@article {18695,
	title = {Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {16},
	year = {2009},
	month = {2009///},
	pages = {883 - 889},
	abstract = {Ubiquitin (denoted Ub) receptor proteins as a group must contain a diverse set of binding specificities to distinguish the many forms of polyubiquitin (polyUb) signals. Previous studies suggested that the large class of ubiquitin-associated (UBA) domains contains members with intrinsic specificity for Lys63-linked polyUb or Lys48-linked polyUb, thus explaining how UBA-containing proteins can mediate diverse signaling events. Here we show that previously observed Lys63-polyUb selectivity in UBA domains is the result of an artifact in which the dimeric fusion partner, glutathione S-transferase (GST), positions two UBAs for higher affinity, avid interactions with Lys63-polyUb, but not with Lys48-polyUb. Freed from GST, these UBAs are either nonselective or prefer Lys48-polyUb. Accordingly, NMR experiments reveal no Lys63-polyUb{\textendash}specific binding epitopes for these UBAs. We reexamine previous conclusions based on GST-UBAs and present an alternative model for how UBAs achieve a diverse range of linkage specificities.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb.1637},
	url = {http://www.nature.com/nsmb/journal/v16/n8/abs/nsmb.1637.html},
	author = {Sims,Joshua J. and Haririnia,Aydin and Dickinson,Bryan C. and Fushman, David and Cohen,Robert E.}
}
@conference {16275,
	title = {Inexact Local Alignment Search over Suffix Arrays},
	booktitle = {IEEE International Conference on Bioinformatics and Biomedicine, 2009. BIBM {\textquoteright}09},
	year = {2009},
	month = {2009/11/01/4},
	pages = {83 - 87},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may contain insertions and deletions. We present a generalized heuristic for finding such seeds efficiently and prove that the heuristic does not affect sensitivity. We show how to adapt this algorithm to work over the memory efficient suffix array with provably minimal overhead in running time. We demonstrate the effectiveness of our algorithm on two tasks: whole genome alignment of bacteria and alignment of the DNA sequences of 177 genes that are orthologous in human and mouse. We show our algorithm achieves better sensitivity and uses less memory than other commonly used local alignment tools.},
	keywords = {bacteria, Bioinformatics, biology computing, Computational Biology, Costs, DNA, DNA homology searches, DNA sequences, Educational institutions, generalized heuristic, genes, Genetics, genome alignment, Genomics, human, inexact local alignment search, inexact seeds, local alignment, local alignment tools, memory efficient suffix array, microorganisms, molecular biophysics, mouse, Organisms, Sensitivity and Specificity, sequences, suffix array, USA Councils},
	isbn = {978-0-7695-3885-3},
	doi = {10.1109/BIBM.2009.25},
	author = {Ghodsi,M. and Pop, Mihai}
}
@article {12888,
	title = {Microbial oceanography in a sea of opportunity},
	journal = {Nature},
	volume = {459},
	year = {2009},
	month = {2009/05/13/},
	pages = {180 - 184},
	abstract = {Plankton use solar energy to drive the nutrient cycles that make the planet habitable for larger organisms. We can now explore the diversity and functions of plankton using genomics, revealing the gene repertoires associated with survival in the oceans. Such studies will help us to appreciate the sensitivity of ocean systems and of the ocean{\textquoteright}s response to climate change, improving the predictive power of climate models.},
	keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling, climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
	isbn = {0028-0836},
	doi = {10.1038/nature08056},
	url = {http://www.nature.com/nature/journal/v459/n7244/abs/nature08056.html},
	author = {Bowler,Chris and Karl,David M. and Rita R Colwell}
}
@article {18717,
	title = {Structural Biology: Analysis of {\textquoteright}downhill{\textquoteright} protein folding; Analysis of protein-folding cooperativity (Reply)},
	journal = {Nature},
	volume = {445},
	year = {2007},
	month = {2007/02/15/},
	pages = {E17-E18 - E17-E18},
	abstract = {Ferguson et al. and Zhou and Bai criticize the quality of our nuclear magnetic resonance (NMR) data and atom-by-atom analysis of global {\textquoteright}downhill{\textquoteright} folding, also claiming that the data are compatible with two-state folding.},
	keywords = {Astronomy, astrophysics, Biochemistry, Bioinformatics, Biology, biotechnology, cancer, cell cycle, cell signalling., climate change, Computational Biology, development, developmental biology, DNA, drug discovery, earth science, ecology, environmental science, Evolution, evolutionary biology, functional genomics, Genetics, Genomics, geophysics, immunology, interdisciplinary science, life, marine biology, materials science, medical research, medicine, metabolomics, molecular biology, molecular interactions, nanotechnology, Nature, neurobiology, neuroscience, palaeobiology, pharmacology, Physics, proteomics, quantum physics, RNA, Science, science news, science policy, signal transduction, structural biology, systems biology, transcriptomics},
	isbn = {0028-0836},
	doi = {10.1038/nature05645},
	url = {http://www.nature.com/nature/journal/v445/n7129/full/nature05645.html?lang=en},
	author = {Sadqi,Mourad and Fushman, David and Mu{\~n}oz,Victor}
}
@article {16949,
	title = {A telescope for high-dimensional data},
	journal = {Computing in Science \& Engineering},
	volume = {8},
	year = {2006},
	month = {2006/04//March},
	pages = {48 - 53},
	abstract = {Muscular dystrophy is a degenerative disease that destroys muscles and ultimately kills its victims. Researchers worldwide are racing to find a cure by trying to uncover the genetic processes that cause it. Given that a key process is muscle development, researchers at a consortium of 10 institutions are studying 1,000 men and women, ages 18 to 40 years, to see how their muscles enlarge with exercise. The 150 variables collected for each participant will make this data analysis task challenging for users of traditional statistical software tools. However, a new approach to visual data analysis is helping these researchers speed up their work. At the University of Maryland{\textquoteright}s Human-Computer Interaction Library, we developed an interactive approach to let researchers explore high-dimensional data in an orderly manner, focusing on specific features one at a time. The rank-by-feature framework lets them adjust controls to specify what they{\textquoteright}re looking for, and then, with only a glance, they can spot strong relationships among variables, find tight data clusters, or identify unexpected gaps. Sometimes surprising outliers invite further study as to whether they represent errors or an unusual outcome. Similar data analysis problems come up in meteorology, finance, chemistry, and other sciences in which complex relationships among many variables govern outcomes. The rank-by-feature framework could be helpful to many researchers, engineers, and managers because they can then steer their analyses toward the action},
	keywords = {Chemistry, Data analysis, data mining, data visualisation, degenerative disease, Degenerative diseases, diseases, Finance, genetic process, Genetics, high-dimensional data, interactive data analysis, medical computing, Meteorology, muscle, muscle development, Muscles, muscular dystrophy, Rank-by-feature framework, software, software libraries, software tools, Telescopes, visual data, visual data analysis},
	isbn = {1521-9615},
	doi = {10.1109/MCSE.2006.21},
	author = {Shneiderman, Ben}
}
@article {18699,
	title = {Diverse polyubiquitin interaction properties of ubiquitin-associated domains},
	journal = {Nature Structural \& Molecular Biology},
	volume = {12},
	year = {2005},
	month = {2005///},
	pages = {708 - 714},
	abstract = {The ubiquitin-associated (UBA) domain occurs frequently in proteins involved in ubiquitin-dependent signaling pathways. Although polyubiquitin chain binding is considered to be a defining feature of the UBA domain family, the generality of this property has not been established. Here we have surveyed the polyubiquitin interaction properties of 30 UBA domains, including 16 of 17 occurrences in budding yeast. The UBA domains sort into four classes that include linkage-selective polyubiquitin binders and domains that bind different chains (and monoubiquitin) in a nondiscriminatory manner; one notable class (30\%) did not bind any ubiquitin ligand surveyed. The properties of a given UBA domain are conserved from yeast to mammals. Their functional relevance is further suggested by the ability of an ectopic UBA domain to alter the specificity of a deubiquitylating enzyme in a predictable manner. Conversely, non-UBA sequences can modulate the interaction properties of a UBA domain.},
	keywords = {apoptosis, basic cellular processes, Biochemistry, biophysics, cell biology, cell cycle, cell surface proteins, cell-cell interactions, checkpoints, chromatin, chromatin remodeling, chromatin structure, content, DNA recombination, DNA repair, DNA replication, Gene expression, Genetics, intracellular signaling, journal, macromolecules, mechanism, membrane processes, molecular, molecular basis of disease, molecular biology, molecular interactions, multi-component complexes, nature publishing group, nature structural molecular biology, nucleic acids, protein degradation, protein folding, protein processing, Proteins, regulation of transcription, regulation of translation, RNA, RNA processing, RNAi, signal transduction, single molecule studies, structure and function of proteins, transcription, translation},
	isbn = {1545-9993},
	doi = {10.1038/nsmb962},
	url = {http://www.nature.com/nsmb/journal/v12/n8/full/nsmb962.html},
	author = {Raasi,Shahri and Varadan,Ranjani and Fushman, David and Pickart,Cecile M.}
}
@article {12973,
	title = {A book like its cover},
	journal = {Heredity},
	volume = {93},
	year = {2004},
	month = {2004/08/01/},
	pages = {234 - 235},
	abstract = {An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News \& Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.},
	keywords = {animal and plant breeding, biometrical and statistical genetics, cytogenetics, ecological, eukaryotes, Genetics, Genomics, human population genetics, population and evolutionary genetics, post-genomics},
	isbn = {0018-067X},
	doi = {10.1038/sj.hdy.6800475},
	url = {http://www.nature.com/hdy/journal/v93/n2/full/6800475a.html},
	author = {Cummings, Michael P.}
}
@conference {17113,
	title = {Dynamic querying for pattern identification in microarray and genomic data},
	booktitle = {2003 International Conference on Multimedia and Expo, 2003. ICME {\textquoteright}03. Proceedings},
	volume = {3},
	year = {2003},
	month = {2003/07/06/9},
	pages = {III- 453-6 vol.3 - III- 453-6 vol.3},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals.},
	keywords = {Bioinformatics, data sets, Displays, dynamic querying, expression profiles, Frequency, Gene expression, genes, Genetics, genomic data, Genomics, linear ordered sequences, macromolecules, medical signal processing, Mice, Microarray, pattern identification, pattern recognition, premRNA splicing, Query processing, sequences, Signal processing, splicing, TimeSearcher},
	isbn = {0-7803-7965-9},
	doi = {10.1109/ICME.2003.1221346},
	author = {Hochheiser,H. and Baehrecke,E. H and Mount, Stephen M. and Shneiderman, Ben}
}
@article {17259,
	title = {Interactively exploring hierarchical clustering results [gene identification]},
	journal = {Computer},
	volume = {35},
	year = {2002},
	month = {2002/07//},
	pages = {80 - 86},
	abstract = {To date, work in microarrays, sequenced genomes and bioinformatics has focused largely on algorithmic methods for processing and manipulating vast biological data sets. Future improvements will likely provide users with guidance in selecting the most appropriate algorithms and metrics for identifying meaningful clusters-interesting patterns in large data sets, such as groups of genes with similar profiles. Hierarchical clustering has been shown to be effective in microarray data analysis for identifying genes with similar profiles and thus possibly with similar functions. Users also need an efficient visualization tool, however, to facilitate pattern extraction from microarray data sets. The Hierarchical Clustering Explorer integrates four interactive features to provide information visualization techniques that allow users to control the processes and interact with the results. Thus, hybrid approaches that combine powerful algorithms with interactive visualization tools will join the strengths of fast processors with the detailed understanding of domain experts},
	keywords = {algorithmic methods, arrays, Bioinformatics, biological data sets, biology computing, Data analysis, data mining, data visualisation, Data visualization, DNA, Fluorescence, gene functions, gene identification, gene profiles, Genetics, Genomics, Hierarchical Clustering Explorer, hierarchical systems, interactive exploration, interactive information visualization tool, interactive systems, Large screen displays, meaningful cluster identification, metrics, microarray data analysis, pattern clustering, pattern extraction, Process control, Sensor arrays, sequenced genomes, Tiles},
	isbn = {0018-9162},
	doi = {10.1109/MC.2002.1016905},
	author = {Seo,Jinwook and Shneiderman, Ben}
}
@article {14648,
	title = {Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals},
	journal = {J. ACM},
	volume = {46},
	year = {1999},
	month = {1999/01//},
	pages = {1 - 27},
	abstract = {Genomes frequently evolve by reversals \&rgr;(i,j) that transform a gene order \&pgr;1 {\textellipsis} \&pgr;i\&pgr;i+1 {\textellipsis} \&pgr;j-1\&pgr;j {\textellipsis} \&pgr;n into \&pgr;1 {\textellipsis} \&pgr;i\&pgr;j-1 {\textellipsis} \&pgr;i+1\&pgr;j {\textellipsis} \&pgr;n. Reversal distance between permutations \&pgr; and \&sgr;is the minimum number of reversals to transform \&pgr; into \&Agr;. Analysis of genome rearrangements in molecular biology started in the late 1930{\textquoteright}s, when Dobzhansky  and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions between the species of Drosophilia. Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. We study sorting of signed permutations by reversals, a problem that adequately models rearrangements in a small genomes like chloroplast or mitochondrial DNA. The previously suggested approximation algorithms for sorting signed permutations by reversals compute the reversal distance between permutations with an astonishing accuracy for both simulated and biological data. We prove a duality theorem explaining this intriguing performance and show that there exists a  {\textquotedblleft}hidden{\textquotedblright} parameter that allows one to compute the reversal distance between signed permutations in polynomial time.},
	keywords = {Computational Biology, Genetics},
	isbn = {0004-5411},
	doi = {10.1145/300515.300516},
	url = {http://doi.acm.org/10.1145/300515.300516},
	author = {Hannenhalli, Sridhar and Pevzner,Pavel A.}
}
@conference {14565,
	title = {Transforming men into mice (polynomial algorithm for genomic distance problem)},
	booktitle = {Foundations of Computer Science, Annual IEEE Symposium on},
	year = {1995},
	month = {1995///},
	pages = {581 - 581},
	publisher = {IEEE Computer Society},
	organization = {IEEE Computer Society},
	address = {Los Alamitos, CA, USA},
	abstract = {Many people believe that transformations of humans into mice happen only in fairy tales. However, despite some differences in appearance and habits, men and mice are genetically very similar. In the pioneering paper, J.H. Nadeau and B.A. Taylor (1984) estimated that surprisingly few genomic rearrangements (178/spl plusmn/39) happened since the divergence of human and mouse 80 million years ago. However, their analysis is nonconstructive and no rearrangement scenario for human-mouse evolution has been suggested yet. The problem is complicated by the fact that rearrangements in multi chromosomal genomes include inversions, translocations, fusions and fissions of chromosomes, a rather complex set of operations. As a result, at first glance, a polynomial algorithm for the genomic distance problem with all these operations looks almost as improbable as the transformation of a (real) man into a (real) mouse. We prove a duality theorem which expresses the genomic distance in terms of easily computable parameters reflecting different combinatorial properties of sets of strings. This theorem leads to a polynomial time algorithm for computing most parsimonious rearrangement scenarios. Based on this result and the latest comparative physical mapping data we have constructed a scenario of human-mouse evolution with 131 reversals/translocaitons/fusions/fissions. A combination of the genome rearrangement algorithm with the recently proposed experimental technique called ZOO FISH suggests a new constructive approach to the 100 year old problem of reconstructing mammalian evolution.},
	keywords = {biology computing, combinatorial properties, comparative physical mapping data, computable parameters, duality (mathematics), duality theorem, evolution (biological), Genetics, genome rearrangement algorithm, genomic distance problem, genomic rearrangements, human-mouse evolution, mammalian evolution, multi chromosomal genomes, parsimonious rearrangement scenarios, pattern matching, polynomial algorithm, polynomial time algorithm, set theory, sorting, string matching, strings, zoo fish},
	doi = {http://doi.ieeecomputersociety.org/10.1109/SFCS.1995.492588},
	author = {Hannenhalli, Sridhar and Pevzner,P.A.}
}
@conference {14579,
	title = {A SIMD solution to the sequence comparison problem on the MGAP},
	booktitle = {International Conference on Application Specific Array Processors, 1994. Proceedings},
	year = {1994},
	month = {1994/08/22/24},
	pages = {336 - 345},
	publisher = {IEEE},
	organization = {IEEE},
	abstract = {Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar, with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long, even for moderate length sequences. In this paper, we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor (MGAP), a fine-grained massively parallel array of processors with nearest-neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N, in O(M+N+K) time with O(MN) processors, which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128},
	keywords = {AT-optimal algorithm, Biological information theory, biology computing, biosequence comparison problem, computational complexity, Computer science, Costs, database size, Databases, DNA computing, dynamic programming, dynamic programming algorithms, fine-grained massively parallel processor array, Genetics, Heuristic algorithms, maximally similar sequence, MGAP parallel computer, Micro-Grain Array Processor, Military computing, molecular biology, molecular biophysics, Nearest neighbor searches, nearest-neighbor connections, Parallel algorithms, pipeline processing, pipelined SIMD solution, sequence alignment problem, sequences},
	isbn = {0-8186-6517-3},
	doi = {10.1109/ASAP.1994.331791},
	author = {Borah,M. and Bajwa,R. S and Hannenhalli, Sridhar and Irwin,M. J}
}
