A. Agung Julius, Ádám Halász, M. Selman Sakar, Student Member, Harvey Rubin, Vijay Kumar, ...
Abstract—In this paper, we present a comprehensive framework for stochastic modeling, model abstraction, and controller design for a biological system. The first half of the paper concerns modeling...
analysis of Escherichia (2008)
Marcin Imieliński, Călin Belta, Ádám Halász, Harvey Rubin
Vol. 21 no. 9 2005, pages 2008–2016 doi:10.1093/bioinformatics/bti245 Investigating metabolite essentiality through genome-scale
Marcin Imielinski, Calin Belta, Adam Halasz, Harvey Rubin
network reveals novel growth media
A PCR-based Protocol for In Vitro Selection of (2008)
Non-crosshybridizing Oligonucleotides, Russell Deaton, Junghuei Chen, Hong Bi, Max Garzon, Harvey Rubin, ...
Abstract. DNA computing often requires oligonucleotides that do not produce erroneous cross-hybridizations. By using in vitro evolution, huge libraries of non-crosshybridizing oligonucleotides might...
MODELING AND ANALYZING BIOMOLECULAR NETWORKS (2007)
George J. Pappas, Harvey Rubin, Jonathan Schug
The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the...
High-Confidence Medical Device Software and Systems (2006)
Lee, Insup, Pappas, George J, Cleaveland, Rance, Hatcliff, John, Krogh, Bruce H, Lee, Peter, ...
Given the shortage of caregivers and the increase in an aging US population, the future of US healthcare quality does not look promising and definitely is unlikely to be cheaper. Advances in health...
Imielinski, Marcin, Belta, Calin, Halász, Ádám, Rubin, Harvey
Motivation: A phenotype mechanism is classically derived through the study of a set of mutants and comparison of their biochemical capabilities. One method of comparing mutant capabilities is to...
Imieliski, Marcin, Belta, Clin, Halász, Ádám, Rubin, Harvey
Motivation: A phenotype mechanism is classically derived through the study of a set of mutants and comparison of their biochemical capabilities. One method of comparing mutant capabilities is to...
Pearce, Mary C., Cabrita, Lisa D., Rubin, Harvey, Gore, Michael G., Bottomley, Stephen P.
The native serpin fold is metastable and possesses the inherent ability to convert into more stable, but inactive, conformations. In order to understand why serpins attain the native fold instead of...
UNIVERSITY OF PENNSYLVANIA- SCHOOL OF MEDICINE Curriculum Vitae (2004)
Postgraduate Training and Fellowship Appointments:
Understanding the bacterial stringent response using reachability analysis of hybrid systems (2004)
Călin Belta, Peter Finin, Ádám M. Halász, R. Vijay Kumar, Harvey Rubin
Abstract. In this paper we model coupled genetic and metabolic networks as hybrid systems. The vector fields are multi- affine, i.e., have only product- type nonlinearities to accommodate chemical...
Ribonucleotide Reductases, Stephanie S. Dawes, Digby F. Warner, Liana Tsenova, Juliano Timm, John D. Mckinney, ...
Mycobacterium tuberculosis, the causative agent of tuberculosis, possesses a class Ib ribonucleotide reductase (RNR), encoded by the nrdE and nrdF2 genes, in addition to a putative class II RNR,...
Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks (2002)
Alur, Rajeev, Belta, Calin, Ivancic, Franjo, Kumar, R. Vijay, Rubin, Harvey, Schug, Jonathan, ...
In this paper we introduce our new tool BIOSKETCHPAD that allows visual programming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks...
Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks (2002)
Alur, Rajeev, Belta, Calin, Ivancic, Franjo, Kumar, Vijay, Rubin, Harvey, Schug, Jonathan, ...
In this paper we introduce our new tool BIOSKETCHPAD that allows visual progamming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks...
Modeling and Analyzing Biomolecular Networks (2002)
Alur, Rajeev, Belta, Calin, Kumar, R. Vijay, Mintz, Max L, Pappas, George J, Rubin, Harvey, ...
The authors argue for the need to model and analyze biological networks at molecular and cellular levels. They propose a computational toolbox for biologists. Central to their approach is the...
Belta, Calin, Schug, Jonathan, Dang, Thao, Kumar, R. Vijay, Pappas, George J, Rubin, Harvey, ...
This paper addresses the mathematical modeling and analysis of the quorum sensing system found in unicellular bacteria that exhibit bioluminescence. The luminescence is governed by the expression of...
Hybrid modeling and simulation of biomolecular networks (2001)
Rajeev Alur, Calin Belta, Franjo Ivančić, Vijay Kumar, Max Mintz, Harvey Rubin, ...
Abstract. In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control...
Hybrid modeling and simulation of biomolecular networks (2001)
Rajeev Alur, Calin Belta, Franjo Ivanifi, Vijay Kumar, Max Mintz, Harvey Rubin, ...
Abstract. In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by a network of chemical reactions in which regulatory proteins can control...
Joshua P. Klein, Thomas H. Leete, Harvey Rubin
Energy dissipation associated with logic operations imposes a fundamental physical limit on computation and is generated by the entropic cost of information erasure, which is a consequence of...
Joshua P. Klein, Thomas H. Leete, Harvey Rubin
Energy dissipation associated with logic operations imposes a fundamental physical limit on computation and is generated by the entropic cost of information erasure, which is a consequence of...
On the conformation of single stranded RNA. (1974)
Thesis (Ph.D. in Molecular Biology)--Graduate School of Arts and Sciences, University of Pennsylvania, 1974.
Characterization of the cydAB-Encoded Cytochrome bd Oxidase from Mycobacterium smegmatis
Kana, Bavesh D., Weinstein, Edward A., Avarbock, David, Dawes, Stephanie S., Rubin, Harvey, Mizrahi, Valerie
The cydAB genes from Mycobacterium smegmatis have been cloned and characterized. The cydA and cydB genes encode the two subunits of a cytochrome bd oxidase belonging to the widely distributed family...
The Stringent Response of Mycobacterium tuberculosis Is Required for Long-Term Survival
Primm, Todd P., Andersen, Susan J., Mizrahi, Valerie, Avarbock, David, Rubin, Harvey, Barry, Clifton E.
The stringent response utilizes hyperphosphorylated guanine [(p)ppGpp] as a signaling molecule to control bacterial gene expression involved in long-term survival under starvation conditions. In...
Dahl, John L., Kraus, Carl N., Boshoff, Helena I. M., Doan, Bernard, Foley, Korrie, Avarbock, David, ...
Long-term survival of nonreplicating Mycobacterium tuberculosis (Mtb) is ensured by the coordinated shutdown of active metabolism through a broad transcriptional program called the stringent...
Dawes, Stephanie S., Warner, Digby F., Tsenova, Liana, Timm, Juliano, McKinney, John D., Kaplan, Gilla, ...
Mycobacterium tuberculosis, the causative agent of tuberculosis, possesses a class Ib ribonucleotide reductase (RNR), encoded by the nrdE and nrdF2 genes, in addition to a putative class II RNR,...
Inhibitors of type II NADH:menaquinone oxidoreductase represent a class of antitubercular drugs
Weinstein, Edward A., Yano, Takahiro, Li, Lin-Sheng, Avarbock, David, Avarbock, Andrew, Helm, Douglas, ...
Mycobacterium tuberculosis (Mtb) is an obligate aerobe that is capable of long-term persistence under conditions of low oxygen tension. Analysis of the Mtb genome predicts the existence of a branched...
Matsoso, Limenako G., Kana, Bavesh D., Crellin, Paul K., Lea-Smith, David J., Pelosi, Assunta, Powell, David, ...
The aerobic electron transport chain in Mycobacterium smegmatis can terminate in one of three possible terminal oxidase complexes. The structure and function of the electron transport pathway leading...
Characterization of the cydAB-Encoded Cytochrome bd Oxidase from Mycobacterium smegmatis
Kana, Bavesh D., Weinstein, Edward A., Avarbock, David, Dawes, Stephanie S., Rubin, Harvey, Mizrahi, Valerie
The cydAB genes from Mycobacterium smegmatis have been cloned and characterized. The cydA and cydB genes encode the two subunits of a cytochrome bd oxidase belonging to the widely distributed family...
The Stringent Response of Mycobacterium tuberculosis Is Required for Long-Term Survival
Primm, Todd P., Andersen, Susan J., Mizrahi, Valerie, Avarbock, David, Rubin, Harvey, Barry, Clifton E.
The stringent response utilizes hyperphosphorylated guanine [(p)ppGpp] as a signaling molecule to control bacterial gene expression involved in long-term survival under starvation conditions. In...
Dahl, John L., Kraus, Carl N., Boshoff, Helena I. M., Doan, Bernard, Foley, Korrie, Avarbock, David, ...
Long-term survival of nonreplicating Mycobacterium tuberculosis (Mtb) is ensured by the coordinated shutdown of active metabolism through a broad transcriptional program called the stringent...
Dawes, Stephanie S., Warner, Digby F., Tsenova, Liana, Timm, Juliano, McKinney, John D., Kaplan, Gilla, ...
Mycobacterium tuberculosis, the causative agent of tuberculosis, possesses a class Ib ribonucleotide reductase (RNR), encoded by the nrdE and nrdF2 genes, in addition to a putative class II RNR,...
Inhibitors of type II NADH:menaquinone oxidoreductase represent a class of antitubercular drugs
Weinstein, Edward A., Yano, Takahiro, Li, Lin-Sheng, Avarbock, David, Avarbock, Andrew, Helm, Douglas, ...
Mycobacterium tuberculosis (Mtb) is an obligate aerobe that is capable of long-term persistence under conditions of low oxygen tension. Analysis of the Mtb genome predicts the existence of a branched...
Matsoso, Limenako G., Kana, Bavesh D., Crellin, Paul K., Lea-Smith, David J., Pelosi, Assunta, Powell, David, ...
The aerobic electron transport chain in Mycobacterium smegmatis can terminate in one of three possible terminal oxidase complexes. The structure and function of the electron transport pathway leading...
Imieliński, Marcin, Belta, Calin, Rubin, Harvey, Halász, Ádam
A biochemical species is called producible in a constraints-based metabolic model if a feasible steady-state flux configuration exists that sustains its nonzero concentration during growth. Extreme...
Characterization of Nucleotide Pools as a Function of Physiological State in Escherichia coli▿
Buckstein, Michael H., He, Jian, Rubin, Harvey
Using a modified method that involves minimal manipulation of cells, we report new information about nucleotide pool sizes and changes throughout the Escherichia coli growth curve. Nucleotide pool...