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10.1101/001602 | p97-dependent retrotranslocation and proteolytic processing govern formation of active Nrf1 upon proteasome inhibition | Senthil K Radhakrishnan;Willem den Besten;Raymond J Deshaies; | Raymond J Deshaies | California Institute of Technology | 2014-01-23 | 3 | New Results | cc_no | Cell Biology | https://www.biorxiv.org/content/early/2014/01/23/001602.source.xml | Proteasome inhibition elicits an evolutionarily conserved response wherein proteasome subunit mRNAs are upregulated, resulting in recovery of proteasome activity. We previously demonstrated that the transcription factor Nrf1 mediates this homeostatic response in mammalian cells. We show here that Nrf1 is initially tran... | 10.7554/eLife.01856.001 | biorxiv |
10.1101/000141 | Microenvironmental variables must influence intrinsic phenotypic parameters of cancer stem cells to affect tumourigenicity | Jacob Scott;Anita Hjelmeland;Prakash Chinnaiyan;Alexander R A Anderson;David Basanta; | Jacob Scott | H. Lee Moffitt Cancer Center and Research Institute and University of Oxford | 2013-11-07 | 1 | New Results | cc_by_nc | Cancer Biology | https://www.biorxiv.org/content/early/2013/11/07/000141.source.xml | Since the discovery of tumour initiating cells (TICs) in solid tumours, studies focussing on their role in cancer initiation and progression have abounded. The biological interrogation of these cells continues to yield volumes of information on their pro-tumourigenic behaviour, but actionable generalised conclusions ha... | 10.1371/journal.pcbi.1003433 | biorxiv |
10.1101/000125 | A filter-flow perspective of hematogenous metastasis offers a non-genetic paradigm for personalized cancer therapy | Jacob G Scott;Alexander G Fletcher;Philip K Maini;Alexander R A Anderson;Philip Gerlee; | Jacob G Scott | H. Lee Moffitt Cancer Center and Research Institute and University of Oxford | 2013-11-07 | 1 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2013/11/07/000125.source.xml | Translational RelevanceSince the discovery of circulating tumor cells (CTC), we have struggled for ways to use them to inform treatment. The only currently accepted method for this is a more is worse paradigm by which clinicians measure CTC burden before and after treatment to assess efficacy. Research efforts are cur... | 10.1016/j.ejca.2014.08.019 | biorxiv |
10.1101/000992 | Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas | Alejandro Reyes;Carolin Blume;Vicent Pelechano;Petra Jakob;Lars M Steinmetz;Thorsten Zenz;Wolfgang Huber; | Alejandro Reyes | European Molecular Biology Laboratory | 2013-12-02 | 1 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2013/12/02/000992.source.xml | BackgroundGenome sequencing studies of chronic lympoid leukemia (CLL) have provided a comprehensive overview of recurrent somatic mutations in coding genes. One of the most intriguing discoveries has been the prevalence of mutations in the HEAT-repeat domain of the splicing factor SF3B1. A frequently observed variant i... | null | biorxiv |
10.1101/000992 | Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas | Alejandro Reyes;Carolin Blume;Vicent Pelechano;Petra Jakob;Lars M Steinmetz;Thorsten Zenz;Wolfgang Huber; | Alejandro Reyes | European Molecular Biology Laboratory | 2014-06-12 | 2 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2014/06/12/000992.source.xml | BackgroundGenome sequencing studies of chronic lympoid leukemia (CLL) have provided a comprehensive overview of recurrent somatic mutations in coding genes. One of the most intriguing discoveries has been the prevalence of mutations in the HEAT-repeat domain of the splicing factor SF3B1. A frequently observed variant i... | null | biorxiv |
10.1101/000992 | Mutated SF3B1 is associated with transcript isoform changes of the genes UQCC and RPL31 both in CLLs and uveal melanomas | Alejandro Reyes;Carolin Blume;Vicent Pelechano;Petra Jakob;Lars M Steinmetz;Thorsten Zenz;Wolfgang Huber; | Alejandro Reyes | European Molecular Biology Laboratory | 2014-07-13 | 3 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2014/07/13/000992.source.xml | BackgroundGenome sequencing studies of chronic lympoid leukemia (CLL) have provided a comprehensive overview of recurrent somatic mutations in coding genes. One of the most intriguing discoveries has been the prevalence of mutations in the HEAT-repeat domain of the splicing factor SF3B1. A frequently observed variant i... | null | biorxiv |
10.1101/001107 | U2AF1 mutations alter splice site recognition in hematological malignancies | Janine O Ilagan;Aravind Ramakrishnan;Brian Hayes;Michele E Murphy;Ahmad S Zebari;Philip Bradley;Robert K Bradley; | Robert K Bradley | FHCRC | 2013-12-03 | 1 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2013/12/03/001107.source.xml | Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1 muta... | 10.1101/gr.181016.114 | biorxiv |
10.1101/001107 | U2AF1 mutations alter splice site recognition in hematological malignancies | Janine O Ilagan;Aravind Ramakrishnan;Brian Hayes;Michele E Murphy;Ahmad S Zebari;Philip Bradley;Robert K Bradley; | Robert K Bradley | FHCRC | 2014-06-28 | 2 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2014/06/28/001107.source.xml | Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1 muta... | 10.1101/gr.181016.114 | biorxiv |
10.1101/001107 | U2AF1 mutations alter splice site recognition in hematological malignancies | Janine O Ilagan;Aravind Ramakrishnan;Brian Hayes;Michele E Murphy;Ahmad S Zebari;Philip Bradley;Robert K Bradley; | Robert K Bradley | FHCRC | 2014-09-29 | 3 | New Results | cc_by | Cancer Biology | https://www.biorxiv.org/content/early/2014/09/29/001107.source.xml | Whole-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 3' splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1 muta... | 10.1101/gr.181016.114 | biorxiv |
10.1101/001321 | Effect of glycogen synthase kinase-3 inactivation on mouse mammary gland development and oncogenesis | Joanna Dembowy;Hibret A Adissu;Jeff C Liu;Eldad Zacksenhaus;James Robert Woodgett; | James Robert Woodgett | Lunenfeld-Tanenbaum Research Institute | 2013-12-10 | 1 | New Results | cc_no | Cancer Biology | https://www.biorxiv.org/content/early/2013/12/10/001321.source.xml | Many components of Wnt/{beta}-catenin signaling pathway have critical functions in mammary gland development and tumor formation, yet the contribution of glycogen synthase kinase-3 (GSK-3 and GSK-3{beta}) to mammopoiesis and oncogenesis is unclear. Here, we report that WAP-Cre-mediated deletion of GSK-3 in the mammary ... | 10.1038/onc.2014.279 | biorxiv |
10.1101/001321 | Effect of glycogen synthase kinase-3 inactivation on mouse mammary gland development and oncogenesis | Joanna Dembowy;Hibret A Adissu;Jeff C Liu;Eldad Zacksenhaus;James Robert Woodgett; | James Robert Woodgett | Lunenfeld-Tanenbaum Research Institute | 2014-07-26 | 2 | New Results | cc_no | Cancer Biology | https://www.biorxiv.org/content/early/2014/07/26/001321.source.xml | Many components of Wnt/{beta}-catenin signaling pathway have critical functions in mammary gland development and tumor formation, yet the contribution of glycogen synthase kinase-3 (GSK-3 and GSK-3{beta}) to mammopoiesis and oncogenesis is unclear. Here, we report that WAP-Cre-mediated deletion of GSK-3 in the mammary ... | 10.1038/onc.2014.279 | biorxiv |
10.1101/001651 | Power-law Null Model for Bystander Mutations in Cancer | Loes Olde Loohuis;Andreas Witzel;Bud Mishra; | Loes Olde Loohuis | City University New York | 2014-01-02 | 1 | New Results | cc_no | Cancer Biology | https://www.biorxiv.org/content/early/2014/01/02/001651.source.xml | In this paper we study Copy Number Variation (CNV) data. The underlying process generating CNV segments is generally assumed to be memory-less, giving rise to an exponential distribution of segment lengths. In this paper, we provide evidence from cancer patient data, which suggests that this generative model is too sim... | null | biorxiv |
10.1101/000786 | Cycling Physicochemical Gradients as ‘Evolutionary Drivers’: From Complex Matter to Complex Living States | Jan Spitzer; | Jan Spitzer | MCP Inc | 2013-11-20 | 1 | New Results | cc_by_nc_nd | Biophysics | https://www.biorxiv.org/content/early/2013/11/20/000786.source.xml | HighlightsO_LIBiological complexity cannot be reduced to chemistry and physics\nC_LIO_LIComplex living states are: multicomponent, multiphase, crowded, and re-emergent\nC_LIO_LILiving states arise naturally only by the action of cycling physicochemical gradients\nC_LIO_LIBacterial cells can be modeled as viscoelastic ... | null | biorxiv |
10.1101/001297 | Aerodynamic characteristics of a feathered dinosaur measured using physical models. Effects of form on static stability and control effectiveness. | Dennis Evangelista;Griselda Cardona;Eric Guenther-Gleason;Tony Huynh;Austin Kwong;Dylan Marks;Neil Ray;Adrian Tisbe;Kyle Tse;Mimi Kohl; | Dennis Evangelista | UC Berkeley | 2013-12-10 | 1 | New Results | cc_by_nc_nd | Biophysics | https://www.biorxiv.org/content/early/2013/12/10/001297.source.xml | We report the effects of posture and morphology on the static aerodynamic stability and control effectiveness of physical models based on the feathered dinosaur, {dagger}Microraptor gui, from the Cretaceous of China. Postures had similar lift and drag coefficients and were broadly similar when simplified metrics of gli... | 10.1371/journal.pone.0085203 | biorxiv |
10.1101/001297 | Aerodynamic characteristics of a feathered dinosaur measured using physical models. Effects of form on static stability and control effectiveness. | Dennis Evangelista;Griselda Cardona;Eric Guenther-Gleason;Tony Huynh;Austin Kwong;Dylan Marks;Neil Ray;Adrian Tisbe;Kyle Tse;Mimi Kohl; | Dennis Evangelista | UC Berkeley | 2013-12-10 | 2 | New Results | cc_by_nc_nd | Biophysics | https://www.biorxiv.org/content/early/2013/12/10/001297.source.xml | We report the effects of posture and morphology on the static aerodynamic stability and control effectiveness of physical models based on the feathered dinosaur, {dagger}Microraptor gui, from the Cretaceous of China. Postures had similar lift and drag coefficients and were broadly similar when simplified metrics of gli... | 10.1371/journal.pone.0085203 | biorxiv |
10.1101/001297 | Aerodynamic characteristics of a feathered dinosaur measured using physical models. Effects of form on static stability and control effectiveness. | Dennis Evangelista;Griselda Cardona;Eric Guenther-Gleason;Tony Huynh;Austin Kwong;Dylan Marks;Neil Ray;Adrian Tisbe;Kyle Tse;Mimi Kohl; | Dennis Evangelista | UC Berkeley | 2014-01-16 | 3 | New Results | cc_by_nc_nd | Biophysics | https://www.biorxiv.org/content/early/2014/01/16/001297.source.xml | We report the effects of posture and morphology on the static aerodynamic stability and control effectiveness of physical models based on the feathered dinosaur, {dagger}Microraptor gui, from the Cretaceous of China. Postures had similar lift and drag coefficients and were broadly similar when simplified metrics of gli... | 10.1371/journal.pone.0085203 | biorxiv |
10.1101/001396 | Parametric inference in the large data limit using maximally informative models | Justin B. Kinney;Gurinder S. Atwal; | Justin B. Kinney | Cold Spring Harbor Laboratory | 2013-12-13 | 1 | New Results | cc_by_nc_nd | Biophysics | https://www.biorxiv.org/content/early/2013/12/13/001396.source.xml | Motivated by data-rich experiments in transcriptional regulation and sensory neuro-science, we consider the following general problem in statistical inference. When exposed to a high-dimensional signal S, a system of interest computes a representation R of that signal which is then observed through a noisy measurement ... | 10.1162/NECO_a_00568 | biorxiv |
10.1101/001461 | RNA Structure Refinement using the ERRASER-Phenix pipeline | Fang-Chieh Chou;Nathaniel Echols;Thomas C. Terwilliger;Rhiju Das; | Rhiju Das | Stanford | 2013-12-19 | 1 | New Results | cc_by_nd | Biophysics | https://www.biorxiv.org/content/early/2013/12/19/001461.source.xml | The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatica... | 10.1007/978-1-4939-2763-0_17 | biorxiv |
10.1101/001065 | A null model for Pearson coexpression networks | Andrea Gobbi;Giuseppe Jurman; | Giuseppe Jurman | Fondazione Bruno Kessler | 2013-12-02 | 1 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/02/001065.source.xml | Gene coexpression networks inferred by correlation from high-throughput profiling such as microarray data represent a simple but effective technique for discovering and interpreting linear gene relationships. In the last years several approach have been proposed to tackle the problem of deciding when the resulting corr... | 10.1371/journal.pone.0128115 | biorxiv |
10.1101/001065 | A null model for Pearson coexpression networks | Andrea Gobbi;Giuseppe Jurman; | Giuseppe Jurman | Fondazione Bruno Kessler | 2013-12-03 | 2 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/03/001065.source.xml | Gene coexpression networks inferred by correlation from high-throughput profiling such as microarray data represent a simple but effective technique for discovering and interpreting linear gene relationships. In the last years several approach have been proposed to tackle the problem of deciding when the resulting corr... | 10.1371/journal.pone.0128115 | biorxiv |
10.1101/001081 | PyRAD: assembly of de novo RADseq loci for phylogenetic analyses | Deren A. R. Eaton; | Deren A. R. Eaton | University of Chicago | 2013-12-03 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/03/001081.source.xml | Restriction-site associated genomic markers are a powerful tool for investigating evolutionary questions at the population level, but are limited in their utility at deeper phylogenetic scales where fewer orthologous loci are typically recovered across disparate taxa. While this limitation stems in part from mutations ... | 10.1093/bioinformatics/btu121 | biorxiv |
10.1101/000984 | A Bayesian Method to Incorporate Hundreds of Functional Characteristics with Association Evidence to Improve Variant Prioritization | Sarah A Gagliano;Michael R Barnes;Michael E Weale;Jo Knight; | Jo Knight | Centre for Addiction and Mental Health | 2013-12-04 | 1 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/04/000984.source.xml | The increasing quantity and quality of functional genomic information motivate the assessment and integration of these data with association data, including data originating from genome-wide association studies (GWAS). We used previously described GWAS signals (\"hits\") to train a regularized logistic model in order t... | 10.1371/journal.pone.0098122 | biorxiv |
10.1101/001230 | libRoadRunner: A High Performance SBML Compliant Simulator | Herbert M Sauro;Totte T Karlsson;Maciej Swat;Michal Galdzicki;Andy Somogyi; | Herbert M Sauro | University of Washington | 2013-12-12 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/12/001230.source.xml | SummaryWe describe libRoadRunner, a cross-platform, open-source, high performance C++ library for running and analyzing SBML-compliant models. libRoadRunner was created primarily to achieve high performance, ease of use, portability and an extensible architecture. libRoadRunner includes a comprehensive API, Plugin supp... | 10.1093/bioinformatics/btv363 | biorxiv |
10.1101/001370 | Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly | Giuseppe Narzisi;Jason A O'Rawe;Ivan Iossifov;Han Fang;Yoon-ha Lee;Zihua Wang;Yiyang Wu;Gholson J Lyon;Michael Wigler;Michael C Schatz; | Giuseppe Narzisi | Cold Spring Harbor Laboratory | 2013-12-13 | 1 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/13/001370.source.xml | We present a new open-source algorithm, Scalpel, for sensitive and specific discovery of INDELs in exome-capture data. By combining the power of mapping and assembly, Scalpel searches the de Bruijn graph for sequence paths (contigs) that span each exon. The algorithm creates a single path for exons with no INDEL, two p... | 10.1038/nmeth.3069 | biorxiv |
10.1101/001370 | Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly | Giuseppe Narzisi;Jason A O'Rawe;Ivan Iossifov;Han Fang;Yoon-ha Lee;Zihua Wang;Yiyang Wu;Gholson J Lyon;Michael Wigler;Michael C Schatz; | Giuseppe Narzisi | Cold Spring Harbor Laboratory | 2014-04-15 | 2 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2014/04/15/001370.source.xml | We present a new open-source algorithm, Scalpel, for sensitive and specific discovery of INDELs in exome-capture data. By combining the power of mapping and assembly, Scalpel searches the de Bruijn graph for sequence paths (contigs) that span each exon. The algorithm creates a single path for exons with no INDEL, two p... | 10.1038/nmeth.3069 | biorxiv |
10.1101/001370 | Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly | Giuseppe Narzisi;Jason A O'Rawe;Ivan Iossifov;Han Fang;Yoon-ha Lee;Zihua Wang;Yiyang Wu;Gholson J Lyon;Michael Wigler;Michael C Schatz; | Giuseppe Narzisi | Cold Spring Harbor Laboratory | 2014-06-18 | 3 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2014/06/18/001370.source.xml | We present a new open-source algorithm, Scalpel, for sensitive and specific discovery of INDELs in exome-capture data. By combining the power of mapping and assembly, Scalpel searches the de Bruijn graph for sequence paths (contigs) that span each exon. The algorithm creates a single path for exons with no INDEL, two p... | 10.1038/nmeth.3069 | biorxiv |
10.1101/001495 | A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations | Vincent Frappier;Rafael Najmanovich; | Rafael Najmanovich | Université de Sherbrooke | 2013-12-20 | 1 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/20/001495.source.xml | Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. Two critical components of NMA methods are coarse-graining in the level of simplification used to represent protein structures and the choice of potential energy functional form. There is a trade-off between speed and acc... | 10.1371/journal.pcbi.1003569 | biorxiv |
10.1101/000422 | On the optimal trimming of high-throughput mRNAseq data | Matthew D MacManes; | Matthew D MacManes | University of New Hampshire | 2013-11-14 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/11/14/000422.source.xml | The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in... | 10.3389/fgene.2014.00013 | biorxiv |
10.1101/000422 | On the optimal trimming of high-throughput mRNAseq data | Matthew D MacManes; | Matthew D MacManes | University of New Hampshire | 2013-12-23 | 2 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/23/000422.source.xml | The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in... | 10.3389/fgene.2014.00013 | biorxiv |
10.1101/000422 | On the optimal trimming of high-throughput mRNAseq data | Matthew D MacManes; | Matthew D MacManes | University of New Hampshire | 2014-01-14 | 3 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/14/000422.source.xml | The widespread and rapid adoption of high-throughput sequencing technologies has afforded researchers the opportunity to gain a deep understanding of genome level processes that underlie evolutionary change, and perhaps more importantly, the links between genotype and phenotype. In particular, researchers interested in... | 10.3389/fgene.2014.00013 | biorxiv |
10.1101/001545 | Exploring community structure in biological networks with random graphs | Pratha Sah;Lisa O. Singh;Aaron Clauset;Shweta Bansal; | Shweta Bansal | Georgetown University | 2013-12-22 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/22/001545.source.xml | BackgroundCommunity structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a systems functional components and the impact of local structures on dynamics at a global scale. Choosing an app... | 10.1186/1471-2105-15-220 | biorxiv |
10.1101/001545 | Exploring community structure in biological networks with random graphs | Pratha Sah;Lisa O. Singh;Aaron Clauset;Shweta Bansal; | Shweta Bansal | Georgetown University | 2013-12-24 | 2 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/24/001545.source.xml | BackgroundCommunity structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a systems functional components and the impact of local structures on dynamics at a global scale. Choosing an app... | 10.1186/1471-2105-15-220 | biorxiv |
10.1101/001545 | Exploring community structure in biological networks with random graphs | Pratha Sah;Lisa O. Singh;Aaron Clauset;Shweta Bansal; | Shweta Bansal | Georgetown University | 2014-06-02 | 3 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2014/06/02/001545.source.xml | BackgroundCommunity structure is ubiquitous in biological networks. There has been an increased interest in unraveling the community structure of biological systems as it may provide important insights into a systems functional components and the impact of local structures on dynamics at a global scale. Choosing an app... | 10.1186/1471-2105-15-220 | biorxiv |
10.1101/001669 | Algorithms in Stringomics (I): Pattern-Matching against "Stringomes" | Paolo Ferragina;Bud (Bhubaneswar) Mishra; | Bud (Bhubaneswar) Mishra | New York University | 2014-01-02 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/02/001669.source.xml | This paper reports an initial design of new data-structures that generalizes the idea of pattern-matching in stringology, from its traditional usage in an (unstructured) set of strings to the arena of a well-structured family of strings. In particular, the object of interest is a family of strings composed of blocks/cl... | null | biorxiv |
10.1101/001305 | Ordered, Random, Monotonic, and Non-Monotonic Digital Nanodot Gradients | Grant Ongo;Sebastien G Ricoult;Timothy E Kennedy;David Juncker; | David Juncker | McGill University | 2013-12-10 | 1 | New Results | cc_no | Bioengineering | https://www.biorxiv.org/content/early/2013/12/10/001305.source.xml | Cell navigation is directed by inhomogeneous distributions of extracellular cues. It is well known that noise plays a key role in biology and is present in naturally occurring gradients at the micro- and nanoscale, yet it has not been studied with gradients in vitro. Here, we introduce novel algorithms to produce order... | 10.1371/journal.pone.0106541 | biorxiv |
10.1101/001305 | Ordered, Random, Monotonic, and Non-Monotonic Digital Nanodot Gradients | Grant Ongo;Sebastien G Ricoult;Timothy E Kennedy;David Juncker; | David Juncker | McGill University | 2013-12-13 | 2 | New Results | cc_by | Bioengineering | https://www.biorxiv.org/content/early/2013/12/13/001305.source.xml | Cell navigation is directed by inhomogeneous distributions of extracellular cues. It is well known that noise plays a key role in biology and is present in naturally occurring gradients at the micro- and nanoscale, yet it has not been studied with gradients in vitro. Here, we introduce novel algorithms to produce order... | 10.1371/journal.pone.0106541 | biorxiv |
10.1101/001305 | Ordered, Random, Monotonic, and Non-Monotonic Digital Nanodot Gradients | Grant Ongo;Sebastien G Ricoult;Timothy E Kennedy;David Juncker; | David Juncker | McGill University | 2014-03-28 | 3 | New Results | cc_by | Bioengineering | https://www.biorxiv.org/content/early/2014/03/28/001305.source.xml | Cell navigation is directed by inhomogeneous distributions of extracellular cues. It is well known that noise plays a key role in biology and is present in naturally occurring gradients at the micro- and nanoscale, yet it has not been studied with gradients in vitro. Here, we introduce novel algorithms to produce order... | 10.1371/journal.pone.0106541 | biorxiv |
10.1101/000547 | Varing chemical equilibrium gives kinetic parameters | Edward Flach;Santiago Schnell; | Edward Flach | Ronin Institute | 2013-11-16 | 1 | New Results | cc_by | Biochemistry | https://www.biorxiv.org/content/early/2013/11/16/000547.source.xml | We are interested in finding the kinetic parameters of a chemical reaction. Previous methods for finding these parameters rely on the dynamic behaviour of the system. This means that the methods are time-sensitive and often rely on non-linear curve fitting. | null | biorxiv |
10.1101/001966 | Correcting a SHAPE-directed RNA structure by a mutate-map-rescue approach | Siqi Tian;Pablo Cordero;Wipapat Kladwang;Rhiju Das; | Rhiju Das | Stanford University | 2014-01-22 | 1 | New Results | cc_no | Biochemistry | https://www.biorxiv.org/content/early/2014/01/22/001966.source.xml | The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput chemical mapping enables rapid RNA structure inference with unusually strong validat... | 10.1261/rna.044321.114 | biorxiv |
10.1101/002022 | ATOMIC STRUCTURES OF GLUCOSE, FRUCTOSE AND SUCROSE AND EXPLANATION OF ANOMERIC CARBON | Raji Heyrovska; | Raji Heyrovska | *(Retired) Academy of Sciences of the Czech Republic | 2014-01-23 | 1 | New Results | cc_no | Biochemistry | https://www.biorxiv.org/content/early/2014/01/23/002022.source.xml | Presented here are the structures of three biologically important sweet sugars, based on the additivity of covalent atomic radii in bond lengths. The observed smaller carbon-oxygen distances involving the anomeric carbons of the open chain hexoses are explained here, for the first time, as due to the smaller covalent ... | null | biorxiv |
10.1101/002014 | Estimate of Within Population Incremental Selection Through Branch Imbalance in Lineage Trees | Gilad Liberman;Jennifer Benichou;Lea Tsaban;yaakov maman;Jacob Glanville;yoram louzoun; | Jennifer Benichou | Bar Ilan University | 2014-01-23 | 1 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/23/002014.source.xml | Incremental selection within a population, defined as a limited fitness change following a mutation, is an important aspect of many evolutionary processes and can significantly affect a large number of mutations through the genome. Strongly advantageous or deleterious mutations are detected through the fixation of muta... | 10.1093/nar/gkv1198 | biorxiv |
10.1101/001990 | An Improved Search Algorithm to Find G-Quadruplexes in Genome Sequences | Anna Varizhuk;Dmitry Ischenko;Igor Smirnov;Olga Tatarinova;Vyacheslav Severov;Roman Novikov;Vladimir Tsvetkov;Vladimir Naumov;Dmitry Kaluzhny;Galina Pozmogova; | Galina Pozmogova | Institute for Physical-Chemical Medicine | 2014-01-23 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/23/001990.source.xml | A growing body of data suggests that the secondary structures adopted by G-rich polynucleotides may be more diverse than previously thought and that the definition of G-quadruplex-forming sequences should be broadened. We studied solution structures of a series of naturally occurring and model single-stranded DNA fragm... | null | biorxiv |
10.1101/001958 | Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data | John G Cleary;Ross Braithwaite;Kurt Gaastra;Brian S Hilbush;Stuart Inglis;Sean A Irvine;Alan Jackson;Richard Littin;Sahar Nohzadeh-Malakshah;Minita Shah;Mehul Rathod;David Ware;Len Trigg;Francisco M De La Vega; | Francisco M De La Vega | Real Time Genomics, Inc. | 2014-01-22 | 1 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/22/001958.source.xml | The analysis of whole-genome or exome sequencing data from trios and pedigrees has being successfully applied to the identification of disease-causing mutations. However, most methods used to identify and genotype genetic variants from next-generation sequencing data ignore the relationships between samples, resulting ... | 10.1089/cmb.2014.0029 | biorxiv |
10.1101/001958 | Joint variant and de novo mutation identification on pedigrees from high-throughput sequencing data | John G Cleary;Ross Braithwaite;Kurt Gaastra;Brian S Hilbush;Stuart Inglis;Sean A Irvine;Alan Jackson;Richard Littin;Sahar Nohzadeh-Malakshah;Minita Shah;Mehul Rathod;David Ware;Len Trigg;Francisco M De La Vega; | Francisco M De La Vega | Real Time Genomics, Inc. | 2014-01-24 | 2 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/24/001958.source.xml | The analysis of whole-genome or exome sequencing data from trios and pedigrees has being successfully applied to the identification of disease-causing mutations. However, most methods used to identify and genotype genetic variants from next-generation sequencing data ignore the relationships between samples, resulting ... | 10.1089/cmb.2014.0029 | biorxiv |
10.1101/001982 | An accelerated miRNA-based screen implicates Atf-3 in odorant receptor expression | Shreelatha Bhat;Minjung Shin;Suhyoung Bahk;Young-Joon Kim;Walton D. Jones; | Walton D. Jones | Korea Advanced Institute of Science and Technology (KAIST) | 2014-01-22 | 1 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2014/01/22/001982.source.xml | Large scale genetic screening is tedious and time-consuming. To address this problem, we propose a novel two-tiered screening system comprising an initial \"pooling\" screen that identifies miRNAs whose tissue-specific over-expression causes a phenotype of interest followed by a more focused secondary screen that uses ... | 10.1038/srep20109 | biorxiv |
10.1101/001925 | Complex behavioral manipulation drives mismatch between host and parasite diversity | Fabricio Baccaro;João Araújo;Harry Evans;Jorge Souza;Bill Magnusson;David Hughes; | David Hughes | Penn State | 2014-01-21 | 1 | New Results | cc_by_nc | Ecology | https://www.biorxiv.org/content/early/2014/01/21/001925.source.xml | Parasites and hosts are intimately associated such that changes in the diversity of one partner are thought to lead to changes in the other. We investigated this linked diversity hypothesis in a specialized ant-Ophiocordyceps system in three forests across 750 km in Central Amazonia. All species belonging to the fungal... | null | biorxiv |
10.1101/001941 | Particle size distribution and optimal capture of aqueous macrobial eDNA | Cameron R. Turner;Matthew A. Barnes;Charles C.Y. Xu;Stuart E. Jones;Christopher L. Jerde;David M. Lodge; | Cameron R. Turner | University of Notre Dame | 2014-01-21 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2014/01/21/001941.source.xml | O_LIDetecting aquatic macroorganisms with environmental DNA (eDNA) is a new survey method with broad applicability. However, the origin, state, and fate of aqueous macrobial eDNA - which collectively determine how well eDNA can serve as a proxy for directly observing organisms and how eDNA should be captured, purified,... | 10.1111/2041-210X.12206 | biorxiv |
10.1101/001974 | SINGLE NUCLEOTIDE POLYMORPHISMS SHED LIGHT ON CORRELATIONS BETWEEN ENVIRONMENTAL VARIABLES AND ADAPTIVE GENETIC DIVERGENCE AMONG POPULATIONS IN ONCORHYNCHUS KETA | Xilin Deng;Philippe Henry; | Philippe Henry | University of Northern British Columbia | 2014-01-22 | 1 | Confirmatory Results | cc_no | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/22/001974.source.xml | Identifying the genetic and ecological basis of adaptation is of immense importance in evolutionary biology. In our study, we applied a panel of 58 biallelic single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus keta. Samples included 4164 individuals from 43 populat... | null | biorxiv |
10.1101/001933 | Coalescence 2.0: a multiple branching of recent theoretical developments and their applications | Aurelien Tellier;Christophe Lemaire; | Aurelien Tellier | Technische Universit?t M?nchen | 2014-01-21 | 1 | Confirmatory Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/21/001933.source.xml | Population genetics theory has laid the foundations for genomics analyses including the recent burst in genome scans for selection and statistical inference of past demographic events in many prokaryote, animal and plant species. Identifying SNPs under natural selection and underpinning species adaptation relies on dis... | 10.1111/mec.12755 | biorxiv |
10.1101/002006 | Genome-wide patterns of copy number variation in the diversified chicken genomes using next-generation sequencing | Guoqiang Yi;Lujiang Qu;Jianfeng Liu;Yiyuan Yan;Guiyun Xu;Ning Yang; | Ning Yang | China Agricultural University | 2014-01-23 | 1 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/01/23/002006.source.xml | Copy number variation (CNV) is important and widespread in the genome, and is a major cause of disease and phenotypic diversity. Herein, we perform genome-wide CNV analysis in 12 diversified chicken genomes based on whole genome sequencing. A total of 9,025 CNV regions (CNVRs) covering 100.1 Mb and representing 9.6% of... | 10.1186/1471-2164-15-962 | biorxiv |
10.1101/001834 | Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | Rajiv C McCoy;Ryan W Taylor;Timothy A Blauwkamp;Joanna L Kelley;Michael Kertesz;Dmitry Pushkarev;Dmitri A Petrov;Anna-Sophie Fiston-Lavier; | Rajiv C McCoy | Stanford University | 2014-01-21 | 1 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/01/21/001834.source.xml | High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements... | 10.1371/journal.pone.0106689 | biorxiv |
10.1101/001834 | Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | Rajiv C McCoy;Ryan W Taylor;Timothy A Blauwkamp;Joanna L Kelley;Michael Kertesz;Dmitry Pushkarev;Dmitri A Petrov;Anna-Sophie Fiston-Lavier; | Rajiv C McCoy | Stanford University | 2014-01-21 | 2 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/01/21/001834.source.xml | High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements... | 10.1371/journal.pone.0106689 | biorxiv |
10.1101/001834 | Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | Rajiv C McCoy;Ryan W Taylor;Timothy A Blauwkamp;Joanna L Kelley;Michael Kertesz;Dmitry Pushkarev;Dmitri A Petrov;Anna-Sophie Fiston-Lavier; | Rajiv C McCoy | Stanford University | 2014-04-29 | 3 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/04/29/001834.source.xml | High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements... | 10.1371/journal.pone.0106689 | biorxiv |
10.1101/001834 | Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | Rajiv C McCoy;Ryan W Taylor;Timothy A Blauwkamp;Joanna L Kelley;Michael Kertesz;Dmitry Pushkarev;Dmitri A Petrov;Anna-Sophie Fiston-Lavier; | Rajiv C McCoy | Stanford University | 2014-04-30 | 4 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/04/30/001834.source.xml | High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements... | 10.1371/journal.pone.0106689 | biorxiv |
10.1101/001834 | Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | Rajiv C McCoy;Ryan W Taylor;Timothy A Blauwkamp;Joanna L Kelley;Michael Kertesz;Dmitry Pushkarev;Dmitri A Petrov;Anna-Sophie Fiston-Lavier; | Rajiv C McCoy | Stanford University | 2014-04-30 | 5 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/04/30/001834.source.xml | High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements... | 10.1371/journal.pone.0106689 | biorxiv |
10.1101/001834 | Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly repetitive transposable elements | Rajiv C McCoy;Ryan W Taylor;Timothy A Blauwkamp;Joanna L Kelley;Michael Kertesz;Dmitry Pushkarev;Dmitri A Petrov;Anna-Sophie Fiston-Lavier; | Rajiv C McCoy | Stanford University | 2014-06-17 | 6 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/06/17/001834.source.xml | High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements... | 10.1371/journal.pone.0106689 | biorxiv |
10.1101/001917 | Modelling and analysis of bacterial tracks suggest an active reorientation mechanism in Rhodobacter sphaeroides | Gabriel Rosser;Ruth E. Baker;Judith P. Armitage;Alexander George Fletcher; | Alexander George Fletcher | University of Oxford | 2014-01-21 | 1 | New Results | cc_by_nc | Microbiology | https://www.biorxiv.org/content/early/2014/01/21/001917.source.xml | Most free-swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. A key open question concerns varying mechanisms by which reorientation occurs. We combine mathematical modelling with analysis of a large tracking dataset to study the poorly-understood reorientation mechani... | 10.1098/rsif.2014.0320 | biorxiv |
10.1101/002097 | A Powerful Approach for Identification of Differentially Transcribed mRNA Isoforms | Yuande Tan; | Yuande Tan | Department of Molecular Physiology and Biophysics and Dan L. Duncan Cancer Center, Baylor College of | 2014-01-26 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/26/002097.source.xml | Next generation sequencing is being increasingly used for transcriptome-wide analysis of differential gene expression. The primary goal in profiling expression is to identify genes or RNA isoforms differentially expressed between specific conditions. Yet, the next generation sequence-based count data are essentially di... | null | biorxiv |
10.1101/002048 | Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles | Kyle Beauchamp;Vijay Pande;Rhiju Das; | Rhiju Das | Stanford University | 2014-01-24 | 1 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/01/24/002048.source.xml | Predicting biological structure has remained challenging for systems such as disordered proteins that take on myriad conformations. Hybrid simulation/experiment strategies have been undermined by difficulties in evaluating errors from computa- tional model inaccuracies and data uncertainties. Building on recent proposa... | 10.1016/j.bpj.2014.02.009 | biorxiv |
10.1101/002063 | Holsteins Favor Heifers, Not Bulls: Biased Milk Production Programmed during Pregnancy as a Function of Fetal Sex | Katie Hinde;Abigail J Carpenter;John C Clay;Barry J Bradford; | Katie Hinde | Harvard University | 2014-01-24 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/24/002063.source.xml | Mammalian females pay high energetic costs for reproduction, the greatest of which is imposed by lactation. The synthesis of milk requires, in part, the mobilization of bodily reserves to nourish developing young. Numerous hypotheses have been advanced to predict how mothers will differentially invest in sons and daugh... | 10.1371/journal.pone.0086169 | biorxiv |
10.1101/002071 | A microRNA profile in Fmr1 knockout mice reveals microRNA expression alterations with possible roles in fragile X syndrome | Ting Liu;Rui-Ping Wan;Ling-Jia Tang;Shu-Jing Liu;Hai-Jun Li;Qi-Hua Zhao;Wei-Ping Liao;Xiao-Fang Sun;Yong-Hong Yi;Yue-Sheng Long; | Yue-Sheng Long | The Second Affiliated Hospital of Guangzhou Medical University | 2014-01-26 | 1 | New Results | cc_no | Neuroscience | https://www.biorxiv.org/content/early/2014/01/26/002071.source.xml | Fragile X syndrome (FXS), a common form of inherited mental retardation, is caused by a loss of expression of the fragile X mental retardation protein (FMRP). FMRP is involved in brain functions by interacting with mRNAs and microRNAs (miRNAs) that selectively control gene expression at translational level. However, li... | 10.1007/s12035-014-8770-1 | biorxiv |
10.1101/002139 | VgeneRepertoire.org identifies and stores variable genes of immunoglobulins and T-cell receptors from the genomes of jawed vertebrates | David N Olivieri;Francisco Gambón-Deza; | David N Olivieri | Universidad de Vigo, School of Computer Science | 2014-01-27 | 1 | New Results | cc_no | Immunology | https://www.biorxiv.org/content/early/2014/01/27/002139.source.xml | The VgeneRepertoire.org platform (http://vgenerepertoire.org) is a new public database repository for variable (V) gene sequences that encode immunoglobulin and T-cell receptor molecules. It identifies the nucleic and amino acid sequences of more than 20,000 genes, providing their exon location in either the contig, sc... | null | biorxiv |
10.1101/002147 | The determinants of alpine butterfly richness and composition vary according to the ecological traits of species | Vincent Sonnay;Loïc Pellissier;Jean-Nicolas Pradervand;Luigi Maiorano;Anne Dubuis;Mary S. Wisz;Antoine Guisan; | Lo?c Pellissier | University of Fribourg | 2014-01-27 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2014/01/27/002147.source.xml | Predicting spatial patterns of species diversity and composition using suitable environmental predictors is an essential element in conservation planning. Although species have distinct relationships to environmental conditions, some similarities may exist among species that share functional characteristics or traits. ... | null | biorxiv |
10.1101/002204 | Genome-wide DNA methylome analysis reveals novel epigenetically dysregulated non-coding RNAs in human breast cancer | Yongsheng Li;Yunpeng Zhang;Shengli Li;Jianping Lu;Juan Chen;Zheng Zhao;Jing Bai;Juan Xu;Xia Li; | Xia Li | Harbin Medical University | 2014-01-28 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/28/002204.source.xml | The development of human breast cancer is driven by changes in the genetic and epigenetic landscape of the cell. Despite growing appreciation of the importance of epigenetics in breast cancers, our knowledge of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancers remains limited. Here, we explored the e... | 10.1038/srep08790 | biorxiv |
10.1101/002196 | Cytoplasmic nanojunctions between lysosomes and sarcoplasmic reticulum are required for specific calcium signaling | Nicola Fameli;Oluseye A. Ogunbayo;Cornelis van Breemen;A. Mark Evans; | Nicola Fameli | University of British Columbia | 2014-01-28 | 1 | New Results | cc_by_nc_nd | Cell Biology | https://www.biorxiv.org/content/early/2014/01/28/002196.source.xml | Herein we demonstrate how nanojunctions between lysosomes and sarcoplasmic reticulum (L-SR junctions) serve to couple lysosomal activation to regenerative, ryanodine receptor-mediated cellular Ca2+ waves. In pulmonary artery smooth muscle cells (PASMCs) it has been proposed that nicotinic acid adenine dinucleotide phos... | 10.12688/f1000research.3986 | biorxiv |
10.1101/002170 | Transcriptome pyrosequencing of abnormal phenotypes in Trypanosoma cruzi epimastigotes after ectopic expression of a small zinc finger protein | Gaston Westergaard;Marc Laverriere;Santiago Revale;Marina Reinert;Javier De Gaudenzi;Adriana Jager;Martin P Vazquez; | Martin P Vazquez | INDEAR | 2014-01-28 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/01/28/002170.source.xml | The TcZFPs are a family of small zinc finger proteins harboring WW domains or Proline rich motifs. In Trypanosoma brucei, ZFPs are involved during stage specific differentiation. TcZFPs interact with each other using the WW domain (ZFP2 and ZFP3) and the proline rich motif (ZFP1). The tcZFP1b member is exclusive to Try... | null | biorxiv |
10.1101/002188 | Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data | Guoli Sun;Alexander Krasnitz; | Alexander Krasnitz | Cold Spring Harbor Laboratory | 2014-01-29 | 1 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/29/002188.source.xml | BackgroundOne of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measu... | 10.1186/1471-2164-15-1000 | biorxiv |
10.1101/002188 | Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data | Guoli Sun;Alexander Krasnitz; | Alexander Krasnitz | Cold Spring Harbor Laboratory | 2014-02-10 | 2 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/10/002188.source.xml | BackgroundOne of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measu... | 10.1186/1471-2164-15-1000 | biorxiv |
10.1101/002188 | Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data | Guoli Sun;Alexander Krasnitz; | Alexander Krasnitz | Cold Spring Harbor Laboratory | 2014-02-12 | 3 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/12/002188.source.xml | BackgroundOne of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measu... | 10.1186/1471-2164-15-1000 | biorxiv |
10.1101/002188 | Significantly distinct branches of hierarchical trees: A framework for statistical analysis and applications to biological data | Guoli Sun;Alexander Krasnitz; | Alexander Krasnitz | Cold Spring Harbor Laboratory | 2014-06-05 | 4 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/06/05/002188.source.xml | BackgroundOne of the most common goals of hierarchical clustering is finding those branches of a tree that form quantifiably distinct data subtypes. Achieving this goal in a statistically meaningful way requires (a) a measure of distinctness of a branch and (b) a test to determine the significance of the observed measu... | 10.1186/1471-2164-15-1000 | biorxiv |
10.1101/002105 | The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer | Johannes Engelken;Matthias Altmeyer;Renty B Franklin; | Johannes Engelken | 1.Institute of Evolutionary Biology (CSIC Universitat Pompeu Fabra) 08003 Barcelona, Spain. 2. 3. | 2014-01-29 | 1 | New Results | cc_by_nc | Cancer Biology | https://www.biorxiv.org/content/early/2014/01/29/002105.source.xml | #### #### ABSTRACT FOR SCIENTISTS: While decades of cancer research have firmly established multiple hallmarks of cancer 1,2, cancers genomic landscape remains to be fully understood. Particularly, the phenomenon of aneuploidy gains and losses of large genomic regions, i.e. whole chromosomes or chromosome arms and why ... | null | biorxiv |
10.1101/002105 | The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer | Johannes Engelken;Matthias Altmeyer;Renty B Franklin; | Johannes Engelken | 1.Institute of Evolutionary Biology (CSIC Universitat Pompeu Fabra) 08003 Barcelona, Spain. 2. 3. | 2014-01-30 | 2 | New Results | cc_by_nc | Cancer Biology | https://www.biorxiv.org/content/early/2014/01/30/002105.source.xml | #### #### ABSTRACT FOR SCIENTISTS: While decades of cancer research have firmly established multiple hallmarks of cancer 1,2, cancers genomic landscape remains to be fully understood. Particularly, the phenomenon of aneuploidy gains and losses of large genomic regions, i.e. whole chromosomes or chromosome arms and why ... | null | biorxiv |
10.1101/002105 | The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer | Johannes Engelken;Matthias Altmeyer;Renty B Franklin; | Johannes Engelken | 1.Institute of Evolutionary Biology (CSIC Universitat Pompeu Fabra) 08003 Barcelona, Spain. 2. 3. | 2014-03-13 | 3 | New Results | cc_by_nd | Cancer Biology | https://www.biorxiv.org/content/early/2014/03/13/002105.source.xml | #### #### ABSTRACT FOR SCIENTISTS: While decades of cancer research have firmly established multiple hallmarks of cancer 1,2, cancers genomic landscape remains to be fully understood. Particularly, the phenomenon of aneuploidy gains and losses of large genomic regions, i.e. whole chromosomes or chromosome arms and why ... | null | biorxiv |
10.1101/002105 | The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer | Johannes Engelken;Matthias Altmeyer;Renty B Franklin; | Johannes Engelken | 1.Institute of Evolutionary Biology (CSIC Universitat Pompeu Fabra) 08003 Barcelona, Spain. 2. 3. | 2014-03-13 | 4 | New Results | cc_by_nc_nd | Cancer Biology | https://www.biorxiv.org/content/early/2014/03/13/002105.source.xml | #### #### ABSTRACT FOR SCIENTISTS: While decades of cancer research have firmly established multiple hallmarks of cancer 1,2, cancers genomic landscape remains to be fully understood. Particularly, the phenomenon of aneuploidy gains and losses of large genomic regions, i.e. whole chromosomes or chromosome arms and why ... | null | biorxiv |
10.1101/002105 | The disruption of trace element homeostasis due to aneuploidy as a unifying theme in the etiology of cancer | Johannes Engelken;Matthias Altmeyer;Renty B Franklin; | Johannes Engelken | 1.Institute of Evolutionary Biology (CSIC Universitat Pompeu Fabra) 08003 Barcelona, Spain. 2. 3. | 2014-03-14 | 5 | New Results | cc_by_nc | Cancer Biology | https://www.biorxiv.org/content/early/2014/03/14/002105.source.xml | #### #### ABSTRACT FOR SCIENTISTS: While decades of cancer research have firmly established multiple hallmarks of cancer 1,2, cancers genomic landscape remains to be fully understood. Particularly, the phenomenon of aneuploidy gains and losses of large genomic regions, i.e. whole chromosomes or chromosome arms and why ... | null | biorxiv |
10.1101/002238 | Fast Principal Component Analysis of Large-Scale Genome-Wide Data | Gad Abraham;Michael Inouye; | Gad Abraham | University of Melbourne | 2014-01-30 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/01/30/002238.source.xml | Principal component analysis (PCA) is routinely used to analyze genome-wide single-nucleotide polymorphism (SNP) data, for detecting population structure and potential outliers. However, the size of SNP datasets has increased immensely in recent years and PCA of large datasets has become a time consuming task. We have ... | 10.1371/journal.pone.0093766 | biorxiv |
10.1101/002238 | Fast Principal Component Analysis of Large-Scale Genome-Wide Data | Gad Abraham;Michael Inouye; | Gad Abraham | University of Melbourne | 2014-03-11 | 2 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/03/11/002238.source.xml | Principal component analysis (PCA) is routinely used to analyze genome-wide single-nucleotide polymorphism (SNP) data, for detecting population structure and potential outliers. However, the size of SNP datasets has increased immensely in recent years and PCA of large datasets has become a time consuming task. We have ... | 10.1371/journal.pone.0093766 | biorxiv |
10.1101/002261 | Impact of RNA degradation on measurements of gene expression | Irene Gallego Romero;Athma A. Pai;Jenny Tung;Yoav Gilad; | Yoav Gilad | University of Chicago | 2014-01-30 | 1 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2014/01/30/002261.source.xml | The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potential... | null | biorxiv |
10.1101/002329 | Improving Protein Docking with Constraint Programming and Coevolution Data | Ludwig Krippahl;Fábio Madeira; | Fábio Madeira | Centria-DI, Universidade Nova de Lisboa | 2014-02-03 | 1 | Confirmatory Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/03/002329.source.xml | BackgroundConstraint programming (CP) is usually seen as a rigid approach, focusing on crisp, precise, distinctions between what is allowed as a solution and what is not. At first sight, this makes it seem inadequate for bioinformatics applications that rely mostly on statistical parameters and optimization. The predic... | null | biorxiv |
10.1101/002295 | Modeling bi-modality improves characterization of cell cycle on gene expression in single cells | Lucas Dennis;Andrew McDavid;Patrick Danaher;Greg Finak;Michael Krouse;Alice Wang;Philippa Webster;Joseph Beechem;Raphael Gottardo; | Raphael Gottardo | Fred Hutchinson Cancer Research Center | 2014-02-03 | 1 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/03/002295.source.xml | Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expression in single cells b... | 10.1371/journal.pcbi.1003696 | biorxiv |
10.1101/002295 | Modeling bi-modality improves characterization of cell cycle on gene expression in single cells | Lucas Dennis;Andrew McDavid;Patrick Danaher;Greg Finak;Michael Krouse;Alice Wang;Philippa Webster;Joseph Beechem;Raphael Gottardo; | Raphael Gottardo | Fred Hutchinson Cancer Research Center | 2014-07-10 | 2 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/07/10/002295.source.xml | Advances in high-throughput, single cell gene expression are allowing interrogation of cell heterogeneity. However, there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level. We assess the effect of cell cycle phase on gene expression in single cells b... | 10.1371/journal.pcbi.1003696 | biorxiv |
10.1101/002121 | FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation. | Jerven Bolleman;Christopher J Mungall;Francesco Strozzi;Joachim Baran;Michel Dumontier;Raoul J P Bonnal;Robert Buels;Robert Hoehndorf;Takatomo Fujisawa;Toshiaki Katayama;Peter J A Cock; | Jerven Bolleman | SIB Swiss Institute of Bioinformatics | 2014-01-31 | 1 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/31/002121.source.xml | Background Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate... | 10.1186/s13326-016-0067-z | biorxiv |
10.1101/002121 | FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation. | Jerven Bolleman;Christopher J Mungall;Francesco Strozzi;Joachim Baran;Michel Dumontier;Raoul J P Bonnal;Robert Buels;Robert Hoehndorf;Takatomo Fujisawa;Toshiaki Katayama;Peter J A Cock; | Jerven Bolleman | SIB Swiss Institute of Bioinformatics | 2014-02-01 | 2 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/01/002121.source.xml | Background Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate... | 10.1186/s13326-016-0067-z | biorxiv |
10.1101/002121 | FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation. | Jerven Bolleman;Christopher J Mungall;Francesco Strozzi;Joachim Baran;Michel Dumontier;Raoul J P Bonnal;Robert Buels;Robert Hoehndorf;Takatomo Fujisawa;Toshiaki Katayama;Peter J A Cock; | Jerven Bolleman | SIB Swiss Institute of Bioinformatics | 2014-02-02 | 3 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/02/002121.source.xml | Background Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate... | 10.1186/s13326-016-0067-z | biorxiv |
10.1101/002345 | Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms | Fernando Racimo;Joshua G Schraiber; | Fernando Racimo | University of California, Berkeley | 2014-02-04 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/02/04/002345.source.xml | Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution, disease genetics and the maintenance of variation genome-wide. Here, we develop an approximation to the distribution of fitness effects (DFE) of segregating single-nucleoti... | 10.1371/journal.pgen.1004697 | biorxiv |
10.1101/002345 | Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms | Fernando Racimo;Joshua G Schraiber; | Fernando Racimo | University of California, Berkeley | 2014-06-19 | 2 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/06/19/002345.source.xml | Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution, disease genetics and the maintenance of variation genome-wide. Here, we develop an approximation to the distribution of fitness effects (DFE) of segregating single-nucleoti... | 10.1371/journal.pgen.1004697 | biorxiv |
10.1101/002303 | Stress, heritability, tissue type and human methylome variation in mother-newborn dyads. | David A. Hughes;Nicole C. Rodney;Connie J. Mulligan; | David A. Hughes | Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra) | 2014-01-31 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/01/31/002303.source.xml | DNA methylation variation has been implicated as a factor that influences inter-individual and inter-tissue phenotypic variation in numerous organisms and under various conditions. Here, using a unique collection of three tissues, derived from 24 mother-newborn dyads from war-torn Democratic Republic of Congo, we estim... | null | biorxiv |
10.1101/002279 | Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data | Richard W Lusk; | Richard W Lusk | University of Michigan | 2014-01-30 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/01/30/002279.source.xml | BackgroundTrace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that have rested controversial claims upon sequencing data that appear to support the pre... | 10.1371/journal.pone.0110808 | biorxiv |
10.1101/002279 | Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data | Richard W Lusk; | Richard W Lusk | University of Michigan | 2014-02-06 | 2 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/02/06/002279.source.xml | BackgroundTrace quantities of contaminating DNA are widespread in the laboratory environment, but their presence has received little attention in the context of high throughput sequencing. This issue is highlighted by recent works that have rested controversial claims upon sequencing data that appear to support the pre... | 10.1371/journal.pone.0110808 | biorxiv |
10.1101/002311 | The organization and dynamics of corticostriatal pathways link the medial orbitofrontal cortex to future decisions | Timothy Verstynen; | Timothy Verstynen | CMU | 2014-02-03 | 1 | New Results | cc_no | Neuroscience | https://www.biorxiv.org/content/early/2014/02/03/002311.source.xml | Accurately making a decision in the face of incongruent options increases the efficiency of making similar congruency decisions in the future. This adaptive process is modulated by reward, suggesting that ventral corticostriatal circuits may contribute to the process of conflict adaptation. To evaluate this possibility... | null | biorxiv |
10.1101/002287 | Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli | Viswanadham Sridhara;Austin G. Meyer;Piyush Rai;Jeffrey E. Barrick;Pradeep Ravikumar;Daniel Segrè;Claus O Wilke; | Claus O Wilke | The University of Texas at Austin | 2014-01-31 | 1 | New Results | cc_by_nc_nd | Systems Biology | https://www.biorxiv.org/content/early/2014/01/31/002287.source.xml | A widely studied problem in systems biology is to predict bacterial phenotype from growth conditions, using mechanistic models such as flux balance analysis (FBA). However, the inverse prediction of growth conditions from phenotype is rarely considered. Here we develop a computational framework to carry out this invers... | 10.1371/journal.pone.0114608 | biorxiv |
10.1101/002287 | Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli | Viswanadham Sridhara;Austin G. Meyer;Piyush Rai;Jeffrey E. Barrick;Pradeep Ravikumar;Daniel Segrè;Claus O Wilke; | Claus O Wilke | The University of Texas at Austin | 2014-01-31 | 2 | New Results | cc_by_nc_nd | Systems Biology | https://www.biorxiv.org/content/early/2014/01/31/002287.source.xml | A widely studied problem in systems biology is to predict bacterial phenotype from growth conditions, using mechanistic models such as flux balance analysis (FBA). However, the inverse prediction of growth conditions from phenotype is rarely considered. Here we develop a computational framework to carry out this invers... | 10.1371/journal.pone.0114608 | biorxiv |
10.1101/002287 | Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli | Viswanadham Sridhara;Austin G. Meyer;Piyush Rai;Jeffrey E. Barrick;Pradeep Ravikumar;Daniel Segrè;Claus O Wilke; | Claus O Wilke | The University of Texas at Austin | 2014-10-14 | 3 | New Results | cc_by_nc_nd | Systems Biology | https://www.biorxiv.org/content/early/2014/10/14/002287.source.xml | A widely studied problem in systems biology is to predict bacterial phenotype from growth conditions, using mechanistic models such as flux balance analysis (FBA). However, the inverse prediction of growth conditions from phenotype is rarely considered. Here we develop a computational framework to carry out this invers... | 10.1371/journal.pone.0114608 | biorxiv |
10.1101/002352 | SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data | Sandra Steyaert;Wim Van Criekinge;Ayla De Paepe;Simon Denil;Klaas Mensaert;Katrien Vandepitte;Wim Vanden Berghe;Geert Trooskens;Tim De Meyer; | Sandra Steyaert | University of Ghent | 2014-02-04 | 1 | New Results | cc_by_nc | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/04/002352.source.xml | Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but onl... | 10.1093/nar/gku847 | biorxiv |
10.1101/002360 | A phase diagram for gene selection and disease classification | Hong-Dong Li;Qing-Song Xu;Yi-Zeng Liang; | Hong-Dong Li | Central South University | 2014-02-04 | 1 | New Results | cc_by_nc | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/04/002360.source.xml | Identifying a small subset of discriminate genes is important for predicting clinical outcomes and facilitating disease diagnosis. Based on the model population analysis framework, we present a method, called PHADIA, which is able to output a phase diagram displaying the predictive ability of each variable, which provi... | null | biorxiv |
10.1101/002360 | A phase diagram for gene selection and disease classification | Hong-Dong Li;Qing-Song Xu;Yi-Zeng Liang; | Hong-Dong Li | Central South University | 2014-02-05 | 2 | New Results | cc_by_nc | Bioinformatics | https://www.biorxiv.org/content/early/2014/02/05/002360.source.xml | Identifying a small subset of discriminate genes is important for predicting clinical outcomes and facilitating disease diagnosis. Based on the model population analysis framework, we present a method, called PHADIA, which is able to output a phase diagram displaying the predictive ability of each variable, which provi... | null | biorxiv |
10.1101/002378 | Evolutionary dynamics of shared niche construction | Philip Gerlee;Alexander RA Anderson; | Philip Gerlee | Moffitt Cancer Center | 2014-02-05 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/02/05/002378.source.xml | Many species engage in niche construction that ultimately leads to an increase in the carrying capacity of the population. We have investigated how the specificity of this behaviour affects evolutionary dynamics using a set of coupled logistic equations, where the carrying capacity of each genotype consists of two comp... | null | biorxiv |
10.1101/002386 | Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis | Bethann S Hromatka;Joyce Y Tung;Amy K Kiefer;Chuong B Do;David A Hinds;Nicholas Eriksson; | Nicholas Eriksson | 23andMe | 2014-02-04 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/02/04/002386.source.xml | Roughly one in three individuals is highly susceptible to motion sickness and yet the underlying causes of this condition are not well understood. Despite high heritability, no associated genetic factors have been discovered to date. Here, we conducted the first genome-wide association study on motion sickness in 80,49... | 10.1093/hmg/ddv028 | biorxiv |
10.1101/002444 | Methods to study toxic transgenes in C. elegans: an analysis of protease-dead separase in the C. elegans embryo | Diana M Mitchell;Lindsey R Uehlein;Joshua Bembenek; | Joshua Bembenek | UT Knoxville | 2014-02-06 | 1 | New Results | cc_no | Cell Biology | https://www.biorxiv.org/content/early/2014/02/06/002444.source.xml | We investigated whether the protease activity of separase, which is required for chromosome segregation, is also required for its other roles during anaphase in C. elegans given that non-proteolytic functions of separase have been identified in other organisms. We find that expression of protease-dead separase is domin... | 10.1371/journal.pone.0108188 | biorxiv |
10.1101/002436 | Biochemical ‘Cambrian’ explosion-implosions: the generation and pruning of genetic codes | Rodrick Wallace; | Rodrick Wallace | New York State Psychiatric Institute | 2014-02-06 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/02/06/002436.source.xml | Tlusty's topological analysis of the genetic code suggests ecosystem changes in available metabolic free energy that predated the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. These coevolved via a `Cambrian explosion' until, very early on, the ancestor ... | null | biorxiv |
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