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10.1101/001891 | Population genomics of Saccharomyces cerevisiae human isolates: passengers, colonizers, invaders. | Carlotta De Filippo;Monica Di Paola;Irene Stefanini;Lisa Rizzetto;Luisa Berná;Matteo Ramazzotti;Leonardo Dapporto;Damariz Rivero;Ivo G Gut;Marta Gut;Mónica Bayés;Jean-Luc Legras;Roberto Viola;Cristina Massi-Benedetti;Antonella De Luca;Luigina Romani;Paolo Lionetti;Duccio Cavalieri; | Duccio Cavalieri | Fondazione E. Mach (FEM) | 2014-01-17 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/17/001891.source.xml | The quest for the ecological niches of Saccharomyces cerevisiae ranged from wineries to oaks and more recently to the gut of Crabro Wasps. Here we propose the role of the human gut in shaping S. cerevisiae evolution, presenting the genetic structure of a previously unknown population of yeasts, associated with Crohns d... | null | biorxiv |
10.1101/001867 | Estimating seed bank accumulation and dynamics in three obligate-seeder Proteaceae species | Meaghan E. Jenkins;David Morrison;Tony D. Auld; | David Morrison | Swedish University of Agricultural Sciences | 2014-01-17 | 1 | New Results | cc_by_nc | Ecology | https://www.biorxiv.org/content/early/2014/01/17/001867.source.xml | The seed bank dynamics of the three co-occurring obligate-seeder (i.e. fire-sensitive) Proteaceae species, Banksia ericifolia, Banksia marginata and Petrophile pulchella, were examined at sites of varying time since the most recent fire (i.e. plant age) in the Sydney region. Significant variation among species was foun... | null | biorxiv |
10.1101/001875 | How and where to look for tRNAs in Metazoan mitochondrial genomes, and what you might find when you get there | David Morrison; | David Morrison | Swedish University of Agricultural Sciences | 2014-01-17 | 1 | New Results | cc_by_nc | Molecular Biology | https://www.biorxiv.org/content/early/2014/01/17/001875.source.xml | The ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to be problematic because they often vary in number (genes missing or duplicated) a... | null | biorxiv |
10.1101/001875 | How and where to look for tRNAs in Metazoan mitochondrial genomes, and what you might find when you get there | David Morrison; | David Morrison | Swedish University of Agricultural Sciences | 2014-01-22 | 2 | New Results | cc_by_nc | Molecular Biology | https://www.biorxiv.org/content/early/2014/01/22/001875.source.xml | The ability to locate and annotate mitochondrial genes is an important practical issue, given the rapidly increasing number of mitogenomes appearing in the public databases. Unfortunately, tRNA genes in Metazoan mitochondria have proved to be problematic because they often vary in number (genes missing or duplicated) a... | null | biorxiv |
10.1101/001883 | Tracking global changes induced in the CD4 T cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence. | Niclas Thomas;Katharine Best;Mattia Cinelli;Shlomit Reich-Zeliger;Hila Gal;Eric Shifrut;Asaf Madi;Nir Friedman;John Shawe-Taylor;Benny Chain; | Benny Chain | UCL | 2014-01-17 | 1 | New Results | cc_no | Immunology | https://www.biorxiv.org/content/early/2014/01/17/001883.source.xml | The clonal theory of adaptive immunity proposes that immunological responses are encoded by increases in the frequency of lymphocytes carrying antigen-specific receptors. In this study, we measure the frequency of different TcRs in CD4+ T cell populations of mice immunized with a complex antigen, killed Mycobacterium t... | 10.1093/bioinformatics/btu523 | biorxiv |
10.1101/001909 | The shrinking human protein coding complement: are there fewer than 20,000 genes? | Iakes Ezkurdia;David Juan;Jose Manuel Rodriguez;Adam Frankish;Mark Deikhans;Jennifer L Harrow;Jesus Vazquez;Alfonso Valencia;Michael Tress; | Michael Tress | Spanish National Cancer Research Centre | 2014-01-17 | 1 | New Results | cc_by_nc | Genomics | https://www.biorxiv.org/content/early/2014/01/17/001909.source.xml | Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein coding potential is the detection of cellular protein expression through peptide mass spectrometry experiments. Here we map the peptides detected in 7 large-scale proteomics stud... | 10.1093/hmg/ddu309 | biorxiv |
10.1101/001818 | Emergence of structural and dynamical properties of ecological mutualistic networks | Samir Suweis;Filippo Simini;Jayanth Banavar;Amos Maritan; | Samir Suweis | Universiyt of Padova | 2014-01-14 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2014/01/14/001818.source.xml | Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the organization of ecological communities1-3. Such networks in ecology have generically ... | null | biorxiv |
10.1101/001826 | Expertly validated models suggest responses to climate change are related to species traits: a phylogenetically-controlled analysis of the Order Lagomorpha | Katie Leach;Ruth Kelly;Alison Cameron;W.Ian Montgomery;Neil Reid; | Katie Leach | Queen's University Belfast | 2014-01-14 | 1 | New Results | cc_no | Ecology | https://www.biorxiv.org/content/early/2014/01/14/001826.source.xml | Climate change during the last five decades has impacted significantly on natural ecosystems and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species bioclimatic envelopes under future climate scenari... | 10.1371/journal.pone.0122267 | biorxiv |
10.1101/001826 | Expertly validated models suggest responses to climate change are related to species traits: a phylogenetically-controlled analysis of the Order Lagomorpha | Katie Leach;Ruth Kelly;Alison Cameron;W.Ian Montgomery;Neil Reid; | Katie Leach | Queen's University Belfast | 2014-10-01 | 2 | New Results | cc_no | Ecology | https://www.biorxiv.org/content/early/2014/10/01/001826.source.xml | Climate change during the last five decades has impacted significantly on natural ecosystems and the rate of current climate change is of great concern among conservation biologists. Species Distribution Models (SDMs) have been used widely to project changes in species bioclimatic envelopes under future climate scenari... | 10.1371/journal.pone.0122267 | biorxiv |
10.1101/001842 | The emergence of the rescue effect from explicit within- and between-patch dynamics in a metapopulation | Anders Eriksson;Federico Elías-Wolff;Bernhard Mehlig;Andrea Manica; | Anders Eriksson | University of Cambridge | 2014-01-15 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2014/01/15/001842.source.xml | Immigration can rescue local populations from extinction, helping to stabilise a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very li... | 10.1098/rspb.2013.3127 | biorxiv |
10.1101/001842 | The emergence of the rescue effect from explicit within- and between-patch dynamics in a metapopulation | Anders Eriksson;Federico Elías-Wolff;Bernhard Mehlig;Andrea Manica; | Anders Eriksson | University of Cambridge | 2014-03-05 | 2 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2014/03/05/001842.source.xml | Immigration can rescue local populations from extinction, helping to stabilise a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very li... | 10.1098/rspb.2013.3127 | biorxiv |
10.1101/001800 | The Toxoplasma Acto-MyoA Motor Complex Is Important but Not Essential for Gliding Motility and Host Cell Invasion | Saskia Egarter;Nicole Andenmatten;Allison J Jackson;Jamie A Whitelaw;Gurmann Pall;Jennifer A Black;David JP Ferguson;Isabelle Tardieux;Alex Mogilner;Markus Meissner; | Markus Meissner | University of Glasgow | 2014-01-15 | 1 | New Results | cc_by_nc_nd | Cell Biology | https://www.biorxiv.org/content/early/2014/01/15/001800.source.xml | Apicomplexan parasites are thought to actively invade the host cell by gliding motility. This movement is powered by the parasite own actomyosin system and depends on the regulated polymerisation and depolymerisation of actin to generate the force for gliding and host cell penetration. Recent studies demonstrated that ... | 10.1371/journal.pone.0091819 | biorxiv |
10.1101/001800 | The Toxoplasma Acto-MyoA Motor Complex Is Important but Not Essential for Gliding Motility and Host Cell Invasion | Saskia Egarter;Nicole Andenmatten;Allison J Jackson;Jamie A Whitelaw;Gurmann Pall;Jennifer A Black;David JP Ferguson;Isabelle Tardieux;Alex Mogilner;Markus Meissner; | Markus Meissner | University of Glasgow | 2014-02-12 | 2 | New Results | cc_by_nc_nd | Cell Biology | https://www.biorxiv.org/content/early/2014/02/12/001800.source.xml | Apicomplexan parasites are thought to actively invade the host cell by gliding motility. This movement is powered by the parasite own actomyosin system and depends on the regulated polymerisation and depolymerisation of actin to generate the force for gliding and host cell penetration. Recent studies demonstrated that ... | 10.1371/journal.pone.0091819 | biorxiv |
10.1101/001800 | The Toxoplasma Acto-MyoA Motor Complex Is Important but Not Essential for Gliding Motility and Host Cell Invasion | Saskia Egarter;Nicole Andenmatten;Allison J Jackson;Jamie A Whitelaw;Gurmann Pall;Jennifer A Black;David JP Ferguson;Isabelle Tardieux;Alex Mogilner;Markus Meissner; | Markus Meissner | University of Glasgow | 2014-03-18 | 3 | New Results | cc_by_nc_nd | Cell Biology | https://www.biorxiv.org/content/early/2014/03/18/001800.source.xml | Apicomplexan parasites are thought to actively invade the host cell by gliding motility. This movement is powered by the parasite own actomyosin system and depends on the regulated polymerisation and depolymerisation of actin to generate the force for gliding and host cell penetration. Recent studies demonstrated that ... | 10.1371/journal.pone.0091819 | biorxiv |
10.1101/001792 | Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences | Sebastian Lippold;Hongyang Xu;Albert Ko;Mingkun Li;Gabriel Renaud;Anne Butthof;Roland Schroeder;Mark Stoneking; | Mark Stoneking | MPI-EVA | 2014-01-13 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/01/13/001792.source.xml | To investigate in detail the paternal and maternal demographic histories of humans, we obtained [~]500 kb of non-recombining Y chromosome (NRY) sequences and complete mtDNA genome sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). Our results: confirm the controversial asserti... | 10.1186/2041-2223-5-13 | biorxiv |
10.1101/001784 | Global Epistasis Makes Adaptation Predictable Despite Sequence-Level Stochasticity | Sergey Kryazhimskiy;Daniel Paul Rice;Elizabeth Jerison;Michael M Desai; | Michael M Desai | Harvard University | 2014-01-13 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/13/001784.source.xml | Epistasis can make adaptation highly unpredictable, rendering evolutionary trajectories contingent on the chance effects of initial mutations. We used experimental evolution in Saccharomyces cerevisiae to quantify this effect, finding dramatic differences in adaptability between 64 closely related genotypes. Despite th... | 10.1126/science.1250939 | biorxiv |
10.1101/001784 | Global Epistasis Makes Adaptation Predictable Despite Sequence-Level Stochasticity | Sergey Kryazhimskiy;Daniel Paul Rice;Elizabeth Jerison;Michael M Desai; | Michael M Desai | Harvard University | 2014-08-25 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/08/25/001784.source.xml | Epistasis can make adaptation highly unpredictable, rendering evolutionary trajectories contingent on the chance effects of initial mutations. We used experimental evolution in Saccharomyces cerevisiae to quantify this effect, finding dramatic differences in adaptability between 64 closely related genotypes. Despite th... | 10.1126/science.1250939 | biorxiv |
10.1101/001776 | Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens | Haoyang Cai;Nitin Kumar;Homayoun C Bagheri;Christian von Mering;Mark Robinson;Michael Baudis; | Michael Baudis | University of Zurich | 2014-01-13 | 1 | New Results | cc_by_nc | Genomics | https://www.biorxiv.org/content/early/2014/01/13/001776.source.xml | BackgroundChromothripsis is a recently discovered phenomenon of genomic rearrangement, possibly arising during a single genome-shattering event. This could provide an alternative paradigm in cancer development, replacing the gradual accumulation of genomic changes with a \"one-off\" catastrophic event. However, the ter... | 10.1186/1471-2164-15-82 | biorxiv |
10.1101/001776 | Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens | Haoyang Cai;Nitin Kumar;Homayoun C Bagheri;Christian von Mering;Mark Robinson;Michael Baudis; | Michael Baudis | University of Zurich | 2014-01-13 | 2 | New Results | cc_by_nc | Genomics | https://www.biorxiv.org/content/early/2014/01/13/001776.source.xml | BackgroundChromothripsis is a recently discovered phenomenon of genomic rearrangement, possibly arising during a single genome-shattering event. This could provide an alternative paradigm in cancer development, replacing the gradual accumulation of genomic changes with a \"one-off\" catastrophic event. However, the ter... | 10.1186/1471-2164-15-82 | biorxiv |
10.1101/001768 | Quantification of nuclear transport in single cells | Lucía Durrieu;Rikard Johansson;Alan Bush;David L.I. Janzén;Martin Gollvik;Gunnar Cedersund;Alejandro Colman-Lerner; | Alejandro Colman-Lerner | IFIByNE, DFBMC, FCEN, UBA, Buenos Aires, Argentine | 2014-01-13 | 1 | New Results | cc_by_nc_nd | Biophysics | https://www.biorxiv.org/content/early/2014/01/13/001768.source.xml | Nuclear transport is an essential part of eukaryotic cell function. Several assays exist to measure the rate of this process, but not at the single-cell level. Here, we developed a fluorescent recovery after photobleaching (FRAP)- based method to determine nuclear import and export rates independently in individual liv... | 10.1016/j.isci.2022.105906 | biorxiv |
10.1101/001768 | Characterization of cell-to-cell variation in nuclear transport rates and identification of its sources | Durrieu, L.; Bush, A.; Grande, A.; Johansson, R.; Janzen, D. L. I.; Gollvik, M.; Katz, A.; Cedersund, G.; Colman-Lerner, A. | Alejandro Colman-Lerner | IFIByNE, DFBMC, FCEN, UBA, Buenos Aires, Argentine | 2022-06-24 | 2 | new results | cc_by_nc_nd | systems biology | https://www.biorxiv.org/content/early/2022/06/24/001768.source.xml | Nuclear transport is an essential part of eukaryotic cell function. Several assays exist to measure the rate of this process, but not at the single-cell level. Here, we developed a fluorescent recovery after photobleaching (FRAP)- based method to determine nuclear import and export rates independently in individual liv... | 10.1016/j.isci.2022.105906 | biorxiv |
10.1101/001750 | Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins | Dennis Evangelista;Sharlene Cam;Tony Huynh;Austin Kwong;Homayun Mehrabani;Kyle Tse;Robert Dudley; | Dennis Evangelista | University of North Carolina at Chapel Hill | 2014-01-13 | 1 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/01/13/001750.source.xml | The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds... | 10.7717/peerj.632 | biorxiv |
10.1101/001750 | Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins | Dennis Evangelista;Sharlene Cam;Tony Huynh;Austin Kwong;Homayun Mehrabani;Kyle Tse;Robert Dudley; | Dennis Evangelista | University of North Carolina at Chapel Hill | 2014-01-14 | 2 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/01/14/001750.source.xml | The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds... | 10.7717/peerj.632 | biorxiv |
10.1101/001750 | Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins | Dennis Evangelista;Sharlene Cam;Tony Huynh;Austin Kwong;Homayun Mehrabani;Kyle Tse;Robert Dudley; | Dennis Evangelista | University of North Carolina at Chapel Hill | 2014-01-16 | 3 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/01/16/001750.source.xml | The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds... | 10.7717/peerj.632 | biorxiv |
10.1101/001750 | Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins | Dennis Evangelista;Sharlene Cam;Tony Huynh;Austin Kwong;Homayun Mehrabani;Kyle Tse;Robert Dudley; | Dennis Evangelista | University of North Carolina at Chapel Hill | 2014-04-22 | 4 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/04/22/001750.source.xml | The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds... | 10.7717/peerj.632 | biorxiv |
10.1101/001750 | Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins | Dennis Evangelista;Sharlene Cam;Tony Huynh;Austin Kwong;Homayun Mehrabani;Kyle Tse;Robert Dudley; | Dennis Evangelista | University of North Carolina at Chapel Hill | 2014-07-11 | 5 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/07/11/001750.source.xml | The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds... | 10.7717/peerj.632 | biorxiv |
10.1101/001750 | Shifts in stability and control effectiveness during evolution of Paraves support aerial maneuvering hypotheses for flight origins | Dennis Evangelista;Sharlene Cam;Tony Huynh;Austin Kwong;Homayun Mehrabani;Kyle Tse;Robert Dudley; | Dennis Evangelista | University of North Carolina at Chapel Hill | 2014-10-03 | 6 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/10/03/001750.source.xml | The capacity for aerial maneuvering was likely a major influence on the evolution of flying animals. Here we evaluate consequences of paravian morphology for aerial performance by quantifying static stability and control effectiveness of physical models for numerous taxa sampled from within the lineage leading to birds... | 10.7717/peerj.632 | biorxiv |
10.1101/001719 | Modeling the functional relationship network at the splice isoform level through heterogeneous data integration | Hongdong Li;Rajasree Menon;Ridvan Eksi;Aysam Guerler;Yang Zhang;Gilbert S. Omenn;Yuanfang Guan; | Yuanfang Guan | University of Michigan, Ann Arbor | 2014-01-09 | 1 | New Results | cc_by_nc_nd | Genomics | https://www.biorxiv.org/content/early/2014/01/09/001719.source.xml | Functional relationship networks, which reveal the collaborative roles between genes, have significantly accelerated our understanding of gene functions and phenotypic relevance. However, establishing such networks for alternatively spliced isoforms remains a difficult, unaddressed problem due to the lack of systematic... | null | biorxiv |
10.1101/001719 | Modeling the functional relationship network at the splice isoform level through heterogeneous data integration | Hongdong Li;Rajasree Menon;Ridvan Eksi;Aysam Guerler;Yang Zhang;Gilbert S. Omenn;Yuanfang Guan; | Yuanfang Guan | University of Michigan, Ann Arbor | 2014-03-07 | 2 | New Results | cc_by_nc_nd | Genomics | https://www.biorxiv.org/content/early/2014/03/07/001719.source.xml | Functional relationship networks, which reveal the collaborative roles between genes, have significantly accelerated our understanding of gene functions and phenotypic relevance. However, establishing such networks for alternatively spliced isoforms remains a difficult, unaddressed problem due to the lack of systematic... | null | biorxiv |
10.1101/001735 | Ecological and Evolutionary Oscillations in Host-Parasite Population Dynamics, and The Red Queen | Jomar Fajardo Rabajante; | Jomar Fajardo Rabajante | University of the Philippines | 2014-01-10 | 1 | New Results | cc_no | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/10/001735.source.xml | In a host-parasite system, the constitutive interaction among the species, regulated by the growth rates and functional response, may induce populations to approach equilibrium or sometimes to exhibit simple cycles or peculiar oscillations, such as chaos. A large carrying capacity coupled with appropriate parasitism ef... | null | biorxiv |
10.1101/001735 | Ecological and Evolutionary Oscillations in Host-Parasite Population Dynamics, and The Red Queen | Jomar Fajardo Rabajante; | Jomar Fajardo Rabajante | University of the Philippines | 2014-01-25 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/25/001735.source.xml | In a host-parasite system, the constitutive interaction among the species, regulated by the growth rates and functional response, may induce populations to approach equilibrium or sometimes to exhibit simple cycles or peculiar oscillations, such as chaos. A large carrying capacity coupled with appropriate parasitism ef... | null | biorxiv |
10.1101/001743 | OPPOSING MICROTUBULE MOTORS CONTROL MOTILITY, MORPHOLOGY, AND CARGO SEGREGATION DURING ER-TO-GOLGI TRANSPORT. | Anna K Brown;Sylvie D Hunt;David J Stephens; | David J Stephens | University of Bristol | 2014-01-10 | 1 | New Results | cc_by | Cell Biology | https://www.biorxiv.org/content/early/2014/01/10/001743.source.xml | We recently demonstrated that dynein and kinesin motors drive multiple aspects of endosomal function in mammalian cells. These functions include driving motility, maintaining morphology (notably through providing longitudinal tension to support vesicle fission), and driving cargo sorting. Microtubule motors drive bidir... | 10.1242/bio.20147633 | biorxiv |
10.1101/001727 | SIANN: Strain Identification by Alignment to Near Neighbors | Samuel Minot;Stephen D Turner;Krista L Ternus;Dana R Kadavy; | Samuel Minot | Signature Science, LLC | 2014-01-10 | 1 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2014/01/10/001727.source.xml | Next-generation sequencing is increasingly being used to study samples composed of mixtures of organisms, such as in clinical applications where the presence of a pathogen at very low abundance may be highly important. We present an analytical method (SIANN: Strain Identification by Alignment to Near Neighbors) specifi... | null | biorxiv |
10.1101/001701 | An unmet actin requirement explains the mitotic inhibition of clathrin-mediated endocytosis | Satdip Kaur;Andrew B Fielding;Gisela Gassner;Nicholas J Carter;Stephen J Royle; | Stephen J Royle | University of Warwick | 2014-01-09 | 1 | New Results | cc_by | Cell Biology | https://www.biorxiv.org/content/early/2014/01/09/001701.source.xml | Clathrin-mediated endocytosis (CME) is the major internalisation route for many different receptor types in mammalian cells. CME is shut down during early mitosis, but the mechanism of this inhibition is unclear. Here we show that the mitotic shutdown is due to an unmet requirement for actin in CME. In mitotic cells, m... | 10.7554/eLife.00829 | biorxiv |
10.1101/001701 | An unmet actin requirement explains the mitotic inhibition of clathrin-mediated endocytosis | Satdip Kaur;Andrew B Fielding;Gisela Gassner;Nicholas J Carter;Stephen J Royle; | Stephen J Royle | University of Warwick | 2014-02-18 | 2 | New Results | cc_by | Cell Biology | https://www.biorxiv.org/content/early/2014/02/18/001701.source.xml | Clathrin-mediated endocytosis (CME) is the major internalisation route for many different receptor types in mammalian cells. CME is shut down during early mitosis, but the mechanism of this inhibition is unclear. Here we show that the mitotic shutdown is due to an unmet requirement for actin in CME. In mitotic cells, m... | 10.7554/eLife.00829 | biorxiv |
10.1101/001693 | A statistical mechanics model for the collective epigenetic histone modification dynamics | Hang Zhang;XIAO-JUN TIAN;Abhishek Mukhopadhyay;Kenneth S Kim;Jianhua Xing; | Jianhua Xing | Virginia Tech | 2014-01-08 | 1 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/01/08/001693.source.xml | Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a Potts-type model based on experimentally observed nearest-neighbor enzyme lateral inte... | 10.1103/PhysRevLett.112.068101 | biorxiv |
10.1101/001693 | A statistical mechanics model for the collective epigenetic histone modification dynamics | Hang Zhang;XIAO-JUN TIAN;Abhishek Mukhopadhyay;Kenneth S Kim;Jianhua Xing; | Jianhua Xing | Virginia Tech | 2014-01-08 | 2 | New Results | cc_no | Biophysics | https://www.biorxiv.org/content/early/2014/01/08/001693.source.xml | Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a Potts-type model based on experimentally observed nearest-neighbor enzyme lateral inte... | 10.1103/PhysRevLett.112.068101 | biorxiv |
10.1101/000109 | Speciation and introgression between Mimulus nasutus and Mimulus guttatus | Yaniv Brandvain;Amanda M Kenney;Lex Fagel;Graham Coop;Andrea L Sweigart; | Yaniv Brandvain | Department of Evolution and Ecology & Center for Population Biology, University of California -Davis | 2013-11-07 | 1 | New Results | cc_by | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/07/000109.source.xml | Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a nov... | 10.1371/journal.pgen.1004410 | biorxiv |
10.1101/000075 | A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease | Vanessa Jonsson;Anders Rantzer;Richard M Murray; | Vanessa Jonsson | Caltech | 2013-11-07 | 1 | New Results | cc_by_nc | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/07/000075.source.xml | It has been shown that optimal controller synthesis for positive systems can be formulated as a linear program. Leveraging these results, we propose a scalable iterative algorithm for the systematic design of sparse, small gain feedback strategies that stabilize the evolutionary dynamics of a generic disease model. We ... | 10.1109/ACC.2014.6859452 | biorxiv |
10.1101/000075 | A Scalable Formulation for Engineering Combination Therapies for Evolutionary Dynamics of Disease | Vanessa Jonsson;Anders Rantzer;Richard M Murray; | Vanessa Jonsson | Caltech | 2014-03-30 | 2 | New Results | cc_by_nc | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/03/30/000075.source.xml | It has been shown that optimal controller synthesis for positive systems can be formulated as a linear program. Leveraging these results, we propose a scalable iterative algorithm for the systematic design of sparse, small gain feedback strategies that stabilize the evolutionary dynamics of a generic disease model. We ... | 10.1109/ACC.2014.6859452 | biorxiv |
10.1101/000240 | Genome-wide targets of selection: female response to experimental removal of sexual selection in Drosophila melanogaster | Paolo Innocenti;Ilona Flis;Edward H Morrow; | Edward H Morrow | University of Sussex | 2013-11-12 | 1 | New Results | cc_by | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/12/000240.source.xml | Despite the common assumption that promiscuity should in general be favored in males, but not in females, to date there is no consensus on the general impact of multiple mating on female fitness. Notably, very little is known about the genetic and physiological features underlying the female response to sexual selectio... | null | biorxiv |
10.1101/000208 | Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato | Nicola Nadeau;Mayte Ruiz;Patricio Salazar;Brian Counterman;Jose Alejandro Medina;Humberto Ortiz-Zuazaga;Anna Morrison;W. Owen McMillan;Chri Jiggins;Riccardo Papa; | Chri Jiggins | Cambridge | 2013-11-12 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/12/000208.source.xml | Hybrid zones can be valuable tools for studying evolution and identifying genomic regions responsible for adaptive divergence and underlying phenotypic variation. Hybrid zones between subspecies of Heliconius butterflies can be very narrow and are maintained by strong selection acting on colour pattern. The co-mimetic ... | 10.1101/gr.169292.113 | biorxiv |
10.1101/000398 | The Origin of Human-infecting Avian Influenza A H6N1 Virus | Liangsheng Zhang;Zhenguo Zhang; | Zhenguo Zhang | Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA | 2013-11-14 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/14/000398.source.xml | In this study, we retraced the origin of the reported avian influenza A H6N1 virus infecting a 20-year-old woman in Taiwan. As we know, this is the first reported case of human infection by the H6N1 virus, because this subtype virus usually circulates in birds and poultry. Therefore it is crucial to know how this virus... | null | biorxiv |
10.1101/000406 | Universality and predictability in molecular quantitative genetics | Armita Nourmohammad;Torsten Held;Michael Lassig; | Michael Lassig | University of Cologne | 2013-11-14 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/14/000406.source.xml | Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent d... | 10.1016/j.gde.2013.11.001 | biorxiv |
10.1101/000406 | Universality and predictability in molecular quantitative genetics | Armita Nourmohammad;Torsten Held;Michael Lassig; | Michael Lassig | University of Cologne | 2013-11-15 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/15/000406.source.xml | Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary point of view, are important as targets of natural selection. We review recent d... | 10.1016/j.gde.2013.11.001 | biorxiv |
10.1101/000521 | Pathways to social evolution: reciprocity, relatedness, and synergy | Jeremy Van Cleve;Erol Akcay; | Jeremy Van Cleve | National Evolutionary Synthesis Center | 2013-11-16 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/16/000521.source.xml | Many organisms live in populations structured by space and by class, exhibit plastic responses to their social partners, and are subject to non-additive ecological and fitness effects. Social evolution theory has long recognized that all of these factors can lead to different selection pressures but has only recently a... | 10.1111/evo.12438 | biorxiv |
10.1101/000521 | Pathways to social evolution: reciprocity, relatedness, and synergy | Jeremy Van Cleve;Erol Akcay; | Jeremy Van Cleve | National Evolutionary Synthesis Center | 2014-04-17 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/04/17/000521.source.xml | Many organisms live in populations structured by space and by class, exhibit plastic responses to their social partners, and are subject to non-additive ecological and fitness effects. Social evolution theory has long recognized that all of these factors can lead to different selection pressures but has only recently a... | 10.1111/evo.12438 | biorxiv |
10.1101/000588 | On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al. | Claudiu I Bandea; | Claudiu I Bandea | Centers for Disease Control and Prevention | 2013-11-18 | 1 | Contradictory Results | cc_by_nc | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/18/000588.source.xml | In a recent article entitled \"On the immortality of television sets: \"function\" in the human genome according to the evolution-free gospel of ENCODE\", Graur et al. dismantle ENCODEs evidence and conclusion that 80% of the human genome is functional. However, the article by Graur et al. contains assumptions and stat... | null | biorxiv |
10.1101/000661 | Natural Allelic Variations of Xenobiotic Enzymes Pleiotropically Affect Sexual Dimorphism in Oryzias latipes | Takafumi Katsumura;Shoji Oda;Shigeki Nakagome;Tsunehiko Hanihara;Hiroshi Kataoka;Hiroshi Mitani;Shoji Kawamura;Hiroki Oota; | Hiroki Oota | Kitasato University School of Medicine | 2013-11-19 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/19/000661.source.xml | Summary Summary Highlights Results and Discussion Accession Numbers Reference Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection [1, 2]. Interestingly, sexually selected traits show geographic variations within species despite strong directional selective pres... | 10.1098/rspb.2014.2259 | biorxiv |
10.1101/000661 | Natural Allelic Variations of Xenobiotic Enzymes Pleiotropically Affect Sexual Dimorphism in Oryzias latipes | Takafumi Katsumura;Shoji Oda;Shigeki Nakagome;Tsunehiko Hanihara;Hiroshi Kataoka;Hiroshi Mitani;Shoji Kawamura;Hiroki Oota; | Hiroki Oota | Kitasato University School of Medicine | 2013-11-19 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/19/000661.source.xml | Summary Summary Highlights Results and Discussion Accession Numbers Reference Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection [1, 2]. Interestingly, sexually selected traits show geographic variations within species despite strong directional selective pres... | 10.1098/rspb.2014.2259 | biorxiv |
10.1101/000661 | Natural Allelic Variations of Xenobiotic Enzymes Pleiotropically Affect Sexual Dimorphism in Oryzias latipes | Takafumi Katsumura;Shoji Oda;Shigeki Nakagome;Tsunehiko Hanihara;Hiroshi Kataoka;Hiroshi Mitani;Shoji Kawamura;Hiroki Oota; | Hiroki Oota | Kitasato University School of Medicine | 2013-11-25 | 3 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/11/25/000661.source.xml | Summary Summary Highlights Results and Discussion Accession Numbers Reference Sexual dimorphisms, which are phenotypic differences between males and females, are driven by sexual selection [1, 2]. Interestingly, sexually selected traits show geographic variations within species despite strong directional selective pres... | 10.1098/rspb.2014.2259 | biorxiv |
10.1101/001016 | Predictability of adaptive evolution under the successive fixation assumption | Sandeep Venkataram;Diamantis Sellis;Dmitri A Petrov; | Dmitri A Petrov | Stanford University | 2013-12-02 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/02/001016.source.xml | Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and the evolution of drug resistant pathogens. One approach to studying evolutionary predictability is to observe repeated, independent evolutionary trajectories of similar organisms under similar selection pressures... | null | biorxiv |
10.1101/001016 | Predictability of adaptive evolution under the successive fixation assumption | Sandeep Venkataram;Diamantis Sellis;Dmitri A Petrov; | Dmitri A Petrov | Stanford University | 2013-12-04 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/04/001016.source.xml | Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and the evolution of drug resistant pathogens. One approach to studying evolutionary predictability is to observe repeated, independent evolutionary trajectories of similar organisms under similar selection pressures... | null | biorxiv |
10.1101/001016 | Predictability of adaptive evolution under the successive fixation assumption | Sandeep Venkataram;Diamantis Sellis;Dmitri A Petrov; | Dmitri A Petrov | Stanford University | 2014-08-21 | 3 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/08/21/001016.source.xml | Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and the evolution of drug resistant pathogens. One approach to studying evolutionary predictability is to observe repeated, independent evolutionary trajectories of similar organisms under similar selection pressures... | null | biorxiv |
10.1101/001016 | Predictability of adaptive evolution under the successive fixation assumption | Sandeep Venkataram;Diamantis Sellis;Dmitri A Petrov; | Dmitri A Petrov | Stanford University | 2015-07-28 | 4 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2015/07/28/001016.source.xml | Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and the evolution of drug resistant pathogens. One approach to studying evolutionary predictability is to observe repeated, independent evolutionary trajectories of similar organisms under similar selection pressures... | null | biorxiv |
10.1101/001016 | On the study of evolutionary predictability using historical reconstruction | Venkataram, S.; Sellis, D.; Petrov, D. A. | Dmitri A Petrov | Stanford University | 2017-06-01 | 5 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2017/06/01/001016.source.xml | Predicting the course of evolution is critical for solving current biomedical challenges such as cancer and the evolution of drug resistant pathogens. One approach to studying evolutionary predictability is to observe repeated, independent evolutionary trajectories of similar organisms under similar selection pressures... | null | biorxiv |
10.1101/000091 | Designing Robustness to Temperature in a Feedforward Loop Circuit | Shaunak Sen;Jongmin Kim;Richard M. Murray; | Shaunak Sen | Indian Institute of Technology Delhi | 2013-11-07 | 1 | New Results | cc_by_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/11/07/000091.source.xml | Incoherent feedforward loops represent important biomolecular circuit elements capable of a rich set of dynamic behavior including adaptation and pulsed responses. Temperature can modulate some of these properties through its effect on the underlying reaction rate parameters. It is generally unclear how to design such ... | null | biorxiv |
10.1101/000430 | Negative autoregulation matches production and demand in synthetic transcriptional networks | Elisa Franco;Giulia Giordano;Per-Ola Forsberg;Richard M Murray; | Elisa Franco | University of California at Riverside | 2013-11-14 | 1 | New Results | cc_by_nc_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/11/14/000430.source.xml | We propose a negative feedback architecture that regulates activity of artificial genes, or \"genelets\", to meet their output downstream demand, achieving robustness with respect to uncertain open-loop output production rates. In particular, we consider the case where the outputs of two genelets interact to form a sin... | 10.1021/sb400157z | biorxiv |
10.1101/000430 | Negative autoregulation matches production and demand in synthetic transcriptional networks | Elisa Franco;Giulia Giordano;Per-Ola Forsberg;Richard M Murray; | Elisa Franco | University of California at Riverside | 2013-11-15 | 2 | New Results | cc_by_nc_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/11/15/000430.source.xml | We propose a negative feedback architecture that regulates activity of artificial genes, or \"genelets\", to meet their output downstream demand, achieving robustness with respect to uncertain open-loop output production rates. In particular, we consider the case where the outputs of two genelets interact to form a sin... | 10.1021/sb400157z | biorxiv |
10.1101/001008 | Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria | Iman Farasat;Manish Kushwaha;Jason Collens;Michael Easterbrook;Matthew Guido;Howard M Salis; | Howard M Salis | Penn State University | 2013-12-02 | 1 | New Results | cc_no | Synthetic Biology | https://www.biorxiv.org/content/early/2013/12/02/001008.source.xml | Engineering multi-protein genetic systems to maximize their performance remains a combinatorial challenge, particularly when measurement throughput is limited. We have developed a computational design and modeling approach to build predictive models and identify optimal expression levels, while circumventing combinator... | 10.15252/msb.20134955 | biorxiv |
10.1101/001008 | Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria | Iman Farasat;Manish Kushwaha;Jason Collens;Michael Easterbrook;Matthew Guido;Howard M Salis; | Howard M Salis | Penn State University | 2014-03-03 | 2 | New Results | cc_no | Synthetic Biology | https://www.biorxiv.org/content/early/2014/03/03/001008.source.xml | Engineering multi-protein genetic systems to maximize their performance remains a combinatorial challenge, particularly when measurement throughput is limited. We have developed a computational design and modeling approach to build predictive models and identify optimal expression levels, while circumventing combinator... | 10.15252/msb.20134955 | biorxiv |
10.1101/001008 | Efficient Search, Mapping, and Optimization of Multi-protein Genetic Systems in Diverse Bacteria | Iman Farasat;Manish Kushwaha;Jason Collens;Michael Easterbrook;Matthew Guido;Howard M Salis; | Howard M Salis | Penn State University | 2014-08-05 | 3 | New Results | cc_no | Synthetic Biology | https://www.biorxiv.org/content/early/2014/08/05/001008.source.xml | Engineering multi-protein genetic systems to maximize their performance remains a combinatorial challenge, particularly when measurement throughput is limited. We have developed a computational design and modeling approach to build predictive models and identify optimal expression levels, while circumventing combinator... | 10.15252/msb.20134955 | biorxiv |
10.1101/000885 | Resource usage and gene circuit performance characterization in a cell-free ?breadboard? | Dan Siegal-Gaskins;Zoltan A. Tuza;Jongmin Kim;Vincent Noireaux;Richard M. Murray; | Dan Siegal-Gaskins | California Institute of Technology | 2013-11-25 | 1 | New Results | cc_by_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/11/25/000885.source.xml | The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as t... | 10.1021/sb400203p | biorxiv |
10.1101/000885 | Resource usage and gene circuit performance characterization in a cell-free ?breadboard? | Dan Siegal-Gaskins;Zoltan A. Tuza;Jongmin Kim;Vincent Noireaux;Richard M. Murray; | Dan Siegal-Gaskins | California Institute of Technology | 2013-11-26 | 2 | New Results | cc_by_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/11/26/000885.source.xml | The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as t... | 10.1021/sb400203p | biorxiv |
10.1101/000885 | Resource usage and gene circuit performance characterization in a cell-free ?breadboard? | Dan Siegal-Gaskins;Zoltan A. Tuza;Jongmin Kim;Vincent Noireaux;Richard M. Murray; | Dan Siegal-Gaskins | California Institute of Technology | 2013-12-10 | 3 | New Results | cc_by_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/12/10/000885.source.xml | The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as t... | 10.1021/sb400203p | biorxiv |
10.1101/000885 | Resource usage and gene circuit performance characterization in a cell-free ?breadboard? | Dan Siegal-Gaskins;Zoltan A. Tuza;Jongmin Kim;Vincent Noireaux;Richard M. Murray; | Dan Siegal-Gaskins | California Institute of Technology | 2014-03-09 | 4 | New Results | cc_by_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2014/03/09/000885.source.xml | The many successes of synthetic biology have come in a manner largely different from those in other engineering disciplines; in particular, without well-characterized and simplified prototyping environments to play a role analogous to wind-tunnels in aerodynamics and breadboards in electrical engineering. However, as t... | 10.1021/sb400203p | biorxiv |
10.1101/000448 | Design and implementation of a synthetic biomolecular concentration tracker | Victoria Hsiao;Emmanuel LC de los Santos;Weston R Whitaker;John E Dueber;Richard M Murray; | Victoria Hsiao | California Institute of Technology | 2013-11-15 | 1 | New Results | cc_by_nc_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/11/15/000448.source.xml | As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we design, model, and implement a biomolecu... | 10.1021/sb500024b | biorxiv |
10.1101/000448 | Design and implementation of a synthetic biomolecular concentration tracker | Victoria Hsiao;Emmanuel LC de los Santos;Weston R Whitaker;John E Dueber;Richard M Murray; | Victoria Hsiao | California Institute of Technology | 2013-12-10 | 2 | New Results | cc_by_nc_nd | Synthetic Biology | https://www.biorxiv.org/content/early/2013/12/10/000448.source.xml | As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we design, model, and implement a biomolecu... | 10.1021/sb500024b | biorxiv |
10.1101/000455 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | Stephen Eglen;Michael Weeks;Mark Jessop;Jennifer Simonotto;Tom Jackson;Evelyne Sernagor; | Stephen Eglen | University of Cambridge | 2013-11-15 | 1 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/11/15/000455.source.xml | BackgroundDuring early development, neural circuits fire spontaneously, generating activity episodes with complex spatiotemporal patterns. Recordings of spontaneous activity have been made in many parts of the nervous system over the last 25 years, reporting developmental changes in activity patterns and the effects of... | 10.1186/2047-217X-3-3 | biorxiv |
10.1101/000455 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | Stephen Eglen;Michael Weeks;Mark Jessop;Jennifer Simonotto;Tom Jackson;Evelyne Sernagor; | Stephen Eglen | University of Cambridge | 2013-11-27 | 2 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/11/27/000455.source.xml | BackgroundDuring early development, neural circuits fire spontaneously, generating activity episodes with complex spatiotemporal patterns. Recordings of spontaneous activity have been made in many parts of the nervous system over the last 25 years, reporting developmental changes in activity patterns and the effects of... | 10.1186/2047-217X-3-3 | biorxiv |
10.1101/000455 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | Stephen Eglen;Michael Weeks;Mark Jessop;Jennifer Simonotto;Tom Jackson;Evelyne Sernagor; | Stephen Eglen | University of Cambridge | 2014-02-18 | 3 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2014/02/18/000455.source.xml | BackgroundDuring early development, neural circuits fire spontaneously, generating activity episodes with complex spatiotemporal patterns. Recordings of spontaneous activity have been made in many parts of the nervous system over the last 25 years, reporting developmental changes in activity patterns and the effects of... | 10.1186/2047-217X-3-3 | biorxiv |
10.1101/000067 | Genetics of single-cell protein abundance variation in large yeast populations | Frank Albert;Sebastian Treusch;Arthur H Shockley;Joshua S Bloom;Leonid Kruglyak; | Leonid Kruglyak | UCLA | 2013-11-07 | 1 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/11/07/000067.source.xml | Many DNA sequence variants influence phenotypes by altering gene expression. Our understanding of these variants is limited by sample sizes of current studies and by measurements of mRNA rather than protein abundance. We developed a powerful method for identifying genetic loci that influence protein expression in very ... | 10.1038/nature12904 | biorxiv |
10.1101/000265 | A genome wide dosage suppressor network reveals genetic robustness and a novel mechanism for Huntington’s disease | Biranchi Patra;Yoshiko Kon;Gitanjali Yadav;Anthony Sevold;Jesse P Frumkin;Ravishankar R Vallabhajosyula;Arend Hintze;Bjørn Østman;Jory Schossau;Ashish Bhan;Bruz Marzolf;Jenna K Tamashiro;Amardeep Kaur;Nitin S Baliga;Elizabeth J Grayhack;Christoph Adami;David J Galas;Alpan Raval;Eric M Phizicky;Animesh Ray; | Animesh Ray | Keck Graduate Institute | 2013-11-12 | 1 | New Results | cc_by_nd | Genomics | https://www.biorxiv.org/content/early/2013/11/12/000265.source.xml | Mutational robustness is the extent to which an organism has evolved to withstand the effects of deleterious mutations. We explored the extent of mutational robustness in the budding yeast by genome wide dosage suppressor analysis of 53 conditional lethal mutations in cell division cycle and RNA synthesis related genes... | 10.1093/nar/gkw1148 | biorxiv |
10.1101/000216 | A Complete Public Domain Family Genomics Dataset | Manuel Corpas;Mike Cariaso;Alain Coletta;David Weiss;Andrew P Harrison;Federico Moran;Huanming Yang; | Manuel Corpas | Independent | 2013-11-12 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/12/000216.source.xml | BackgroundThe availability of open access genomic data is essential for the personal genomics field. Public genomic data allow comparative analyses, testing of new tools and genotype-phenotype association studies. Personal genomics data of unrelated individuals are available in the public domain, notably the Personal G... | null | biorxiv |
10.1101/000315 | On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles | Ying-Wooi Wan;Claire Mach;Genevera I. Allen;Matthew Anderson;Zhandong Liu; | Zhandong Liu | Baylor College of Medicine | 2013-11-13 | 1 | Contradictory Results | cc_by_nc_nd | Genomics | https://www.biorxiv.org/content/early/2013/11/13/000315.source.xml | Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian... | 10.1371/journal.pone.0087782 | biorxiv |
10.1101/000752 | Joint analysis of functional genomic data and genome-wide association studies of 18 human traits | Joseph Pickrell; | Joseph Pickrell | New York Genome Center | 2013-11-19 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/19/000752.source.xml | Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a statistical model that uses association statistics computed across the genome to ... | 10.1016/j.ajhg.2014.03.004 | biorxiv |
10.1101/000752 | Joint analysis of functional genomic data and genome-wide association studies of 18 human traits | Joseph Pickrell; | Joseph Pickrell | New York Genome Center | 2013-11-22 | 2 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/22/000752.source.xml | Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a statistical model that uses association statistics computed across the genome to ... | 10.1016/j.ajhg.2014.03.004 | biorxiv |
10.1101/000752 | Joint analysis of functional genomic data and genome-wide association studies of 18 human traits | Joseph Pickrell; | Joseph Pickrell | New York Genome Center | 2014-01-22 | 3 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/01/22/000752.source.xml | Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a statistical model that uses association statistics computed across the genome to ... | 10.1016/j.ajhg.2014.03.004 | biorxiv |
10.1101/000752 | Joint analysis of functional genomic data and genome-wide association studies of 18 human traits | Joseph Pickrell; | Joseph Pickrell | New York Genome Center | 2014-02-25 | 4 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2014/02/25/000752.source.xml | Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a statistical model that uses association statistics computed across the genome to ... | 10.1016/j.ajhg.2014.03.004 | biorxiv |
10.1101/000364 | Sampling principles for biodiversity study | Xubin Pan; | Xubin Pan | Chinese Academy of Inspection and Quarantine | 2013-11-14 | 1 | New Results | cc_by | Ecology | https://www.biorxiv.org/content/early/2013/11/14/000364.source.xml | Sampling is a fundamental tool in ecology and critical for biodiversity measurement. However, basic principles of biodiversity sampling have been overlooked for many years. In this paper, I proposed and explored five principles of sampling for a specific area and biodiversity study. The first principle of sampling, spe... | null | biorxiv |
10.1101/000158 | Functional Annotation Signatures of Disease Susceptibility Loci Improve SNP Association Analysis | Edwin S Iversen;Gary Lipton;Merlise A. Clyde;Alvaro N. A. Monteiro; | Edwin S Iversen | Duke University | 2013-11-11 | 1 | New Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2013/11/11/000158.source.xml | We describe the development and application of a Bayesian statistical model for the prior probability of phenotype-genotype association that incorporates data from past association studies and publicly available functional annotation data regarding the susceptibility variants under study. The model takes the form of a ... | 10.1186/1471-2164-15-398 | biorxiv |
10.1101/000489 | Gappy TotalReCaller for RNASeq Base-Calling and Mapping | Bud (Bhubaneswar) Mishra; | Bud (Bhubaneswar) Mishra | New York University | 2013-11-15 | 1 | New Results | cc_by | Bioinformatics | https://www.biorxiv.org/content/early/2013/11/15/000489.source.xml | Understanding complex mammalian biology depends crucially on our ability to define a precise map of all the transcripts encoded in a genome, and to measure their relative abundances. A promising assay depends on RNASeq approaches, which builds on next generation sequencing pipelines capable of interrogating cDNAs extra... | null | biorxiv |
10.1101/000497 | Unexpected links reflect the noise in networks | Anatoly Yambartsev;Michael Perlin;Yevgeniy Kovchegov;Natalia Shulzhenko;Karina Mine;Andrey Morgun; | Andrey Morgun | Oregon State University | 2013-11-15 | 1 | New Results | cc_by_nc | Bioinformatics | https://www.biorxiv.org/content/early/2013/11/15/000497.source.xml | Gene regulatory networks are commonly used for modeling biological processes and revealing underlying molecular mechanisms. The reconstruction of gene regulatory networks from observational data is a challenging task, especially, considering the large number of involved players (e.g. genes) and much fewer biological re... | 10.1186/s13062-016-0155-0 | biorxiv |
10.1101/000851 | Comment on “TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions” by Kim et al. | Alexander Dobin;Thomas R Gingeras; | Alexander Dobin | Cold Spring Harbor Laboratory | 2013-11-22 | 1 | Contradictory Results | cc_by_nd | Bioinformatics | https://www.biorxiv.org/content/early/2013/11/22/000851.source.xml | In the recent paper [1] (thereafter referred to as \"TopHat2paper\") the accuracy of TopHat2 was compared to other RNA-seq aligners. In this comment we re-examine most important analyses from the TopHat2paper and identify several deficiencies that significantly diminished performance of some of the aligners, including ... | null | biorxiv |
10.1101/000919 | Inferring tree causal models of cancer progression with probability raising | Loes Olde Loohuis;Giulio Caravagna;Alex Graudenzi;Daniele Ramazzotti;Giancarlo Mauri;Marco Antoniotti;Bud Mishra; | Bud Mishra | Courant Institute of Mathematical Sciences | 2013-11-25 | 1 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2013/11/25/000919.source.xml | Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel theoretical framework called CAPRESE (CAncer PRogression Extraction with Single Ed... | 10.1371/journal.pone.0108358 | biorxiv |
10.1101/000919 | Inferring tree causal models of cancer progression with probability raising | Loes Olde Loohuis;Giulio Caravagna;Alex Graudenzi;Daniele Ramazzotti;Giancarlo Mauri;Marco Antoniotti;Bud Mishra; | Bud Mishra | Courant Institute of Mathematical Sciences | 2014-08-19 | 2 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2014/08/19/000919.source.xml | Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel theoretical framework called CAPRESE (CAncer PRogression Extraction with Single Ed... | 10.1371/journal.pone.0108358 | biorxiv |
10.1101/000919 | Inferring tree causal models of cancer progression with probability raising | Loes Olde Loohuis;Giulio Caravagna;Alex Graudenzi;Daniele Ramazzotti;Giancarlo Mauri;Marco Antoniotti;Bud Mishra; | Bud Mishra | Courant Institute of Mathematical Sciences | 2014-08-26 | 3 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2014/08/26/000919.source.xml | Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel theoretical framework called CAPRESE (CAncer PRogression Extraction with Single Ed... | 10.1371/journal.pone.0108358 | biorxiv |
10.1101/000919 | Inferring tree causal models of cancer progression with probability raising | Loes Olde Loohuis;Giulio Caravagna;Alex Graudenzi;Daniele Ramazzotti;Giancarlo Mauri;Marco Antoniotti;Bud Mishra; | Bud Mishra | Courant Institute of Mathematical Sciences | 2014-10-10 | 4 | New Results | cc_no | Bioinformatics | https://www.biorxiv.org/content/early/2014/10/10/000919.source.xml | Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel theoretical framework called CAPRESE (CAncer PRogression Extraction with Single Ed... | 10.1371/journal.pone.0108358 | biorxiv |
10.1101/001024 | Exploring DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data | Sterling Sawaya;James Boocock;Mik Black;Neil Gemmell; | Sterling Sawaya | University of Otago | 2013-12-02 | 1 | New Results | cc_by_nc_nd | Bioinformatics | https://www.biorxiv.org/content/early/2013/12/02/001024.source.xml | Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA structure. The Pacific Biosciences sequencer uses optics to view a polymeras... | 10.1186/s12859-014-0449-0 | biorxiv |
10.1101/000349 | Filling up the tree: considering the self-organization of avian roosting behavior | Bradly J Alicea; | Bradly J Alicea | Michigan State University | 2013-11-13 | 1 | New Results | cc_by_nc | Zoology | https://www.biorxiv.org/content/early/2013/11/13/000349.source.xml | In this paper, models for understanding bird roosting will be considered for purposes of developing better Artificial Life models of complex behavior. Roosting involves multiple flocks of birds picking a single tree limb to rest on for the night, and can be considered an iterative, time-dependent process that unfolds o... | null | biorxiv |
10.1101/000349 | Filling up the tree: considering the self-organization of avian roosting behavior | Bradly J Alicea; | Bradly J Alicea | Michigan State University | 2013-12-01 | 2 | New Results | cc_by_nc | Zoology | https://www.biorxiv.org/content/early/2013/12/01/000349.source.xml | In this paper, models for understanding bird roosting will be considered for purposes of developing better Artificial Life models of complex behavior. Roosting involves multiple flocks of birds picking a single tree limb to rest on for the night, and can be considered an iterative, time-dependent process that unfolds o... | null | biorxiv |
10.1101/001594 | Morphometrics of a wild Asian elephant exhibiting disproportionate dwarfism | Shermin de Silva;Udaya S Weerathunga;Tennekoon Pushpakumara; | Shermin de Silva | Colorado State University, EFECT, Trunks & Leaves (Inc.) | 2013-12-24 | 1 | New Results | cc_by_nc_nd | Zoology | https://www.biorxiv.org/content/early/2013/12/24/001594.source.xml | Dwarfism is a condition characterized by shorter stature, at times accompanied by differential skeletal growth pro-portions relative to the species-typical physical conformation. Causes vary and well-documented in humans as well as certain mammalian species in captive or laboratory conditions, but rarely observed in th... | 10.1186/1756-0500-7-933 | biorxiv |
10.1101/000380 | A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction | Steven Watterson;Maria-Luisa Guerriero;Mathieu Blanc;Alexander Mazein;Laurence Loewe;Kevin Robertson;Holly Gibbs;Guanghou Shui;Markus Wenk;Jane Hillston;Peter Ghazal; | Steven Watterson | University of Ulster | 2013-11-14 | 1 | New Results | cc_by | Systems Biology | https://www.biorxiv.org/content/early/2013/11/14/000380.source.xml | Graphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=37 SRC=\"FIGDIR/small/000380_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (14K):\norg.highwire.dtl.DTLVardef@197f26org.highwire.dtl.DTLVardef@1eac3f3org.highwire.dtl.DTLVardef@1e698f1org.highwire.dtl.DTLVardef@42fb4b_HPS_FORMAT_FIGEXP M_FIG C_FIG Highli... | 10.1016/j.biochi.2012.05.024 | biorxiv |
10.1101/000562 | A structural classification of candidate oscillators and multistationary systems | Franco Blanchini;Elisa Franco;Giulia Giordano; | Elisa Franco | University of California at Riverside | 2013-11-18 | 1 | New Results | cc_by_nc_nd | Systems Biology | https://www.biorxiv.org/content/early/2013/11/18/000562.source.xml | Molecular systems are uncertain: the variability of reaction parameters and the presence of unknown interactions can weaken the predictive capacity of solid mathematical models. However, strong conclusions on the admissible dynamic behaviors of a model can often be achieved without detailed knowledge of its specific pa... | 10.1007/s11538-014-0023-y | biorxiv |
10.1101/000778 | Quantifying the turnover of transcriptional subclasses of HIV-1-infected cells | Christian L Althaus;Beda Joos;Alan S Perelson;Huldrych F Günthard; | Christian L Althaus | University of Bern | 2013-11-20 | 1 | New Results | cc_by_nc_nd | Systems Biology | https://www.biorxiv.org/content/early/2013/11/20/000778.source.xml | HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses. Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells. We used previously published data from five pat... | 10.1371/journal.pcbi.1003871 | biorxiv |
10.1101/000778 | Quantifying the turnover of transcriptional subclasses of HIV-1-infected cells | Christian L Althaus;Beda Joos;Alan S Perelson;Huldrych F Günthard; | Christian L Althaus | University of Bern | 2014-01-18 | 2 | New Results | cc_by_nc_nd | Systems Biology | https://www.biorxiv.org/content/early/2014/01/18/000778.source.xml | HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses. Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells. We used previously published data from five pat... | 10.1371/journal.pcbi.1003871 | biorxiv |
10.1101/000927 | Investigating the relation between stochastic differentiation and homeostasis in intestinal crypts via multiscale modeling | Alex Graudenzi;Giulio Caravagna;Giovanni De Matteis;Marco Antoniotti; | Alex Graudenzi | Dept. of Informatics, Systems and Communication | 2013-11-25 | 1 | New Results | cc_no | Systems Biology | https://www.biorxiv.org/content/early/2013/11/25/000927.source.xml | Colorectal tumors originate and develop within intestinal crypts. Even though some of the essential phenomena that characterize crypt structure and dynamics have been effectively described in the past, the relation between the differentiation process and the overall crypt homeostasis is still partially understood. We h... | 10.1371/journal.pone.0097272 | biorxiv |
10.1101/000745 | ROS accumulation in cotton ovule epidermal cells is necessary for fiber initiation | mingxiong pang;Nickolas Sanford;Thea Wilkins; | mingxiong pang | Texas Tech University | 2013-11-19 | 1 | New Results | cc_no | Plant Biology | https://www.biorxiv.org/content/early/2013/11/19/000745.source.xml | Cotton (Gossypium hirsutum) fiber, an extremely elongated and thickened single cell of the seed epidermis, is the worlds most important natural and economical textile fiber. Unlike Arabidopsis leaf trichomes, fiber initials are randomly developed and frequently form in adjacent seed epidermal cells and follow no appare... | null | biorxiv |
10.1101/000745 | ROS accumulation in cotton ovule epidermal cells is necessary for fiber initiation | mingxiong pang;Nickolas Sanford;Thea Wilkins; | mingxiong pang | Texas Tech University | 2013-11-20 | 2 | New Results | cc_no | Plant Biology | https://www.biorxiv.org/content/early/2013/11/20/000745.source.xml | Cotton (Gossypium hirsutum) fiber, an extremely elongated and thickened single cell of the seed epidermis, is the worlds most important natural and economical textile fiber. Unlike Arabidopsis leaf trichomes, fiber initials are randomly developed and frequently form in adjacent seed epidermal cells and follow no appare... | null | biorxiv |
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