Scott Christley, Yiming Lu, Chen Li, Xiaohui Xie
Human genomes as email attachments
Resource A Mammalian Organelle Map by Protein Correlation Profiling (2009)
Leonard J. Foster, Yanling Zhang, Yong Zhang, Xiaohui Xie, Vamsi K. Mootha, ...
Protein localization to membrane-enclosed organelles is a central feature of cellular organization. Using protein correlation profiling, we have mapped 1,404 proteins to ten subcellular locations in...
Identifying novel constrained elements by exploiting biased substitution patterns (2009)
Garber, Manuel, Guttman, Mitchell, Clamp, Michele, Zody, Michael C., Friedman, Nir, Xie, Xiaohui
Motivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved...
Common polymorphic transcript variation in human disease (2009)
Fraser, Hunter B., Xie, Xiaohui
Most human genes are thought to express different transcript isoforms in different cell types; however, the full extent and functional consequences of polymorphic transcript variation (PTV), which...
MotifMap: a human genome-wide map of candidate regulatory motif sites (2009)
Xie, Xiaohui, Rigor, Paul, Baldi, Pierre
Motivation: Achieving a comprehensive map of all the regulatory elements encoded in the human genome is a fundamental challenge of biomedical research. So far, only a small fraction of the regulatory...
Human genomes as email attachments (2009)
Christley, Scott, Lu, Yiming, Li, Chen, Xie, Xiaohui
Summary: The amount of genomic sequence data being generated and made available through public databases continues to increase at an ever-expanding rate. Downloading, copying, sharing and...
Justin Werfel, Xiaohui Xie, H. Sebastian Seung
Gradient-following learning methods can encounter problems of implementation in many applications, and stochastic variants are sometimes used to overcome these difficulties. We analyze three online...
Xiaohui Xie, H. Sebastian Seung, Howard Hughes
A theory of neural integration in the
Xiaohui Xie, H. Sebastian Seung, Howard Hughes
A theory of neural integration in the
Justin Werfel, Xiaohui Xie, H. Sebastian Seung
Gradient-following learning methods can encounter problems of implementation in many applications, and stochastic variants are sometimes used to overcome these difficulties. We analyze three online...
Justin Werfel, Xiaohui Xie, H. Sebastian Seung
curves for stochastic gradient descent
Xiaohui Xie, H. Sebastian Seung, Howard Hughes
theory of integration in the head-direction system
Asymmetric lateral connections are one possible mechanism that can account for the direction selectivity of cortical neurons. We present a mathematical analysis for a class of these models....
Abstract Background Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1...
Bradley E. Bernstein, Tarjei S. Mikkelsen, Xiaohui Xie, Michael Kamal, Dana J. Huebert, James Cuff, ...
The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that...
A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands (2006)
Giallourakis, Cosmas, Cao, Zhifang, Green, Todd, Wachtel, Heather, Xie, Xiaohui, Lopez-Illasaca, Marco, ...
PDZ domain-containing proteins and their interaction partners are mutated in numerous human diseases and function in complexes regulating epithelial polarity, ion channels, cochlear hair cell...
A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands (2006)
Giallourakis, Cosmas, Cao, Zhifang, Green, Todd, Wachtel, Heather, Xie, Xiaohui, Lopez-Illasaca, Marco, ...
PDZ domain-containing proteins and their interaction partners are mutated in numerous human diseases and function in complexes regulating epithelial polarity, ion channels, cochlear hair cell...
Justin Werfel, Xiaohui Xie, H. Sebastian Seung
learning problem, such as the input distribution and the target function, and are not universally applicable. Neural Computation 17, 2699--2718 (2005) 2005 Massachusetts Institute of Technology 1...
Learning Curves for Stochastic Gradient Descent in Linear Feedforward Networks (2004)
Justin Werfel, Xiaohui Xie, H. Sebastian Seung
Gradient-following learning methods can encounter problems of implementation in many applications, and stochastic variants are sometimes used to overcome these difficulties. We analyze three online...
Learning in neural networks by reinforcement of irregular spiking (2004)
Xiaohui Xie, H. Sebastian Seung
spiking
Learning Curves for Stochastic Gradient Descent in Linear Feedforward Networks (2003)
Justin Werfel, Xiaohui Xie, H. Sebastian Seung
Gradient-following learning methods can encounter problems of implementation in many applications, and stochastic variants are frequently used to overcome these difficulties. We derive quantitative...
Selectively grouping neurons in recurrent networks of lateral inhibition (2002)
Xiaohui Xie, H. Sebastian Seung
Winner-take-all networks have been proposed to underlie many of the brain’s fundamental computational abilities. However, not much is known about how to extend the grouping of potential winners in...
Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition (2002)
Xiaohui Xie, H. Sebastian Seung
Winner-take-all networks have been proposed to underlie many of the brain's fundamental computation abilities. However...
Equivalence of Backpropagation and Contrastive Hebbian Learning in a Layered Network (2002)
Xiaohui Xie, H. Sebastian Seung
Introduction Backpropagation and contrastive Hebbian learning (CHL) are two supervised learning algorithms for training networks with hidden neurons. They are of interest, because they are generally...
Learning winner-take-all competition between groups of neurons in lateral inhibition networks (2001)
Xiaohui Xie, Richard Hahnloser, H. Sebastian Seung
It has long been known that lateral inhibition in neural networks can lead to a winner-take-all competition, so that only a single neuron is active at a steady state. Here we show how to organize...
Learning winner-take-all competition between groups of neurons in lateral inhibition networks (2001)
Xiaohui Xie, Richard Hahnloser, H. Sebastian Seung
neurons in lateral inhibitory networks
Learning winner-take-all competition between groups of neurons in lateral inhibition networks (2001)
Xiaohui Xie, Richard Hahnloser, H. Sebastian Seung
It has long been known that lateral inhibition in neural networks can lead to a winner-take-all competition, so that only a single neuron is active at a steady state. Here we show how to organize...
Learning winner-take-all competition between groups of neurons in lateral inhibition networks (2001)
Xiaohui Xie, Richard Hahnloser, H. Sebastian Seung
It has long been known that lateral inhibition in neural networks can lead to a winner-take-all competition, so that only a single neuron is active at a steady state. Here we show how to organize...
Spike-Based Learning Rules and Stabilization of Persistent Neural Activity (2000)
Xiaohui Xie, H. Sebastian Seung
We analyze the conditions under which synaptic learning rules based on action potential timing can be approximated by learning rules based on firing rates. In particular, we consider a form of...
Spike-Based Learning Rules and Stabilization of (2000)
Persistent Neural Activity, Xiaohui Xie, H. Sebastian Seung
We analyze the conditions under which synaptic learning rules based on action potential timing can be approximated by learning rules based on firing rates. In particular, we consider a form of...
Mootha, Vamsi K., Handschin, Christoph, Arlow, Dan, Xie, Xiaohui, St. Pierre, Julie, Sihag, Smita, ...
Recent studies have shown that genes involved in oxidative phosphorylation (OXPHOS) exhibit reduced expression in skeletal muscle of diabetic and prediabetic humans. Moreover, these changes may be...
A large family of ancient repeat elements in the human genome is under strong selection
Kamal, Michael, Xie, Xiaohui, Lander, Eric S.
Although conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, they remain poorly understood. CNEs seem to be largely unique, with no...
Mootha, Vamsi K., Handschin, Christoph, Arlow, Dan, Xie, Xiaohui, St. Pierre, Julie, Sihag, Smita, ...
Recent studies have shown that genes involved in oxidative phosphorylation (OXPHOS) exhibit reduced expression in skeletal muscle of diabetic and prediabetic humans. Moreover, these changes may be...
A large family of ancient repeat elements in the human genome is under strong selection
Kamal, Michael, Xie, Xiaohui, Lander, Eric S.
Although conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, they remain poorly understood. CNEs seem to be largely unique, with no...
A family of conserved noncoding elements derived from an ancient transposable element
Xie, Xiaohui, Kamal, Michael, Lander, Eric S.
The evolutionary origin of the conserved noncoding elements (CNEs) in the human genome remains poorly understood but may hold important clues to their biological functions. Here, we report the...
A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands
Giallourakis, Cosmas, Cao, Zhifang, Green, Todd, Wachtel, Heather, Xie, Xiaohui, Lopez-Illasaca, Marco, ...
PDZ domain-containing proteins and their interaction partners are mutated in numerous human diseases and function in complexes regulating epithelial polarity, ion channels, cochlear hair cell...
Using comparative sequence analysis, a network among REST, CREB and brain-related miRNAs is propsed to mediate neuronal gene expression.
Xie, Xiaohui, Mikkelsen, Tarjei S., Gnirke, Andreas, Lindblad-Toh, Kerstin, Kellis, Manolis, Lander, Eric S.
Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Experimental evidence suggests that...
Distinguishing protein-coding and noncoding genes in the human genome
Clamp, Michele, Fry, Ben, Kamal, Mike, Xie, Xiaohui, Cuff, James, Lin, Michael F., ...
Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ≈24,500 putative...
Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains
Ku, Manching, Koche, Richard P., Rheinbay, Esther, Mendenhall, Eric M., Endoh, Mitsuhiro, Mikkelsen, Tarjei S., ...
In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the...
Identifying novel constrained elements by exploiting biased substitution patterns
Garber, Manuel, Guttman, Mitchell, Clamp, Michele, Zody, Michael C., Friedman, Nir, Xie, Xiaohui
Motivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved...
Incorporating Existing Network Information into Gene Network Inference
Christley, Scott, Nie, Qing, Xie, Xiaohui
One methodology that has met success to infer gene networks from gene expression data is based upon ordinary differential equations (ODE). However new types of data continue to be produced, so it is...