690 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- National Institutes of HealthUS46 papers
- Seoul National UniversityKR5 papers
- Korea Institute for Advanced StudyKR4 papers
- Quảng Bình UniversityVN4 papers
- The University of Texas at AustinUS4 papers
- Keimyung UniversityKR3 papers
- Lehigh UniversityUS3 papers
- Princeton UniversityUS3 papers
- University at Buffalo, State University of New YorkUS3 papers
- University of ViennaAT3 papers
- Asia Pacific Center for Theoretical PhysicsKR2 papers
- Centre National de la Recherche ScientifiqueFR2 papers
47 papers
Deep Learning Segmentation of Ascites on Abdominal CT Scans for Automatic Volume Quantification
Benjamin Hou, Sung-Won Lee, Jung-Min Lee +4
Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian…
Tight basis cycle representatives for persistent homology of large data sets
Manu Aggarwal, Vipul Periwal
Persistent homology (PH) is a popular tool for topological data analysis that has found applications across diverse areas of research. It provides a rigorous method to compute robu…
Inference of stochastic time series with missing data
Sangwon Lee, Vipul Periwal, Junghyo Jo
Inferring dynamics from time series is an important objective in data analysis. In particular, it is challenging to infer stochastic dynamics given incomplete data. We propose an e…
The FRET-based structural dynamics challenge -- community contributions to consistent and open science practices
Eitan Lerner, Benjamin Ambrose, Anders Barth +23
Single-molecule Förster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the techni…
Decoding Neural Responses in Mouse Visual Cortex through a Deep Neural Network
Asim Iqbal, Phil Dong, Christopher M Kim +1
Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recen…
Inverse Ising inference from high-temperature re-weighting of observations
Junghyo Jo, Danh-Tai Hoang, Vipul Periwal
Maximum Likelihood Estimation (MLE) is the bread and butter of system inference for stochastic systems. In some generality, MLE will converge to the correct model in the infinite d…
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors
Roberto Covino, Michael T. Woodside, Gerhard Hummer +2
In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monit…
Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas Program
Michael P Snyder, Shin Lin, Amanda Posgai +22
Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years,…
Data-driven inference of hidden nodes in networks
Danh-Tai Hoang, Junghyo Jo, Vipul Periwal
The explosion of activity in finding interactions in complex systems is driven by availability of copious observations of complex natural systems. However, such systems, e.g. the h…
Phase Transition and Interpore Correlations of Water in Nanopore Membranes
Georg Menzl, Jürgen Köfinger, Christoph Dellago
Using computer simulations, we study a membrane of parallel narrow pores filled with one-dimensional wires of hydrogen-bonded water molecules. We show that such a membrane is equiv…
Finite size effects for spiking neural networks with spatially dependent coupling
Siwei Qiu, Carson Chow
We study finite-size fluctuations in a network of spiking deterministic neurons coupled with non-uniform synaptic coupling. We generalize a previously developed theory of finite si…
Learning recurrent dynamics in spiking networks
Christopher Kim, Carson Chow
Spiking activity of neurons engaged in learning and performing a task show complex spatiotemporal dynamics. While the output of recurrent network models can learn to perform variou…
Causality inference in stochastic systems from neurons to currencies: Profiting from small sample size
Danh-Tai Hoang, Juyong Song, Vipul Periwal +1
Success in modeling complex phenomena such as human perception hinges critically on the availability of data and computational power. Significant progress has been made in modeling…
NetREX: Network Rewiring using EXpression - Towards Context Specific Regulatory Networks
Yijie Wang, Dong-Yeon Cho, Hangnoh Lee +3
Understanding gene regulation is a fundamental step towards understanding of how cells function and respond to environmental cues and perturbations. An important step in this direc…
Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
Petra Kührová, Robert B. Best, Sandro Bottaro +4
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motif…
A Local Counter-Regulatory Motif Modulates the Global Phase of Hormonal Oscillations
Dong-Ho Park, Taegeun Song, Danh-Tai Hoang +2
Counter-regulatory elements maintain dynamic equilibrium ubiquitously in living systems. The most prominent example, which is critical to mammalian survival, is that of pancreatic…
Diffusive dynamics of contact formation in disordered polypeptides
Gul Zerze, Jeetain Mittal, Robert B. Best
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, b…
Role of solvation in pressure-induced helix stabilization
Robert B. Best, Cayla Miller, Jeetain Mittal
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated α-helices. However a…
Integer sequence discovery from small graphs
Travis Hoppe, Anna Petrone
We have exhaustively enumerated all simple, connected graphs of a finite order and have computed a selection of invariants over this set. Integer sequences were constructed from th…
The jigsaw puzzle of sequence phenotype inference: Piecing together Shannon entropy, importance sampling, and Empirical Bayes
Zeina Shreif, Deborah A. Striegel, Vipul Periwal
A nucleotide sequence 35 base pairs long can take 1,180,591,620,717,411,303,424 possible values. An example of systems biology datasets, protein binding microarrays, contain activi…
H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation
Ji-Eun Lee, Chaochen Wang, Shiliyang Xu +7
Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. Active enhancers are further marked by H3K27ac. However, the methyltransferases res…
Generalized activity equations for spiking neural network dynamics
Michael A. Buice, Carson C. Chow
Much progress has been made in uncovering the computational capabilities of spiking neural networks. However, spiking neurons will always be more expensive to simulate compared to…
The causal meaning of Fisher's average effect
James J. Lee, Carson C. Chow
In order to formulate the Fundamental Theorem of Natural Selection, Fisher defined the average excess and average effect of a gene substitution. Finding these notions to be somewha…
Pair diffusion, hydrodynamic interactions, and available volume in dense fluids
Jeetain Mittal, Gerhard Hummer
We calculate the pair diffusion coefficient D(r) as a function of the distance r between two hard-sphere particles in a dense monodisperse suspension. The distance-dependent pair d…