12041016
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes
UNLABELLED
Promoter Extraction from GenBank (PEG) extracts promoter sequences for large sets of genes using information present in GenBank. For a gene whose promoter sequence is not found, PEG will attempt to extract promoter sequences of the orthologous genes instead.


AVAILABILITY
It is freely available to academic users at ftp://cshl.org/pub/science/mzhanglab/theresa/.


CONTACT
zhangt@cshl.org; mzhang@cshl.org
1069327
DWE: Discriminating Word Enumerator
MOTIVATION
Tissue-specific transcription factor binding sites give insight into tissue-specific transcription regulation.


RESULTS
We describe a word-counting-based tool for de novo tissue-specific transcription factor binding site discovery using expression information in addition to sequence information. We incorporate tissue-specific gene expression through gene classification to positive expression and repressed expression. We present a direct statistical approach to find overrepresented transcription factor binding sites in a foreground promoter sequence set against a background promoter sequence set. Our approach naturally extends to synergistic transcription factor binding site search. We find putative transcription factor binding sites that are overrepresented in the proximal promoters of liver-specific genes relative to proximal promoters of liver-independent genes. Our results indicate that binding sites for hepatocyte nuclear factors (especially HNF-1 and HNF-4) and CCAAT/enhancer-binding protein (C/EBPbeta) are the most overrepresented in proximal promoters of liver-specific genes. Our results suggest that HNF-4 has strong synergistic relationships with HNF-1, HNF-4 and HNF-3beta and with C/EBPbeta.


AVAILABILITY
Programs are available for use over the Web at http://rulai.cshl.edu/tools/dwe.
17846455
Systematic Design of Original and Modified Mastrovito Multipliers for General Irreducible Polynomials
This paper considers the design of bit-parallel dedicated finite field multipliers using standard basis. An explicit algorithm is proposed for efficient construction of Mastrovito product matrix, based on which we present a systematic design of Mastrovito multiplier applicable to GF(2/sup m/) generated by an arbitrary irreducible polynomial. This design effectively exploits the spatial correlation of elements in Mastrovito product matrix to reduce the complexity. Using a similar methodology, we propose a systematic design of modified Mastrovito multiplier, which is suitable for GF(2/sup m/) generated by high-Hamming weight irreducible polynomials. For both original and modified Mastrovito multipliers, the developed multiplier architectures are highly modular, which is desirable for VLSI hardware implementation. Applying the proposed algorithm and design approach, we study the Mastrovito multipliers for several special irreducible polynomials, such as trinomial and equally-spaced-polynomial, and the obtained complexity results match the best known results. Moreover, we have discovered several new special irreducible polynomials which also lead to low-complexity Mastrovito multipliers.
2589663
Hardware assisted control flow obfuscation for embedded processors
With more applications being deployed on embedded platforms, software protection becomes increasingly important. This problem is crucial on embedded systems like financial transaction terminals, pay-TV access-control decoders, where adversaries may easily gain full physical accesses to the systems and critical algorithms must be protected from being cracked. However, as this paper points out that protecting software with either encryption or obfuscation cannot completely preclude the control flow information from being leaked. Encryption has been widely studied and employed as a traditional approach for software protection, however, the control flow information is not 100% hidden with solely encrypting the code. On the other hand, pure software-based obfuscation has been proved inefficient to protect software due to its lack of theoretical foundation and considerable performance overhead introduced by complicated transformations. Moreover, even though obfuscation can prevent static reverse engineering, attacker can still successfully bypass the obfuscation by monitoring the dynamic program execution.To address all of these shortcomings, this paper presents a hardware assisted obfuscation technique that is capable of obfuscating the control flow information dynamically. Dynamic obfuscation changes memory access sequence on-the-fly and conceals recurrent instruction access sequences from being identified. Our scheme makes it provably difficult for the attacker to extract any useful information. Our results show that a high-level security protection is possible with only minor performance penalty. Finally, we show that our scheme can be implemented on embedded systems with very little hardware overhead.
10193683
Using Branch Correlation to Identify Infeasible Paths for Anomaly Detection
In this paper, we propose a system called infeasible path detection system (IPDS) to combat memory tampering attacks causing invalid program control flows. In our system, the compiler analyzes correlations between branches and then the analyzed information is conveyed to the runtime system. The runtime system detects dynamic infeasible program paths by combining compiler determined information with runtime information to check the legality of the path taken during execution. IPDS achieves a zero false positive rate and can detect a high percentage of memory tampering for many attacks in which the tampering actually causes a change in control flow. Moreover, IPDS only incurs a modest amount of hardware resource and negligible performance penalty
206626032
Association Rules
New association rules are presented for measure of association relationships between patterns. The new association rules are shown to not only measure three well-known association relationships correctly, but also satisfy other criteria for correct measure of association. Comparison with other measures is discussed both theoretically and experimentally. Applications in supervised mining of association rules and in pattern-driven multidimensional pattern analysis are presented.
9131829
Memory Protection through Dynamic Access Control
Current anomaly detection schemes focus on control flow monitoring. Recently, Chen et al. discovered that a large category of attacks tamper program data but do not alter control flows. These attacks are not only realistic, but are also as important as classical attacks tampering control flows. Detecting these attacks is a critical issue but has received little attention so far. In this work, we propose an intrusion detection scheme with both compiler and micro-architecture support detecting data tampering directly. The compiler first identifies program regions in which the data should not be modified as per program semantics. Then the compiler performs an analysis to determine the conditions for modification of variables in different program regions and conveys this information to the hardware and the hardware checks the data accesses based on the information. If the compiler asserts that the data should not be modified but there is an attempt to do so at runtime, an attack is detected. The compiler starts with a basic scheme achieving maximum data protection but such a scheme also suffers from high performance overhead. We then attempt to reduce the performance overhead through different optimization techniques. Our experiments show that our scheme achieves strong memory protection with tight control over the performance degradation. Thus, our major contribution is to provide an efficient scheme to detect data tampering while minimizing the overhead