arXiv subjects

Kai Wang

Publications and source records attributed to Kai Wang.

890 records · Page 50Linked to original sources

arXiv2006

Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes

Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription factor activation by phosphorylation and acetylation, formation of active complexes with one or more co-factors, and mRNA/protein degradation and stabilization processes. This paper presents a first step towards the systematic, genome-wide computational inference of genes that modulate the interactions of specific transcription factors at the post-transcriptional level. The method uses a statistical test based on changes in the mutual information between a transcription factor and each of its candidate targets, conditional on the expression of a third gene. The approach was first validated on a synthetic network model, and then tested in the context of a mammalian cellular system. By analyzing 254 microarray expression profiles of normal and tumor related human B lymphocytes, we investigated the post transcriptional modulators of the MYC proto-oncogene, an important transcription factor involved in tumorigenesis. Our method discovered a set of 100 putative modulator genes, responsible for modulating 205 regulatory relationships between MYC and its targets. The set is significantly enriched in molecules with function consistent with their activities as modulators of cellular interactions, recapitulates established MYC regulation pathways, and provides a notable repertoire of novel regulators of MYC function. The approach has broad applicability and can be used to discover modulators of any other transcription factor, provided that adequate expression profile data are available.

q-bio.MN↗

arXiv2005

Secure Communication Scheme Based on Asymptotic Model of Deterministic Randomness

We propose a new cryptosystem by combing the Lissajous map, which is the asymptotic model of deterministic randomness, with the one-way coupled map lattice (OCML) system. The key space, the encryption efficiency, and the security are investigated. We find that the parameter sensitivity can reach the computational precision when the system size is only three, all the lattice outputs can be treated as key stream parallelly, and the system is resistible against various attacks including the differential-like chosen cipher attack. The findings of this paper are a strong indication of the importance of deterministic randomness in secure communications.

nlin.CD↗

arXiv2004

Conditional Network Analysis Identifies Candidate Regulator Genes in Human B Cells

Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic phenotypes. Existing methods for such "reverse engineering" of genetic networks from microarray expression data have been successful only in prokaryotes (E. coli) and lower eukaryotes (S. cerevisiae) with relatively simple genomes. Additionally, they have mostly attempted to reconstruct average properties about the network connectivity without capturing the highly conditional nature of the interactions. In this paper we extend the ARACNE algorithm, which we recently introduced and successfully applied to the reconstruction of whole-genome transcriptional networks from mammalian cells, precisely to link the existence of specific network structures to the expression or lack thereof of specific regulator genes. This is accomplished by analyzing thousands of alternative network topologies generated by constraining the data set on the presence or absence of putative regulator genes. By considering interactions that are consistently supported across several such constraints, we identify many transcriptional interactions that would not have been detectable by the original method. By selecting genes that produce statistically significant changes in network topology, we identify novel candidate regulator genes. Further analysis shows that transcription factors, kinases, phosphatases, and other gene families known to effect biochemical interactions, are significantly overrepresented among the set of candidate regulator genes identified in silico, indirectly supporting the validity of the approach.

q-bio.MN↗

arXiv2004

Hidden symmetries and their implications for Particle Physics

In this thesis, we study the hidden symmetries in the SM and also use discrete gauge symmetries as model building tools to solve various problems in the SM as well as the MSSM, such as R-parity, mu-term, stabilizing the axion solutions, etc. The flavor independent non-supersymmetric SM at the renormalizable level has a discrete Z_3 gauge symmetry known as baryon parity. It is anomaly free at the discrete level as a result of the existence of three generations. The symmetry can effectively act as the Baryon number up to the ΔB=3 mod 3 level which is also consistent with the prediction from non-perturbative processes corrections in the SM, such as electroweak instanton and sphaleron processes. This symmetry is not consistent with the simple GUTs since those theories explicitly break it. Thus this baryon parity provides a strong hint for new physics like GUTs. Quantum mechanically, we estimate the triple nucleon decay rate which is predicted by the existence of this symmetry. We find a simple U(1) realization with the presence of right-handed neutrinos, from which this baryon parity can naturally emerge. Gauged R-parity is studied in the following chapter. We also study various different approaches to the mu-term problem via a symmetry classification. One explicit example in terms of a Z_4 subgroup of the anomalous U(1) symmetry is given. Another solution arises from a SUSY version of QCD invisible axion. Discrete flavor gauge symmetries are discussed to explain the observed hierarchy fermion masses. D-term splitting problem can then be avoided. In the last part, we show how to use discrete gauge symmetries to stabilize the QCD invisible axion solutions, for both DFSZ and KSVZ invisible axion models.

hep-ph↗

arXiv2004

Stabilizing the axion and a natural solution to the mu problem of supersymmetry

The axion solution to the strong CP problem makes use of a global Peccei-Quinn (PQ) U(1) symmetry which is susceptible to violations from quantum gravitational effects. We show explicitly how discrete gauge symmetries can protect the axion from such violations. PQ symmetry emerges as an accidental global symmetry from discrete gauge symmetries which are subgroups of the anomalous U(1) of string origin. We also show how the Dine-Fischler-Srednicki-Zhitnitsky (DFSZ) axion model provides a natural solution to mu problem of supersymmetry as mu ~ M_{SUSY} ~ M^2_{PQ}/M_{Pl}.

hep-ph↗

arXiv2003

Gauged Baryon Parity and Nucleon Stability

We show that the Standard Model Lagrangian, including small neutrino masses, has an anomaly-free discrete Z_6 symmetry. This symmetry can emerge naturally from I^{3}_{R}+L_i+L_j-2L_k gauge symmetry (L_i is the i-th lepton number) and ensure the stability of the nucleon even when the threshold of new physics Λis low. All ΔB=1 and ΔB=2 (B is the baryon number) effective operators are forbidden by the Z_6 symmetry. ΔB=3 operators are allowed, but they arise only at dimension 15. We estimate the lifetime for "triple nucleon decay" resulting from these operators and find that Λcan be as low as 10^2 GeV. We suggest a simple mechanism for realizing reasonable neutrino masses and mixings even with such a low scale for Λ.

hep-ph↗

arXiv2002

Stabilizing the Axion by Discrete Gauge Symmetries

The axion solution to the strong CP problem makes use of a global Peccei-Quinn U(1) symmetry which is susceptible to violations from quantum gravitational effects. We show how discrete gauge symmetries can protect the axion from such violations. PQ symmetry emerges as an approximate global symmetry from discrete gauge symmetries. Simple models based on Z_N symmetries with N =11,12, etc are presented realizing the DFSZ axion and the KSVZ axion. The discrete gauge anomalies are cancelled by a discrete version of the Green-Schwarz mechanism. In the supersymmetric extension our models provide a natural link between the SUSY breaking scale, the axion scale, and the SUSY-preserving μterm.

hep-ph↗

arXiv2002

Natural R-Parity, μ-term, and Fermion Mass Hierarchy From Discrete Gauge Symmetries

In the minimal supersymmetric Standard Model with seesaw neutrino masses we show how R-parity can emerge naturally as a discrete gauge symmetry. The same discrete symmetry explains the smallness of the μ-term (the Higgsino mass parameter) via the Giudice--Masiero mechanism. The discrete gauge anomalies are cancelled by a discrete version of the Green--Schwarz mechanism. The simplest symmetry group is found to be Z_4 with a charge assignment that is compatible with grand unification. Several other Z_N gauge symmetries are found for N=10,12,18,36 etc, with some models employing discrete anomaly cancellation at higher Kac-Moody levels. Allowing for a flavor structure in Z_N, we show that the same gauge symmetry can also explain the observed hierarchy in the fermion masses and mixings.

hep-ph↗