Papers by Ruzbeh Tusserkani
BMC Systems Biology, 2015
Background: Understanding the mechanisms by which hundreds of diverse cell types develop from a s... more Background: Understanding the mechanisms by which hundreds of diverse cell types develop from a single mammalian zygote has been a central challenge of developmental biology. Conrad H. Waddington, in his metaphoric "epigenetic landscape" visualized the early embryogenesis as a hierarchy of lineage bifurcations. In each bifurcation, a single progenitor cell type produces two different cell lineages. The tristable dynamical systems are used to model the lineage bifurcations. It is also shown that a genetic circuit consisting of two auto-activating transcription factors (TFs) with cross inhibitions can form a tristable dynamical system. Results: We used gene expression profiles of pre-implantation mouse embryos at the single cell resolution to visualize the Waddington landscape of the early embryogenesis. For each lineage bifurcation we identified two clusters of TFsrather than two single TFs as previously proposedthat had opposite expression patterns between the pair of bifurcated cell types. The regulatory circuitry among each pair of TF clusters resembled a genetic circuit of a pair of single TFs; it consisted of positive feedbacks among the TFs of the same cluster, and negative interactions among the members of the opposite clusters. Our analyses indicated that the tristable dynamical system of the two-cluster regulatory circuitry is more robust than the genetic circuit of two single TFs.
PLoS ONE, 2014
We present TripNet, a method for constructing phylogenetic networks from triplets. We will presen... more We present TripNet, a method for constructing phylogenetic networks from triplets. We will present the motivations behind our approach and its theoretical and empirical justification. To demonstrate the accuracy and efficiency of TripNet, we performed two simulations and also applied the method to five published data sets: Kreitman's data, a set of triplets from real yeast data obtained from the Fungal Biodiversity Center in Utrecht, a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, and nrDNA ITS and cpDNA JSA sequence data of New Zealand alpine buttercups of Ranunculus sect. Pseudadonis. Finally, we compare our results with those already obtained by other authors using alternative methods. TripNet, data sets, and supplementary files are freely available for download at (www.bioinf.cs.ipm.ir/softwares/tripnet).
Journal of Graph Theory, 2004
Circular chromatic number, χ c is a natural generalization of chromatic number. It is known that ... more Circular chromatic number, χ c is a natural generalization of chromatic number. It is known that it is NP-hard to determine whether or not an arbitrary graph G satisfies χ(G) = χ c (G). In this paper we prove that this problem is NP-hard even if the chromatic number of the graph is known. This answers a question of Xuding Zhu. Also we prove that for all positive integers k ≥ 2 and n ≥ 3, for a given graph G with χ(G) = n, it is NP-complete to verify if χ c (G) ≤ n − 1 k .
Number of a Graph
In this note a conjecture of P. Johnson Jr., on the Hall condition number is dis- proved.
A Note About Hall-Condition Number of a Graph
In this note a conjecture of P. Johnson Jr., on the Hall condition number is dis- proved.
Biosystems, 2014
One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can ... more One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction.
PLoS ONE, 2014
Decision making at a cellular level determines different fates for isogenic cells. However, it is... more Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.
A Counterexample for Hilton-Johnson's Conjecture on List-Coloring of Graphs
In this paper a conjecture of A. Hilton and P. Johnson on list coloring of graphs is disproved. B... more In this paper a conjecture of A. Hilton and P. Johnson on list coloring of graphs is disproved. By modifying our counterexample, we also answer some other questions concerning Hall numbers.
Efficacy of function specific 3D-motifs in enzyme classification according to their EC-numbers
Journal of Theoretical Biology, 2013
Due to the increasing number of protein structures with unknown function originated from structur... more Due to the increasing number of protein structures with unknown function originated from structural genomics projects, protein function prediction has become an important subject in bioinformatics. Among diverse function prediction methods, exploring known 3D-motifs, which are associated with functional elements in unknown protein structures is one of the most biologically meaningful methods. Homologous enzymes inherit such motifs in their active sites from common ancestors. However, slight differences in the properties of these motifs, results in variation in the reactions and substrates of the enzymes. In this study, we examined the possibility of discriminating highly related active site patterns according to their EC-numbers by 3D-motifs. For each EC-number, the spatial arrangement of an active site, which has minimum average distance to other active sites with the same function, was selected as a representative 3D-motif. In order to characterize the motifs, various points in active site elements were tested. The results demonstrated the possibility of predicting full EC-number of enzymes by 3D-motifs. However, the discriminating power of 3D-motifs varies among different enzyme families and depends on selecting the appropriate points and features.
Journal of Graph Theory, 2005
This paper proves that if G is a graph (parallel edges allowed) of maximum degree 3, then χ ′ c (... more This paper proves that if G is a graph (parallel edges allowed) of maximum degree 3, then χ ′ c (G) ≤ 11/3 provided that G does not contain H1 or H2 as a subgraph, where H1 and H2 are obtained by subdividing one edge of K 3 2 (the graph with three parallel edges between two vertices) and K4, respectively. As χ ′ c (H1) = χ ′ c (H2) = 4, our result implies that there is no graph G with 11/3 < χ ′ c (G) < 4. It also implies that if G is a 2-edge connected cubic graph, then χ ′ (G) ≤ 11/3. c (G) = 2 + 1 k for some positive integer k. Since graphs G with ∆(G) ≥ 3 have χ ′ c (G) ≥ 3, 'most' of the rational numbers in the interval (2, 3) are not the circular chromatic index of any graph. The following question was asked in [6]:
Discrete Mathematics, 1999
A defining set (of vertex coloring) of a graph G is a set of vertices S with an assignment of col... more A defining set (of vertex coloring) of a graph G is a set of vertices S with an assignment of colors to its elements which has a unique completion to a proper coloring of G. We define a minimal defining set to be a defining set which does not properly contain another defining set. If G is a uniquely vertex colorable graph, clearly its minimum defining sets are of size χ(G) − 1. It is shown that for a coloring of G, if all minimal defining sets of G are of size χ(G) − 1, then G is a uniquely vertex colorable graph.
Discrete Mathematics, 2000
Let G be a graph. A minimal coloring of G is a coloring which has the smallest possible sum among... more Let G be a graph. A minimal coloring of G is a coloring which has the smallest possible sum among all proper colorings of G, using natural numbers.
Discrete Mathematics, 2005
The chromatic sum of a graph is the minimum total of the colors on the vertices taken over all po... more The chromatic sum of a graph is the minimum total of the colors on the vertices taken over all possible proper colorings using positive integers. Erdös et al [Graphs that require many colors to achieve their chromatic sum, Congr. Numer. 71 (1990) 17-28.] considered the question of finding graphs with minimum number of vertices that require t colors beyond their chromatic number k to obtain their chromatic sum. The number of vertices of such graphs is denoted by P (k, t). They presented some upper bounds for this parameter by introducing certain constructions. In this paper we give some lower bounds for P (k, t) and considerably improve the upper bounds by introducing a class of graphs, called tabular graphs. Finally, for fixed t and sufficiently large k the exact value of P (k, t) is determined.
Discrete Mathematics, 2000
At the 16th British Combinatorial Conference (1997), Cameron introduced a new concept called 2-si... more At the 16th British Combinatorial Conference (1997), Cameron introduced a new concept called 2-simultaneous coloring. He used this concept to reformulate a conjecture of Keedwell (1994) on the existence of critical partial latin squares of a given type. Using computer programs, we have veriÿed the truth of the above conjecture (the SE conjecture) for all graphs having less than 29 edges. In this paper we prove that SE conjecture is a consequence of the well-known oriented cycle double cover conjecture. This connection helps us to prove that the SE conjecture is true for semieulerian graphs.
Discrete Mathematics, 2000
At the 16th British Combinatorial Conference (1997), Cameron introduced a new concept called 2-si... more At the 16th British Combinatorial Conference (1997), Cameron introduced a new concept called 2-simultaneous edge-coloring and conjectured that every bipartite graphic sequence, with all degrees at least 2, has a 2-simultaneous edge-colorable realization. In fact, this conjecture is a reformulation of a conjecture of Keedwell (Graph Theory, Combinatorics, Algorithms and Apthe existence of critical partial latin squares (CPLS) of a given type. In this paper, using some classical results about nowhere-zero 4-ows and oriented cycle double covers, we prove that this conjecture is true for all bipartite graphic sequences with all degrees at least 4.
Ars Combinatoria -Waterloo then Winnipeg-
In this note a conjecture of P. Johnson Jr., on the Hall condition number is dis- proved.
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Papers by Ruzbeh Tusserkani