Sequence-based prediction of protein-protein interactions by means of codon usage

A new approach based on similarity in codon usage is used to predict protein-protein interactions

Erratum: Thermodynamics of solid and liquid EAM metals: A variational study [J. Chem. Phys. 94, 5090 (1991)]

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70785/2/JCPSA6-95-8-6197-1.pd

Genome-wide computational identification of functional RNA elements in Trypanosoma brucei

<p>Abstract</p> <p>Background</p> <p>Post-transcriptional regulation of gene expression is the dominant regulatory mechanism in trypanosomatids as their mRNAs are transcribed from polycistronic units. A few <it>cis</it>-acting RNA elements in 3'-untranslated regions of mRNAs have been identified in trypanosomatids, which affect the mRNA stability or translation rate in different life stages of these parasites. Other functional RNAs (fRNAs) also play essential roles in these organisms. However, there has been no genome-wide analysis for identification of fRNAs in trypanosomatids.</p> <p>Results</p> <p>Functional RNAs, including non-coding RNAs (ncRNAs) and <it>cis</it>-acting RNA elements involved in post-transcriptional gene regulation, were predicted based on two independent computational analyses of the genome of <it>Trypanosoma brucei</it>. In the first analysis, the predicted candidate ncRNAs were identified based on conservation with the related trypanosomatid <it>Leishmania braziliensis</it>. This prediction had a substantially low estimated false discovery rate, and a considerable number of the predicted ncRNAs represented novel classes with unknown functions. In the second analysis, we identified a number of function-specific regulatory motifs, based on which we devised a classifier that can be used for homology-independent function prediction in <it>T. brucei</it>.</p> <p>Conclusion</p> <p>This first genome-wide analysis of fRNAs in trypanosomatids restricts the search space of experimental approaches and, thus, can significantly expedite the process of characterization of these elements. Our classifier for function prediction based on <it>cis</it>-acting regulatory elements can also, in combination with other methods, provide the means for homology-independent annotation of trypanosomatid genomes.</p

Monte Carlo simulation of structural and mechanical properties of crystal and bicrystal systems at finite temperature

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1983.MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCEBibliography: leaves 135-139.by Reza Najafabadi Farahani.Ph.D

Thermodynamic properties of metastable Ag‐Cu alloys

Copyright 1993 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The article originally appeared in Journal of Applied Physics 74, 3144 (1993) and may be found at http://jap.aip.org/resource/1/japiau/v74/i5/p3144_s1.The enthalpies of formation of metastable fcc Ag‐Cu solid solutions, produced by ball milling of elemental powders, were determined by differential scanning calorimetry. Experimental thermodynamic data for these metastable alloys and for the equilibrium phases are compared with both calculation of phase diagrams (CALPHAD) and atomistic simulation predictions. The atomistic simulations were performed using the free‐energy minimization method (FEMM). The FEMM determination of the equilibrium Ag‐Cu phase diagram and the enthalpy of formation and lattice parameters of the metastable solid solutions are in good agreement with the experimental measurements. CALPHAD calculations made in the same metastable regime, however, significantly overestimate the enthalpy of formation. Thus, the FEMM is a viable alternative approach for the calculation of thermodynamic properties of equilibrium and metastable phases, provided reliable interatomic potentials are available. The FEMM is also capable of determining such properties as the lattice parameter which are not available from CALPHAD calculations.  Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70470/2/JAPIAU-74-5-3144-1.pd

Systematic discovery of structural elements governing stability of mammalian messenger RNAs.

Decoding post-transcriptional regulatory programs in RNA is a critical step towards the larger goal of developing predictive dynamical models of cellular behaviour. Despite recent efforts, the vast landscape of RNA regulatory elements remains largely uncharacterized. A long-standing obstacle is the contribution of local RNA secondary structure to the definition of interaction partners in a variety of regulatory contexts, including--but not limited to--transcript stability, alternative splicing and localization. There are many documented instances where the presence of a structural regulatory element dictates alternative splicing patterns (for example, human cardiac troponin T) or affects other aspects of RNA biology. Thus, a full characterization of post-transcriptional regulatory programs requires capturing information provided by both local secondary structures and the underlying sequence. Here we present a computational framework based on context-free grammars and mutual information that systematically explores the immense space of small structural elements and reveals motifs that are significantly informative of genome-wide measurements of RNA behaviour. By applying this framework to genome-wide human mRNA stability data, we reveal eight highly significant elements with substantial structural information, for the strongest of which we show a major role in global mRNA regulation. Through biochemistry, mass spectrometry and in vivo binding studies, we identified human HNRPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1, also known as HNRNPA2B1) as the key regulator that binds this element and stabilizes a large number of its target genes. We created a global post-transcriptional regulatory map based on the identity of the discovered linear and structural cis-regulatory elements, their regulatory interactions and their target pathways. This approach could also be used to reveal the structural elements that modulate other aspects of RNA behaviour

Order-disorder transitions at and segregation to (001) Ni-Pt surfaces

Order-disorder transitions at and segregation to the (001) surface of Ni-Pt alloys have been investigated by a recently developed free energy simulation method, where the atomic interactions are described using the embedded atom method (EAM) potentials. On the Ni-rich side of the phase diagram, we observe a second order, order-disorder phase transition on the (001) surfaces at temperatures well above the bulk phase transition temperature. At the transition temperature, the first (002) atomic plane changes from a disordered plane to an ordered one with the c(2 x 2) pattern. The second (002) plane changes from a disordered plane to a nearly pure Ni plane. Subsequent planes retain their essentially bulk-like, disordered structure. We also observe first order, order-disorder surface phase transitions on the Pt-rich side of the phase diagram. At the transition temperatures, the first and third (002) planes become nearly pure Pt and the second plane becomes nearly pure Ni. The effect of the surface transitions on the thermodynamic properties of the surfaces, such as enthalpy and vibrational and configurational entropy, are also investigated. It is shown that the ordering surface transition upon cooling the Ni-rich sample is enthalpically driven. The present simulations also show the importance of including atomic vibrations in surface segregation studies. Atomic vibrations have been typically omitted in previous lattice gas descriptions of surface segregation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30837/1/0000499.pd