocking chromatin dyanamics: force-driven salt bridges may spearhead compaction and phase transition.
On the interactions of peptides with gold nanoparticles: effects of sequence and size
Peptide-based self-assembly and synthesis techniques have emerged as a viable approach to designing active and stable inorganic nanostructures in aqueous med...
On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study
The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of ...
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations
Supplementary data are available at Bioinformatics online.
On the nuclear pore complex and its emerging role in cellular mechanotransduction
The nuclear pore complex (NPC) is a large protein assembly that perforates the nuclear envelope and provides a sole gateway for traffic between the cytoplasm...
Nucleoporins’ exclusive amino acid sequence features regulate their transient interaction with and selectivity of cargo complexes in the nuclear pore
Nucleocytoplasmic traffic of nucleic acids and proteins across the nuclear envelop via the nuclear pore complexes (NPCs) is vital for eukaryotic cells. NPCs ...
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks
Pretrained representations have recently gained attention in various machine learning applications. Nonetheless, the high computational costs associated with...
EpitopeVec: linear epitope prediction using deep protein sequence embeddings
Supplementary data are available at Bioinformatics online.
PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks
Understanding the functionality of proteins has emerged as a critical problem in recent years due to significant roles of these macro-molecules in biological...
Killer Cell Immunoglobulin-like Receptor Variants Are Associated with Protection from Symptoms Associated with More Severe Course in Parkinson Disease
Immune dysfunction plays a role in the development of Parkinson disease (PD). NK cells regulate immune functions and are modulated by killer cell immunoglobu...
Bridging Finite Element and Machine Learning Modeling: Stress Prediction of Arterial Walls in Atherosclerosis
Finite element and machine learning modeling are two predictive paradigms that have rarely been bridged. In this study, we develop a parametric model to gene...
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
Supplementary data are available at Bioinformatics online.
A molecular model for LINC complex regulation: activation of SUN2 for KASH binding
Linkers of the nucleoskeleton and cytoskeleton are key molecular complexes that span the nuclear envelope (NE) and provide a direct linkage between the nucle...
ProtDataTherm: A database for thermostability analysis and engineering of proteins
Protein thermostability engineering is a powerful tool to improve resistance of proteins against high temperatures and thereafter broaden their applications....
Abstract 18074: Fast and Accurate View Classification of Cardiac Echocardiograms Using Deep Learning
Background: Echocardiography is essential to modern cardiology. However, human interpretation limits accurate and standardized high-throughput analysis, limi...
Mechanical Contact Characteristics of PC3 Human Prostate Cancer Cells on Complex-Shaped Silicon Micropillars
In this study we investigated the contact characteristics of human prostate cancer cells (PC3) on silicon micropillar arrays with complex shapes by using hig...
The LINC and NPC relationship – it's complicated!
The genetic information of eukaryotic cells is enclosed within a double-layered nuclear envelope, which comprises an inner and outer nuclear membrane. Severa...
Comparing Fifty Natural Languages and Twelve Genetic Languages Using Word Embedding Language Divergence (WELD) as a Quantitative Measure of Language Distance
We introduce a new measure of distance between languages based on word embedding, called word embedding language divergence (WELD). WELD is defined as diverg...
Text Analysis and Automatic Triage of Posts in a Mental Health Forum
We present an approach for automatic triage of message posts in ReachOut.com mental health forum, which was a shared task in the 2016 Computational Linguisti...
Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex
Nucleocytoplasmic transport has been the subject of a large body of research in the past few decades. Recently, the focus of investigations in this field has...
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics
We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in gene...
Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and diffe...
Passive control of cell locomotion using micropatterns: the effect of micropattern geometry on the migratory behavior of adherent cells
Directed cell migration is critical to a variety of biological and physiological processes. Although simple topographical patterns such as parallel grooves a...
An efficient two-stage approach for image-based FSI analysis of atherosclerotic arteries
Patient-specific biomechanical modeling of atherosclerotic arteries has the potential to aid clinicians in characterizing lesions and determining optimal tre...
Master Proof Molecular Dynamics Study of Talin-Vinculin Binding
Cells can sense mechanical force in regulating focal adhesion assembly. One vivid example is the force-induced recruitment of vinculin to reinforce initial c...
Microfabrication of Three-Dimensional Engineered Scaffolds
One of the principal challenges facing the field of tissue engineering over the past 2 decades has been the requirement for large-scale engineered constructs...
A Novel Framework for Elastography and Modulus Estimation: Integration of Tissue Mechanics with Imaging
The feasibility of optical coherence elastography is examined and the steps necessary for registration of optical coherence tomography (OCT) images are devel...
OCT-based arterial elastography: robust estimation exploiting tissue biomechanics
We present a novel multi-resolution variational framework for vascular optical coherence elastography (OCE). This method exploits prior information about art...
Vascular Optical Coherence Elastography: Assessment of Conventional Velocimetry Applied to OCT
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Design of a single capillary-parenchymal co-culture bioreactor
A bioreactor is designed and fabricated for the co-culture of endothelial and hepatic parenchymal cells. The device provides a structured environment mimicki...
Optical Elastography for Determining Strain in Coronary Vessels
The disruption of structurally compromised coronary plaque is thought to be the primary event causing heart attack. We have developed a new method for charac...