complex web-like structures describe a wide variety of systems of high technological and intellectual importance. For example, the cell is best described as a complex network of proteins and small...
Constraint-based network model of pathogen–immune system interactions (2009)
Juilee Thakar, Assieh Saadatpour-moghaddam, Eric T. Harvill, Réka Albert
Pathogenic bacteria such as Bordetella bronchiseptica modulate host immune responses to enable their establishment and persistence; however, the immune response is generally successful in clearing...
the effect of cell division on expression patterns of the segment polarity genes
Sarah M. Assmann, Ph. D, Réka Albert, Ph. D, Sarah M. Assmann
A major aim of systems biology is the study of the inter-relationships found within and between large biological datasets. Here we describe one systems biology method, in which the tools of network...
Journal of Cell Science Commentary Scale-free networks in cell biology (2009)
A cell’s behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory...
Anshuman Gupta, Costas D. Maranas, Réka Albert
Figure S1 shows the co-expression network at the chosen similarity threshold value of 0.90. The network was composed of 262 nodes connected by a total of 530 edges while the remaining 484 nodes were...
Boolean network simulations for life scientists (2008)
Albert, István, Thakar, Juilee, Li, Song, Zhang, Ranran, Albert, Réka
Abstract Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an...
Isabella M. Cattadori, Réka Albert, Brian Boag, Isabella M. Cattadori
myxoma poxvirus, age-intensity relationship, TH1-TH2 paradigm.
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Anshuman Gupta, Costas D. Maranas, Réka Albert
Vol. 22 no. 2 2006, pages 209–214 doi:10.1093/bioinformatics/bti780 Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites
Journal of Cell Science Commentary Scale-free networks in cell biology (2008)
A cell’s behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory...
Sema Kachalo, Ranran Zhang, Eduardo Sontag, Réka Albert, Bhaskar Dasgupta
Summary: We present a software for combined synthesis, inference and simplification of signal transduction networks. The main idea of our method lies in representing observed indirect causal...
Kachalo, Sema, Zhang, Ranran, Sontag, Eduardo, Albert, Réka, DasGupta, Bhaskar
Summary: We present a software for combined synthesis, inference and simplification of signal transduction networks. The main idea of our method lies in representing observed indirect causal...
Dynamic Receptor Team Formation Can Explain the High Signal (2007)
Transduction Gain In, Réka Albert, Yu-wen Chiu, Hans G. Othmer
Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of...
Modeling Systems-Level Regulation of Host Immune Responses (2007)
Juilee Thakar, Mylisa Pilione, Girish Kirimanjeswara, Eric T. Harvill, Réka Albert
Many pathogens are able to manipulate the signaling pathways responsible for the generation of host immune responses. Here we examine and model a respiratory infection system in which disruption of...
Réka Albert, Riccardo Dondi, Eduardo Sontag, Kelly Westbrooks, Bhaskar Dasgupta, Sema Kachalo, ...
In this paper we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal relationships as...
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence (2007)
Réka Albert, Bhaskar Dasgupta, Riccardo Dondi, Eduardo Sontag, Er Zelikovsky, Kelly Westbrooks
Abstract. In this paper we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal...
Réka Albert, Riccardo Dondi, Eduardo Sontag, Kelly Westbrooks, Bhaskar Dasgupta, Sema Kachalo, ...
In this paper we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal relationships as...
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence (2007)
Réka Albert, Bhaskar Dasgupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Er Zelikovsky, ...
Abstract. In this paper we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal...
A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence (2007)
Réka Albert, Bhaskar Dasgupta, Riccardo Dondi, Sema Kachalo, Eduardo Sontag, Alexander Zelikovsky, ...
In this paper, we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal relationships...
Song Li, Sarah M. Assmann, Réka Albert
Plants both lose water and take in carbon dioxide through microscopic stomatal pores, each of which is regulated by a surrounding pair of guard cells. During drought, the plant hormone abscisic acid...
Marilyn Gunner, Peter Jung, Dean Astumian, James Glazier, Shirley Chan, Aps Councilor, ...
In this Issue
Réka Albert, Riccardo Dondi, Bhaskar Dasgupta, Eduardo Sontag
In this paper we consider the p-ary transitive reduction (TRp) problem where p> 0 is an integer; for p = 2 this problem arises in inferring a sparsest possible (biological) signal transduction...
Gupta, Anshuman, Maranas, Costas D., Albert, Réka
Motivation: In this paper, we present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic...
E. Sontag’s research was partly supported by NSF grants EIA 0205116 and DMS-0504557. (2005)
Réka Albert, Bhaskar Dasgupta, Riccardo Dondi, Eduardo Sontag, R. Albert, B. Dasgupta, ...
Abstract In this paper we consider the p-ary transitive reduction (TRp) problem where p>0 is an integer; for p = 2 this problem arises in inferring a sparsest possible (biological) signal...
Gupta, Anshuman, Maranas, Costas D., Albert, Réka
Motivation: In this paper, we present a novel framework for inferring regulatory and sequence-level information from gene co-expression networks. The key idea of our methodology is the systematic...
Dynamic receptor team formation can explain the high signal transduction (2004)
Réka Albert, Yu-wen Chiu, Hans G. Othmer
ABSTRACT Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the...
Boolean modeling of genetic regulatory networks (2004)
Abstract. Biological systems form complex networks of interaction on several scales, ranging from the molecular to the ecosystem level. On the subcellular scale, interaction between genes and gene...
Conserved network motifs allow protein-protein interaction prediction (2004)
Motivation: High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale...
Conserved network motifs allow protein-protein interaction prediction (2004)
Motivation: High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale...
Conserved network motifs allow protein-protein interaction prediction (2004)
Motivation: High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale...
Statistical mechanics of complex networks,” cond-mat/0106096 (2001)
Réka Albert, Albert-lászló Barabási
Complex networks describe a wide range of systems in nature and society, much quoted examples
Scale-free characteristics of random networks: The topology of the world wide web (1999)
Albert-László Barabási, Réka Albert, Hawoong Jeong
The world wide web forms a large directed graph, whose vertices are documents and edges are links pointing from one document to another. Here we demonstrate that despite its apparent random...
Maximum angle of stability in wet and dry spherical granular media (1997)
Réka Albert, István Albert, Daniel Hornbaker, Peter Schiffer, Albert-lászló Barabási
We demonstrate that stability criteria can be used to calculate the maximum angle of stability � m of a granular medium composed of spherical particles in three dimensions and circular disks in two...
Dynamic Receptor Team Formation Can Explain the High Signal Transduction Gain in Escherichia coli
Albert, Réka, Chiu, Yu-wen, Othmer, Hans G.
Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of...
Li, Song, Assmann, Sarah M, Albert, Réka
Plants both lose water and take in carbon dioxide through microscopic stomatal pores, each of which is regulated by a surrounding pair of guard cells. During drought, the plant hormone abscisic acid...
Dynamic Receptor Team Formation Can Explain the High Signal Transduction Gain in Escherichia coli
Albert, Réka, Chiu, Yu-wen, Othmer, Hans G.
Evolution has provided many organisms with sophisticated sensory systems that enable them to respond to signals in their environment. The response frequently involves alteration in the pattern of...
Li, Song, Assmann, Sarah M, Albert, Réka
Plants both lose water and take in carbon dioxide through microscopic stomatal pores, each of which is regulated by a surrounding pair of guard cells. During drought, the plant hormone abscisic acid...
Modeling Systems-Level Regulation of Host Immune Responses
Thakar, Juilee, Pilione, Mylisa, Kirimanjeswara, Girish, Harvill, Eric T, Albert, Réka
Many pathogens are able to manipulate the signaling pathways responsible for the generation of host immune responses. Here we examine and model a respiratory infection system in which disruption of...
Bacteriophage-mediated competition in Bordetella bacteria
Joo, Jaewook, Gunny, Michelle, Cases, Marisa, Hudson, Peter, Albert, Réka, Harvill, Eric
Apparent competition between species is believed to be one of the principal driving forces that structure ecological communities, although the precise mechanisms have yet to be characterized. Here we...
Boolean network simulations for life scientists
Albert, István, Thakar, Juilee, Li, Song, Zhang, Ranran, Albert, Réka
Modern life sciences research increasingly relies on computational solutions, from large scale data analyses to theoretical modeling. Within the theoretical models Boolean networks occupy an...
Cattadori, Isabella M, Albert, Réka, Boag, Brian
One of the conditions that can affect host susceptibility and parasite transmission is the occurrence of concomitant infections. Parasites interact directly or indirectly within an individual host...
Network model of survival signaling in large granular lymphocyte leukemia
Zhang, Ranran, Shah, Mithun Vinod, Yang, Jun, Nyland, Susan B., Liu, Xin, Yun, Jong K., ...
T cell large granular lymphocyte (T-LGL) leukemia features a clonal expansion of antigen-primed, competent, cytotoxic T lymphocytes (CTL). To systematically understand signaling components that...
Studying the effect of cell division on expression patterns of the segment polarity genes
Chaves, Madalena, Albert, Réka
The segment polarity gene family, and its gene regulatory network, is at the basis of Drosophila embryonic development. The network's capacity for generating and robustly maintaining a specific gene...