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Better Alternatives to OSPF Routing

Jessica H. Fong, Anna C. Gilbert, Sampath Kannan, Martin J. Strauss
2005 Algorithmica  
The current standard for intra-domain network routing, Open Shortest Path First (OSPF), suffers from a number of problems-the tunable parameters (the weights) are hard to optimize, the chosen paths are not robust under changes in traffic or network state, and some network links are over-used at the expense of others. We present prototypical scenarios that illustrate these problems. Then we propose several variants of a protocol to eliminate or alleviate them and demonstrate the improvements in
more » ... erformance under those scenarios. We also prove that these protocols never perform significantly worse than OSPF and show that for at least a limited class of network topologies, it is possible to find efficiently the optimal weight settings. Some of the problems with OSPF are well known; indeed, there are several routing protocols that perform better than OSPF in routing quality (i.e., in terms of congestion, delay, etc.). OSPF's popularity persists in part because of its efficiency with respect to several resource bounds. In contrast, many competing protocols that provide routing superior to OSPF are computationally prohibitive. Motivated by this consideration, we designed our protocols not only to achieve better routing quality than OSPF, but also to use resources in amount comparable with OSPF with respect to offline broadcast communication, size of and time to compute routing tables, packet delivery latency, and packet header structure and size.
doi:10.1007/s00453-005-1161-2 fatcat:riz35au4d5e5nblm6b7iobih2q

Protein subfamily assignment using the Conserved Domain Database

Jessica H Fong, Aron Marchler-Bauer
2008 BMC Research Notes  
purposes) Publish with Bio Med Central and every scientist can read your work free of charge"BioMed Central will be the most significant development for disseminating the results of biomedical researc h  ... 
doi:10.1186/1756-0500-1-114 pmid:19014584 pmcid:PMC2632666 fatcat:wvx46fjgpbbqnkafsjozsbrysi

Predicting specificity in bZIP coiled-coil protein interactions

Jessica H Fong, Amy E Keating, Mona Singh
2004 Genome Biology  
R11.4 Genome Biology 2004, Volume 5, Issue 2, Article R11 Fong et al. Genome Biology 2004, 5:R11 R11.8 Genome Biology 2004, Volume 5, Issue 2, Article R11 Fong  ... 
doi:10.1186/gb-2004-5-2-r11 pmid:14759261 pmcid:PMC395749 fatcat:ydx2gvhlmbcthayqkbxqskxh74

Intrinsic disorder and protein multibinding in domain, terminal, and linker regions

Jessica H. Fong, Anna R. Panchenko
2010 Molecular Biosystems  
Intrinsic disorder is believed to contribute to the ability of some proteins to interact with multiple partners which is important for protein functional promiscuity and regulation of the cross-talk between pathways. To better understand the mechanisms of molecular recognition through disordered regions, here, we systematically investigate the coupling between disorder and binding within domain families in a structure interaction network and in terminal and inter-domain linker regions. We
more » ... that the canonical domain-domain interaction model should take into account contributions of N-and C-termini and inter-domain linkers, which may form all or part of the binding interfaces. For the majority of proteins, binding interfaces on domain and terminal regions were predicted to be less disordered than non-interface regions. Analysis of all domain families revealed several exceptions, such as kinases, DNA/RNA binding proteins, certain enzymes, and regulatory proteins, which are candidates for disorder-to-order transitions that can occur upon binding. Domain interfaces that bind single or multiple partners do not exhibit significant difference in disorder content if normalized by the number of interactions. In general, protein families with more diverse interactions exhibit less average disorder over all members of the family. Our results shed light on recent controversies regarding the relationship between disorder and binding of multiple partners at common interfaces. In particular, they support the hypothesis that protein domains with many interacting partners should have a pleiotropic effect on functional pathways and consequently might be more constrained in evolution.
doi:10.1039/c005144f pmid:20544079 pmcid:PMC2955455 fatcat:7zaxkfpnjjahlbd5eubrccu6nq

An Approximate L p-Difference Algorithm for Massive Data Streams [chapter]

Jessica H. Fong, Martin J. Strauss
2000 Lecture Notes in Computer Science  
Several recent papers have shown how to approximate the difference ∑ i |a i − b i | or ∑ |a i − b i | 2 between two functions, when the function values a i and b i are given in a data stream, and their order is chosen by an adversary. These algorithms use little space (much less than would be needed to store the entire stream) and little time to process each item in the stream. They approximate with small relative error. Using different techniques, we show how to approximate the L p -difference
more » ... ∑ i |a i − b i | p for any rational-valued p ∈ (0, 2], with comparable efficiency and error. We also show how to approximate ∑ i |a i − b i | p for larger values of p but with a worse error guarantee. Our results fill in gaps left by recent work, by providing an algorithm that is precisely tunable for the application at hand. These results can be used to assess the difference between two chronologically or physically separated massive data sets, making one quick pass over each data set, without buffering the data or requiring the data source to pause. For example, one can use our techniques to judge whether the traffic on two remote network routers are similar without requiring either router to transmit a copy of its traffic. A web search engine could use such algorithms to construct a library of small "sketches," one for each distinct page on the web; one can approximate the extent to which new web pages duplicate old ones by comparing the sketches of the web pages. Such techniques will become increasingly important as the enormous scale, distributional nature, and one-pass processing requirements of data sets become more commonplace.
doi:10.1007/3-540-46541-3_16 fatcat:anhmjppiwzg2xhpbmvotufvy44

Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony

Jessica H. Fong, Lewis Y. Geer, Anna R. Panchenko, Stephen H. Bryant
2007 Journal of Molecular Biology  
Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which
more » ... architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function.
doi:10.1016/j.jmb.2006.11.017 pmid:17166515 pmcid:PMC1858635 fatcat:kmmbokm6ljarpgfok4gv4kw6za

CORAL: aligning conserved core regions across domain families

Jessica H. Fong, Aron Marchler-Bauer
2009 Computer applications in the biosciences : CABIOS  
The optimal scores from H are normalized into Z-scores as follows.  ...  Let table H contain the maximum similarity score of two profile segments ending in a i and b j in entry H i,j Scoring functions S(a i , b j ) to compute the similarity between profile columns a i and b  ... 
doi:10.1093/bioinformatics/btp334 pmid:19470584 pmcid:PMC2712342 fatcat:ynms36o6nvcjbap2rb46axj7e4

Comparison of RefSeq protein-coding regions in human and vertebrate genomes

Jessica H Fong, Terence D Murphy, Kim D Pruitt
2013 BMC Genomics  
Advances in high-throughput sequencing technology have yielded a large number of publicly available vertebrate genomes, many of which are selected for inclusion in NCBI's RefSeq project and subsequently processed by NCBI's eukaryotic annotation pipeline. Genome annotation results are affected by differences in available support evidence and may be impacted by annotation pipeline software changes over time. The RefSeq project has not previously assessed annotation trends across organisms or over
more » ... time. To address this deficiency, we have developed a comparative protocol which integrates analysis of annotated protein-coding regions across a data set of vertebrate orthologs in genomic sequence coordinates, protein sequences, and protein features. Results: We assessed an ortholog dataset that includes 34 annotated vertebrate RefSeq genomes including human. We confirm that RefSeq protein-coding gene annotations in mammals exhibit considerable similarity. Over 50% of the orthologous protein-coding genes in 20 organisms are supported at the level of splicing conservation with at least three selected reference genomes. Approximately 7,500 ortholog sets include at least half of the analyzed organisms, show highly similar sequence and conserved splicing, and may serve as a minimal set of mammalian "core proteins" for initial assessment of new mammalian genomes. Additionally, 80% of the proteins analyzed pass a suite of tests to detect proteins that lack splicing conservation and have unusual sequence or domain annotation. We use these tests to define an annotation quality metric that is based directly on the annotated proteins thus operates independently of other quality metrics such as availability of transcripts or assembly quality measures. Results are available on the RefSeq FTP site []. Conclusions: Our multi-factored analysis demonstrates a high level of consistency in RefSeq protein representation among vertebrates. We find that the majority of the RefSeq vertebrate proteins for which we have calculated orthology are good as measured by these metrics. The process flow described provides specific information on the scope and degree of conservation for the analyzed protein sequences and annotations and will be used to enrich the quality of RefSeq records by identifying targets for further improvement in the computational annotation pipeline, and by flagging specific genes for manual curation.
doi:10.1186/1471-2164-14-654 pmid:24063302 pmcid:PMC3882889 fatcat:4dtx2aqljjctle2rzc55bayx6m

Using Drones to Assess Volitional Swimming Kinematics of Manta Ray Behaviors in the Wild

Vicky Fong, Sarah L. Hoffmann, Jessica H. Pate
2022 Drones  
Kruskal-Wallis rank sum test indicated a significant difference in velocities between behaviors [H(2) = 17.734, p = 0.0001].  ...  Kruskal-Wallis rank sum test indicated a significant difference in velocities between behaviors [H(2) = 17.734, p = 0.0001].  ... 
doi:10.3390/drones6050111 doaj:a1e7f8c38e4547f182a49d35e9165db6 fatcat:xsojh3js4bgorppx5shiolfczu

Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis

Jessica H. Fong, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Michail Y. Lobanov, Oxana V. Galzitskaya, Anna R. Panchenko, Keith Dunker
2009 PLoS Computational Biology  
We perform a large-scale study of intrinsically disordered regions in proteins and protein complexes using a non-redundant set of hundreds of different protein complexes. In accordance with the conventional view that folding and binding are coupled, in many of our cases the disorder-to-order transition occurs upon complex formation and can be localized to binding interfaces. Moreover, analysis of disorder in protein complexes depicts a significant fraction of intrinsically disordered regions,
more » ... th up to one third of all residues being disordered. We find that the disorder in homodimers, especially in symmetrical homodimers, is significantly higher than in heterodimers and offer an explanation for this interesting phenomenon. We argue that the mechanisms of regulation of binding specificity through disordered regions in complexes can be as common as for unbound monomeric proteins. The fascinating diversity of roles of disordered regions in various biological processes and protein oligomeric forms shown in our study may be a subject of future endeavors in this area. This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
doi:10.1371/journal.pcbi.1000316 pmid:19282967 pmcid:PMC2646137 fatcat:gihi5fmbsjgmjeucpsc2wr6tye

Regulation of protein–protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes

Hafumi Nishi, Jessica H. Fong, Christiana Chang, Sarah A. Teichmann, Anna R. Panchenko
2013 Molecular Biosystems  
We use five different categorical variables: phosphorylation (P), disorder (D), interface (I), type of residue (T), and homo/hetero oligomerization state (H).  ...  It has been shown that its phosphorylation promotes dissociation of RhoA, Rac1, and cdc42 from RhoGDI1 and makes GTPases available for activation. 43 The third example is Na(+)/H(+) exchange regulatory  ... 
doi:10.1039/c3mb25514j pmid:23364837 pmcid:PMC3665713 fatcat:t3ogrk3k7vepfo7jxcctxr4vom

Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures

Inbar Cohen-Gihon, Jessica H. Fong, Roded Sharan, Ruth Nussinov, Teresa M. Przytycka, Anna R. Panchenko
2011 Molecular Biosystems  
Abundance Bigram WNT1 Bilateria - CHRD H. sapiens G. gallus TBOX Bilateria - TF_Otx Euteleostomi Euteleostomi Notch H. sapiens H. sapiens NOD G. gallus Bilateria HH_signal Dipteria  ...  Fong et al. 10 studied the evolution of domain architectures using maximum parsimony to infer architectures in ancestral genomes.  ... 
doi:10.1039/c0mb00182a pmid:21127809 pmcid:PMC3321261 fatcat:4uqrbirwjrdghbkcd3kcu4tf3m

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

Benjamin A. Shoemaker, Dachuan Zhang, Ratna R. Thangudu, Manoj Tyagi, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko
2009 Nucleic Acids Research  
IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query. IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and
more » ... t the same time IBIS infers binding sites/interacting partners by inspecting protein complexes formed by homologous proteins. Similar binding sites are clustered together based on their sequence and structure conservation. To emphasize biologically relevant binding sites, several algorithms are used for verification in terms of evolutionary conservation, biological importance of binding partners, size and stability of interfaces, as well as evidence from the published literature. IBIS is updated regularly and is freely accessible via Structure/ibis/ibis.html.
doi:10.1093/nar/gkp842 pmid:19843613 pmcid:PMC2808861 fatcat:ou6b7ft6rfdahfxns6vfbkroge

Regulatory T Cells and Human Myeloid Dendritic Cells Promote Tolerance via Programmed Death Ligand-1

Shoba Amarnath, Carliann M. Costanzo, Jacopo Mariotti, Jessica L. Ullman, William G. Telford, Veena Kapoor, James L. Riley, Bruce L. Levine, Carl H. June, Timothy Fong, Noel L. Warner, Daniel H. Fowler (+1 others)
2010 PLoS Biology  
After 48 h, responder T cells were harvested, stained with PD-L1 fusion protein, and flow cytometry was performed.  ...  Control CD4 cells or Tregs were generated ex vivo and then utilized to condition allogeneic DC (24-h incubation; 1:1 cell ratio).  ... 
doi:10.1371/journal.pbio.1000302 pmid:20126379 pmcid:PMC2814822 fatcat:rdjgbot2jvailjlmryjk3bjaii

ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder

Michail Yu. Lobanov, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Jessica H. Fong, Anna R. Panchenko, Oxana V. Galzitskaya
2009 Nucleic Acids Research  
Most of the proteins in a cell assemble into complexes to carry out their function. In this work, we have created a new database (named ComSin) of protein structures in bound (complex) and unbound (single) states to provide a researcher with exhaustive information on structures of the same or homologous proteins in bound and unbound states. From the complete Protein Data Bank (PDB), we selected 24 910 pairs of protein structures in bound and unbound states, and identified regions of intrinsic
more » ... sorder. For 2448 pairs, the proteins in bound and unbound states are identical, while 7129 pairs have sequence identity 90% or larger. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity between the corresponding proteins in bound and unbound states, and validation of interaction interfaces of protein complexes. Besides that, through our web server, one can obtain necessary information for studying disorder-to-order and order-to-disorder transitions upon complex formation, and analyze structural differences between proteins in bound and unbound states. The database is available at
doi:10.1093/nar/gkp963 pmid:19906708 pmcid:PMC2808974 fatcat:asdz5crf3bgydgxzwbldcqiwre
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