Yongyi Mao

Informatics Platform for Global Proteomic Profiling and Biomarker Discovery Using Liquid Chromatography-Tandem Mass Spectrometry

We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies, simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.

Rateless coding over fading channels

We propose a framework for communication over fading channels utilizing rateless codes. An implementation using fountain codes is simulated, demonstrating that such a scheme has advantages in efficiency, reliability and robustness over conventional fixed-rate codes, particularly when channel state information is not available at the transmitter.

Rateless Coding for Wireless Relay Channels

We propose a novel coding framework for wireless relay channels based on rateless codes. With a concrete Fountain-code implementation of this framework, we show that rateless codes are both robust and efficient when the channel state information is not available at the transmitters

A heuristic search for good low-density parity-check codes at short block lengths

For a given block length and given degree sequences of the underlying Tanner graph (TG), the ensemble of short low-density parity-check (LDPC) codes can have considerable variation in performance. We present an efficient heuristic method to find good LDPC codes based on what we define as the girth distribution of the TG. This method can be used effectively to design short codes for applications where delay and complexity are of major concern.

Eukaryotic Protein Domains as Functional Units of Cellular Evolution

Clustering proteins into groups on the basis of their domain compositions provides insight into protein evolution. Domains for Change Protein domains endow proteins with specific activities and the ability to interact with specific partners. Most protein domains occur in many proteins and most proteins have multiple domains, but the combinations of domains are far fewer than would be predicted, suggesting that there is evolutionary pressure that preserves certain domain combinations. Jin et al. use a proteome-wide clustering method to identify eukaryotic protein domain combinations that correlate with evolutionary change. Their analysis suggests that reciprocal interactions between a protein and its microenvironment constrain the repertoire of domains that control specific cellular functions. They analyzed the proteins in seven eukaryotic species and organized the domains into 1245 “domain clubs,” with the majority of clubs containing proteins with multiple distinct domains and proteins with rich interrelationships among members of different clubs. They grouped proteins on the basis of their domain clubs into functional trees and were able to place domains of unknown function into functional groups, as well as make predictions about the role domain evolution contributes to the evolution of protein function within a molecular environment, as well as to the evolution of molecular environments. Modular protein domains are functional units that can be modified through the acquisition of new intrinsic activities or by the formation of novel domain combinations, thereby contributing to the evolution of proteins with new biological properties. Here, we assign proteins to groups with related domain compositions and functional properties, termed “domain clubs,” which we use to compare multiple eukaryotic proteomes. This analysis shows that different domain types can take distinct evolutionary trajectories, which correlate with the conservation, gain, expansion, or decay of particular biological processes. Evolutionary jumps are associated with a domain that coordinately acquires a new intrinsic function and enters new domain clubs, thereby providing the modified domain with access to a new cellular microenvironment. We also coordinately analyzed the covalent and noncovalent interactions of different domain types to assess the molecular compartment occupied by each domain. This reveals that specific subsets of domains demarcate particular cellular processes, such as growth factor signaling, chromatin remodeling, apoptotic and inflammatory responses, or vesicular trafficking. We suggest that domains, and the proteins in which they reside, are selected during evolution through reciprocal interactions with protein domains in their local microenvironment. Based on this scheme, we propose a mechanism by which Tudor domains may have evolved to support different modes of epigenetic regulation and suggest a role for the germline group of mammalian Tudor domains in Piwi-regulated RNA biology.

Rateless coding for wireless relay channels

We propose a novel coding framework for wireless relay channels based on rateless codes. With a concrete Fountain-code implementation of this framework, we show that rateless codes are both robust and efficient when the channel state information is not available at the transmitters

A factor graph approach to link loss monitoring in wireless sensor networks

The highly stochastic nature of wireless environments makes it desirable to monitor link loss rates in wireless sensor networks. In a wireless sensor network, link loss monitoring is particularly supported by the data aggregation communication paradigm of network traffic: the data collecting node can infer link loss rates on all links in the network by exploiting whether packets from various sensors are received, and there is no need to actively inject probing packets for inference purposes. In this paper, we present a low complexity algorithmic framework for link loss monitoring based on the recent modeling and computational methodology of factor graphs. The proposed algorithm iteratively updates the estimates of link losses upon receiving (or detecting the loss of) recently sent packets by the sensors. The algorithm exhibits good performance and scalability, and can be easily adapted to different statistical models of networking scenarios. In particular, due to its low complexity, the algorithm is particularly suitable as a long-term monitoring facility.

Rateless Coding and Relay Networks

A framework for coding over relay channels using rateless codes is the intersection of two active areas of research in communications; namely relay networks and rateless coding. We demonstrate that there is a very natural and useful fit between these two areas and describe some design challenges and implementation considerations for this framework. The use of relays in wireless communication networks provide a new dimension to the design space of wireless networks that promises enhancements to both the coverage and throughput of the network. In its simplest form, a relay network is a collection of terminals that are able to transmit, receive, and possibly assist the reliable delivery of information from source terminals to destination terminals. Thus, communication of data through a wireless relay network is not required to be direct; it may pass through a number of other terminals, though direct communication from source to destination is not precluded. In fact, it is possible to simultaneously use single-hop, i.e., direct, and multihop communications paths.

On Rateless Coding over Fading Channels with Delay Constraints

We explore the use of rateless coding for communication over fading channels with delay constraints. Both quasi-static fading and block-fading channels are considered. When only the receiver has channel information, we show there exist rateless codes that are both reliable and efficient for every channel realization of such channels. We then apply these codes to a wireless streaming application with a sequence of playback deadlines. Rateless strategies demonstrate benefits in terms of throughput and outage probability compared to fixed-rate schemes

Normal Factor Graphs and Holographic Transformations

This paper stands at the intersection of two distinct lines of research. One line is “holographic algorithms,” a powerful approach introduced by Valiant for solving various counting problems in computer science; the other is “normal factor graphs,” an elegant framework proposed by Forney for representing codes defined on graphs. We introduce the notion of holographic transformations for normal factor graphs, and establish a very general theorem, called the generalized Holant theorem, which relates a normal factor graph to its holographic transformation. We show that the generalized Holant theorem on the one hand underlies the principle of holographic algorithms, and on the other hand reduces to a general duality theorem for normal factor graphs, a special case of which was first proved by Forney. In the course of our development, we formalize a new semantics for normal factor graphs, which highlights various linear algebraic properties that potentially enable the use of normal factor graphs as a linear algebraic tool.