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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. | NA | biorxiv | 0 |
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 ... | NA | biorxiv | 2 |
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 | 3 |
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 | 4 |
10.1101/000836 | Journey to the Center of the Mitochondria Guided by the Tail Anchor of Protein Tyrosine Phosphatase 1B | Julia Fueller;Mikhail Egorov;Kirstin A. Walther;Ola Sabet;Jana Mallah;Markus Grabenbauer;Ali Kinkhabwala; | Ali Kinkhabwala | Max Planck Institute of Molecular Physiology | 2013-11-22 | 1 | New Results | cc_by | Cell Biology | https://www.biorxiv.org/content/early/2013/11/22/000836.source.xml | The canonical protein tyrosine phosphatase PTP1B has traditionally been considered to exclusively reside on the endoplasmic reticulum (ER). Using confocal microscopy, we show that endogenous PTP1B actually exhibits a higher local concentration at the mitochondria in all mammalian cell lines that we tested. Fluorescentl... | NA | biorxiv | 5 |
10.1101/000570 | Lipoproteins carry endocannabinoids that inhibit the Hedgehog pathway | Helena Khaliullina;Mesut Bilgin;Julio L. Sampaio;Andrej Shevchenko;Suzanne Eaton; | Suzanne Eaton | Max-Planck-Institute of Molecular Cell Biology and Genetics | 2013-11-18 | 1 | New Results | cc_no | Developmental Biology | https://www.biorxiv.org/content/early/2013/11/18/000570.source.xml | Hedgehog proteins are lipid-modified secreted signaling molecules that regulate tissue development and homeostasis. Lipids contained in circulating lipoproteins repress the Hedgehog signaling pathway in the absence of Hedgehog ligand, but the identity of these lipids is unknown. Here, using biochemical fractionation an... | NA | biorxiv | 8 |
10.1101/000307 | Drosophila embryogenesis scales uniformly across temperature and developmentally diverse species | Steven Gregory Kuntz;Michael B Eisen; | Steven Gregory Kuntz | University of California, Berkeley | 2013-11-12 | 1 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2013/11/12/000307.source.xml | Temperature affects both the timing and outcome of animal development, but the detailed effects of temperature on the progress of early development have been poorly characterized. To determine the impact of temperature on the order and timing of events during Drosophila melanogaster embryogenesis, we used time-lapse im... | 10.1371/journal.pgen.1004293 | biorxiv | 9 |
10.1101/000711 | Sap flow through petioles and petioles reveals leaf-level responses to light and vapor pressure deficit in the tropical tree Tabebuia rosea (Bignoniaceae) | Adam Roddy;Klaus Winter;Todd Dawson; | Adam Roddy | University of California, Berkeley | 2013-11-19 | 1 | New Results | cc_by | Ecology | https://www.biorxiv.org/content/early/2013/11/19/000711.source.xml | Continuous measurements of sap flow have been widely used to measure water flux through tree stems and branches. However, these measurements lack the resolution necessary for determining fine-scale, leaf-level responses to environmental variables. We used the heat ratio method to measure sap flow rates through leaf pet... | NA | biorxiv | 11 |
10.1101/000414 | The evolution of sex differences in disease genetics | William P Gilks;Jessica K Abbott;Edward H Morrow; | Jessica K Abbott | Lund University | 2013-11-14 | 1 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2013/11/14/000414.source.xml | There are significant differences in the biology of males and females, ranging from biochemical pathways to behavioural responses, which are relevant to modern medicine. Broad-sense heritability estimates differ between the sexes for many common medical disorders, indicating that genetic architecture can be sex-depende... | 10.1016/j.tig.2014.08.006 | biorxiv | 13 |
10.1101/000844 | Genomics via Optical Mapping (I): 0-1 Laws for Mapping with Single Molecules | Thomas Anantharaman;Bud (Bhubaneswar) Mishra; | Bud (Bhubaneswar) Mishra | Courant Inst., New York University | 2013-11-22 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/22/000844.source.xml | The genomic data that can be collected from a single DNA molecule by the best chemical and optical methods (e.g., using technologies from OpGen, BioNanoGenomics, NABSys, PacBio, etc.) are badly corrupted by many poorly understood noise processes. Thus, single molecule technology derives its utility through powerful pro... | NA | biorxiv | 20 |
10.1101/000604 | Aβ, tau, α-synuclein, huntingtin, TDP-43, PrP and AA are members of the innate immune system: a unifying hypothesis on the etiology of AD, PD, HD, ALS, CJD and RSA as innate immunity disorders | Claudiu I Bandea; | Claudiu I Bandea | Centers for Disease Control and Prevention | 2013-11-18 | 1 | Contradictory Results | cc_by_nc | Immunology | https://www.biorxiv.org/content/early/2013/11/18/000604.source.xml | Despite decades of research, thousands of studies and numerous advances, the etiologies of Alzheimers Disease (AD), Parkinsons Disease (PD), Huntingtons Disease (HD), Amyotrophic Lateral Sclerosis (ALS), Frontotemporal Lobar Degeneration (FTLD-U), Creutzfeldt-Jakob Disease (CJD), Reactive Systemic Amyloidosis (RSA) and... | NA | biorxiv | 21 |
10.1101/000513 | Lack of evidence for the presence of an interferon in invertebrate | Pei-Hui Wang; | Pei-Hui Wang | The University of Hong Kong | 2013-11-16 | 1 | New Results | cc_no | Immunology | https://www.biorxiv.org/content/early/2013/11/16/000513.source.xml | In vertebrates, the interferon (IFN) response is the primary form of innate antiviral defense. Previously (2005), a partial cDNA which could encode an interferon-like protein (IntlP) is reported in shrimp, later Rosa et al. (2008) argue that this partial cDNA should encode a portion of insect mitochondrial ATP synthase... | NA | biorxiv | 22 |
10.1101/000679 | Differentiation-dependent telomeric long non-coding transcription in a model of skeletal myogenesis | Scott Brouilette;Samir Ounzain;Vinit Sawhney;Kenta Yashiro;Yasunori Shintani;Kunihiko Takahashi;Steven Coppen;Takuya Narita;Kelli Torsney;Martin Carrier;Niall Campbell;Ken Suzuki; | Samir Ounzain | University of Lausanne Medical School | 2013-11-18 | 1 | New Results | cc_by_nc_nd | Molecular Biology | https://www.biorxiv.org/content/early/2013/11/18/000679.source.xml | Telomeres comprise the distal ends of eukaryotic chromosomes, serve to maintain genomic integrity and are extended by the ribonucleoprotein telomerase. Recent evidence indicates that telomeres are transcribed to generate long non-coding RNAs (lncRNAs) and that these transcripts (TERRA) may inhibit telomerase activity. ... | NA | biorxiv | 24 |
10.1101/000224 | Water and the biology of *prions* and plaques | Graham K Steel;Phillippa M Wiggins;n/a n/a; | Graham K Steel | n/a | 2013-11-12 | 1 | New Results | cc_by | Molecular Biology | https://www.biorxiv.org/content/early/2013/11/12/000224.source.xml | This is an attempt to account for the insolubility and/or aggregation of prions and plaques in terms of a model of water consisting of an equilibrium between high density and low density microdomains. Hydrophobic molecules, including proteins, accumulate selectively into stable populations, enriched in high density wat... | 10.1038/npre.2007.1381.1 | biorxiv | 25 |
10.1101/000638 | Effects of metsulfuron-methyl on aquatic plant (Lemna gibba L.) and recovery from after prolonged exposure under rice cropping conditions | Raja Rajeswari;Atmakuru Ramesh; | Atmakuru Ramesh | International Institute of bio-technology and toxicology | 2013-11-22 | 2 | Contradictory Results | cc_no | Plant Biology | https://www.biorxiv.org/content/early/2013/11/22/000638.source.xml | The effects and potential recovery of aquatic plant Lemna gibba exposed to a sulfonyl urea herbicide metsulfuron-methyl (MSM) for 120 days under rice cropping condition was investigated. The frond number was decreased by day 15 at the concentration 11 {micro}g/L and 100% inhibition on growth rate of Lemna was observed.... | NA | biorxiv | 27 |
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... | NA | biorxiv | 29 |
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 | 31 |
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 | 32 |
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 ... | NA | biorxiv | 34 |
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 | 35 |
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... | NA | biorxiv | 36 |
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 | 37 |
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... | NA | biorxiv | 38 |
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 | 41 |
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... | NA | biorxiv | 42 |
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 | 43 |
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 | 44 |
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 | 48 |
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 ... | NA | biorxiv | 49 |
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... | NA | biorxiv | 52 |
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 | 55 |
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... | NA | biorxiv | 56 |
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 | 57 |
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... | NA | biorxiv | 58 |
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 | 60 |
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 | 65 |
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 | 67 |
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 | 68 |
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 | 69 |
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 | 71 |
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 | 72 |
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 | 73 |
10.1101/001263 | Climate change triggers morphological and life-history evolution in response to predators | Edmund Hart;Nicholas Gotelli; | Edmund Hart | National Ecological Observatory Network | 2013-12-10 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2013/12/10/001263.source.xml | Although climate change is expected to reorganize entire communities, this restructuring might reflect either direct ecological or evolutionary responses to abiotic conditions or indirect effects mediated through altered species interactions. We tested the hypothesis that changes in trophic interaction strength due to ... | NA | biorxiv | 80 |
10.1101/001032 | Mechanism of β-Aminobutyric Acid-Induced Resistance in Wheat to the Grain Aphid, Sitobion avenae | He-He Cao;Meng Zhang;Hui Zhao;Yi Zhang;Xing-Xing Wang;Shan-Shan Guo;Zhan-Feng Zhang;Tong-Xian Liu; | He-He Cao | Northwest A&F University | 2013-12-02 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2013/12/02/001032.source.xml | The non-protein amino acid {beta}-aminobutyric acid (BABA) could induce plant resistance to a broad spectrum of biotic and abiotic stresses. However, BABA-induced plant resistance to insects is less well-studied, especially its underlying mechanism. In this research, we applied BABA to wheat seedlings and tested its ef... | 10.1371/journal.pone.0091768 | biorxiv | 81 |
10.1101/000893 | The Effectiveness of China’s National Forest Protection Program and National-level Nature Reserves, 2000 to 2010: PREPRINT | Guopeng Ren;Stephen S. Young;Lin Wang;Wei Wang;Yongcheng Long;Ruidong Wu;Junsheng Li;Jianguo Zhu;Douglas W. Yu; | Douglas W. Yu | Kunming Institute of Zoology | 2013-11-25 | 1 | New Results | cc_no | Ecology | https://www.biorxiv.org/content/early/2013/11/25/000893.source.xml | There is profound interest in knowing the degree to which Chinas institutions are capable of protecting its natural forests and biodiversity in the face of economic and political change. Chinas two most important forest protection policies are its National Forest Protection Program (NFPP) and its National-level Nature ... | 10.1111/cobi.12561 | biorxiv | 82 |
10.1101/001487 | Hawkish but helpful: When cultural group selection favors within-group aggression | Ben Hanowell; | Ben Hanowell | Department of Anthropology, University of Washington | 2013-12-20 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/20/001487.source.xml | The origin of cooperation is a central problem in evolutionary biology and social science. Cultural group selection and parochial altruism are popular but controversial evolutionary explanations for large-scale cooperation. Proponents of the cultural group selection hypothesis argue that the human tendency to conform--... | NA | biorxiv | 85 |
10.1101/001446 | Direct Reciprocity Under Uncertainty Does Not Explain One-Shot Cooperation, But It Can Explain Norm Psychology | Matthew Zefferman; | Matthew R Zefferman | National Institute for Mathematical and Biological Synthesis | 2013-12-17 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/17/001446.source.xml | Humans in many societies cooperate in economic experiments at much higher levels than would be expected if their goal was maximizing economic returns even when interactions are anonymous and one-shot. This is a puzzle because paying a cost to benefit another player in one-shot interactions has no direct benefit to the ... | NA | biorxiv | 86 |
10.1101/001289 | An Adaptive Threshold in Mammalian Neocortical Evolution | Eric Lewitus;Iva Kelava;Alex T Kalinka;Pavel Tomancak;Wieland B Huttner; | Wieland B Huttner | Max Planck Institute of Molecular Cell Biology and Genetics | 2013-12-16 | 2 | New Results | cc_no | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/16/001289.source.xml | Expansion of the neocortex is a hallmark of human evolution. However, it remains an open question what adaptive mechanisms facilitated its expansion. Here we show, using gyrencephaly index (GI) and other physiological and life-history data for 102 mammalian species, that gyrencephaly is an ancestral mammalian trait. We... | 10.1371/journal.pbio.1002000 | biorxiv | 88 |
10.1101/001404 | The importance of population growth and regulation in human life history evolution | Ryan Baldini; | Ryan Baldini | UC Davis | 2013-12-14 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/14/001404.source.xml | Explaining the evolution of human life history characteristics remains an outstanding problem to evolutionary anthropologists. Progress is hindered by common misunderstandings of how selection works in age-structured populations. I review two important results of life history theory related to demography. First, differ... | 10.1371/journal.pone.0119789 | biorxiv | 89 |
10.1101/001354 | A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry | Aram Yardumian; | Aram Yardumian | University of Pennsylvania | 2013-12-12 | 1 | Contradictory Results | cc_no | Genetics | https://www.biorxiv.org/content/early/2013/12/12/001354.source.xml | The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportati... | NA | biorxiv | 93 |
10.1101/001099 | OTX2 Dosage Sensitivity is Implicated in Hemifacial Microsomia | Dina Zielinski;Barak Markus;Mona Sheikh;Melissa Gymrek;Clement Chu;Marta Zaks;Balaji Srinivasan;Jodi D. Hoffman;Dror Aizenbud;Yaniv Erlich; | Yaniv Erlich | Whitehead Institute | 2013-12-03 | 1 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2013/12/03/001099.source.xml | Hemifacial microsomia (HFM) is the second most common facial anomaly after cleft lip and palate. The phenotype is highly variable and most cases are sporadic. Here, we investigated the disorder in a large pedigree with five affected individuals spanning eight meioses. We performed whole-exome sequencing and a genome-wi... | 10.1371/journal.pone.0096788 | biorxiv | 94 |
10.1101/001073 | Variational Inference of Population Structure in Large SNP Datasets | Anil Raj;Matthew Stephens;Jonathan K Pritchard; | Anil Raj | Stanford University | 2013-12-02 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2013/12/02/001073.source.xml | Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model under... | 10.1534/genetics.114.164350 | biorxiv | 95 |
10.1101/001511 | The causal meaning of genomic predictors and how it affects the construction and comparison of genome-enabled selection models | Bruno D Valente;Gota Morota;Guilherme JM Rosa;Daniel Gianola;Kent Weigel; | Bruno D Valente | University of Wisconsin - Madison | 2013-12-21 | 1 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/12/21/001511.source.xml | The additive genetic effect is arguably the most important quantity inferred in animal and plant breeding analyses. The term effect indicates that it represents causal information, which is different from standard statistical concepts as regression coefficient and association. The process of inferring causal informatio... | 10.1534/genetics.114.169490 | biorxiv | 96 |
10.1101/001479 | Massively differential bias between two widely used Illumina library preparation methods for small RNA sequencing | Jeanette Baran-Gale;Michael R Erdos;Christina Sison;Alice Young;Emily E Fannin;Peter S Chines;Praveen Sethupathy; | Praveen Sethupathy | University of North Carolina at Chapel HIll | 2013-12-19 | 1 | Confirmatory Results | cc_by_nc_nd | Genomics | https://www.biorxiv.org/content/early/2013/12/19/001479.source.xml | Recent advances in sequencing technology have helped unveil the unexpected complexity and diversity of small RNAs. A critical step in small RNA library preparation for sequencing is the ligation of adapter sequences to both the 5 and 3 ends of small RNAs. Two widely used protocols for small RNA library preparation, Ill... | 10.3389/fgene.2015.00352 | biorxiv | 97 |
10.1101/001388 | Bayesian inference of infectious disease transmission from whole genome sequence data | Xavier Didelot;Jennifer Gardy;Caroline Colijn; | Xavier Didelot | Imperial College London | 2013-12-16 | 1 | New Results | cc_by_nc_nd | Genomics | https://www.biorxiv.org/content/early/2013/12/16/001388.source.xml | Genomics is increasingly being used to investigate disease outbreaks, but an important question remains unanswered - how well do genomic data capture known transmission events, particularly for pathogens with long carriage periods or large within-host population sizes? Here we present a novel Bayesian approach to recon... | 10.1093/molbev/msu121 | biorxiv | 98 |
10.1101/000802 | Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data | Gregory R Magoon;Raymond H Banks;Christian Rottensteiner;Bonnie E Schrack;Vincent O Tilroe;Terry Robb;Andrew J Grierson; | Gregory R Magoon | Aerodyne Research, Inc. | 2013-12-13 | 5 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/12/13/000802.source.xml | An approach for generating high-resolution a priori maximum parsimony Y-chromosome (chrY) phylogenies based on SNP and small INDEL variant data from massively-parallel short-read (next-generation) sequencing data is described; the tree-generation methodology produces annotations localizing mutations to individual branc... | NA | biorxiv | 101 |
10.1101/000042 | Routes for breaching and protecting genetic privacy | Yaniv Erlich;Arvind Narayanan; | Yaniv Erlich | Whitehead Institute | 2013-12-01 | 3 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/12/01/000042.source.xml | We are entering the era of ubiquitous genetic information for research, clinical care, and personal curiosity. Sharing these datasets is vital for rapid progress in understanding the genetic basis of human diseases. However, one growing concern is the ability to protect the genetic privacy of the data originators. Here... | 10.1038/nrg3723 | biorxiv | 102 |
10.1101/000935 | The-LHON-Enigma: explaining the behaviour of Leber’s Hereditary Optic Neuropathy by the use of a simple computer model | IAN S Logan; | IAN S Logan | - | 2013-11-25 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/25/000935.source.xml | Lebers Hereditary Optic Neuropathy (LHON) appears as an enigmatic condition; affecting only certain families and often causing a severe loss of vision seemingly at random amongst family members. The first breakthrough came in 1988 with the linking of the condition to a mutation in the mitochondrial DNA (mtDNA). Now it ... | NA | biorxiv | 103 |
10.1101/001362 | Extensive Phenotypic Changes Associated with Large-scale Horizontal Gene Transfer | Kevin Dougherty;Brian A Smith;Autum F Moore;Shannon Maitland;Chris Fanger;Rachel Murillo;David A Baltrus; | David A Baltrus | University of Arizona | 2013-12-12 | 1 | New Results | cc_by_nc_nd | Microbiology | https://www.biorxiv.org/content/early/2013/12/12/001362.source.xml | Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e. changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmid... | 10.1371/journal.pone.0102170 | biorxiv | 104 |
10.1101/000968 | Functional connectivity networks with and without global signal correction | Satoru Hayasaka; | Satoru Hayasaka | Wake Forest School of Medicine | 2013-12-19 | 2 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/12/19/000968.source.xml | In functional connectivity analyses in BOLD (blood oxygenation level dependent) fMRI data, there is an ongoing debate on whether to correct global signals in fMRI time series data. Although the discussion has been ongoing in the fMRI community since the early days of fMRI data analyses, this subject has gained renewed ... | 10.3389/fnhum.2013.00880 | biorxiv | 107 |
10.1101/001198 | Genomic architecture of human neuroanatomical diversity | Roberto Toro;Jean-Baptiste Poline;Guillaume Huguet;Eva Loth;Vincent Frouin;Tobias Banaschewski;Gareth J Barker;Arun Bokde;Christian Büchel;Fabiana Carvalho;Patricia Conrod;Mira Fauth-Bühler;Herta Flor;Jürgen Gallinat;Hugh Garavan;Penny Gowloan;Andreas Heinz;Bernd Ittermann;Claire Lawrence;Hervé Lemaître;Karl Mann;Frauk... | Roberto Toro | Institut Pasteur | 2013-12-10 | 1 | New Results | cc_no | Neuroscience | https://www.biorxiv.org/content/early/2013/12/10/001198.source.xml | Human brain anatomy is strikingly diverse and highly inheritable: genetic factors may explain up to 80% of its variability. Prior studies have tried to detect genetic variants with a large effect on neuroanatomical diversity, but those currently identified account for <5% of the variance. Here we show, based on our ana... | 10.1038/mp.2014.99 | biorxiv | 111 |
10.1101/001156 | Influence of walking speed on locomotor time production | Fabrice MEGROT;Carole MEGROT; | Fabrice MEGROT | French Red Cross | 2013-12-04 | 1 | Contradictory Results | cc_by_nc | Neuroscience | https://www.biorxiv.org/content/early/2013/12/04/001156.source.xml | The aim of the present study was to determine whether or not walking speed affects temporal perception. It was hypothesized that fast walking would reduce the perceived length of time while slow walking increase production estimates. 16 healthy subjects were included. After a first << calibration >> phase allowing the ... | NA | biorxiv | 112 |
10.1101/001123 | Analysis of the study of the cerebellar pinceau by Korn and Axelrad | Antonin Blot;Boris Barbour; | Boris Barbour | Ecole Normale Supérieure | 2013-12-03 | 1 | Contradictory Results | cc_by | Neuroscience | https://www.biorxiv.org/content/early/2013/12/03/001123.source.xml | The axon initial segment of each cerebellar Purkinje cell is ensheathed by basket cell axons in a structure called the pinceau, which is largely devoid of chemical synapses and gap junctions. These facts and ultrastructural similarities with the axon cap of the teleost Mauthner cell led to the conjecture that the pince... | NA | biorxiv | 113 |
10.1101/001438 | DCL1, a Protein that Produces Plant MicroRNA, Coordinates Meristem Activity | Stephen E. Schauer;Teresa A. Golden;Delwin S. Merchant;Biranchi N. Patra;Jean D. Lang;Sumita Ray;Bulbul Chakravarti;Deb N. Chakravarti;Animesh Ray; | Animesh Ray | Keck Graduate Institute | 2013-12-21 | 2 | New Results | cc_by_nd | Plant Biology | https://www.biorxiv.org/content/early/2013/12/21/001438.source.xml | Abstract Abstract Introduction Results Discussion Materials and Methods Authors' contributions Funding References The ubiquity and importance of short duplex RNAs, termed microRNA (miRNA), for normal development in higher eukaryotes are becoming increasingly clear. We had previously shown that reduction-of-function mut... | NA | biorxiv | 118 |
10.1101/001248 | A conserved oomycete CRN effector targets and modulates tomato TCP14-2 to enhance virulence | Remco Stam;Graham Motion;Petra C. Boevink;Edgar Huitema; | Edgar Huitema | University of Dundee | 2013-12-11 | 1 | New Results | cc_by_nc_nd | Plant Biology | https://www.biorxiv.org/content/early/2013/12/11/001248.source.xml | Phytophthora spp. secrete vast arrays of effector molecules upon infection. A main class of intracellular effectors are the CRNs. They are translocated into the host cell and specifically localise to the nucleus where they are thought to perturb many different cellular processes. Although CRN proteins have been implica... | NA | biorxiv | 119 |
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 | 120 |
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... | NA | biorxiv | 121 |
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 | 122 |
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 | 125 |
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 | 132 |
10.1101/001040 | High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population | Adam L. Bailey;Michael Lauck;Andrea Weiler;Samuel D. Sibley;Jorge M. Dinis;Zachary Bergman;Chase W. Nelson;Michael Correll;Michael Gleicher;David Hyeroba;Alex Tumukunde;Geoffrey Weny;Colin Chapman;Jens Kuhn;Austin Hughes;Thomas C. Friedrich;Tony L. Goldberg;David H. O'Connor; | David H. O'Connor | University of Wisconsin - Madison | 2013-12-03 | 1 | New Results | cc_no | Microbiology | https://www.biorxiv.org/content/early/2013/12/03/001040.source.xml | Key biological properties such as high genetic diversity and high evolutionary rate enhance the potential of certain RNA viruses to adapt and emerge. Identifying viruses with these properties in their natural hosts could dramatically improve disease forecasting and surveillance. Recently, we discovered two novel member... | 10.1371/journal.pone.0090714 | biorxiv | 133 |
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... | NA | biorxiv | 134 |
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 | 136 |
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 | 137 |
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... | NA | biorxiv | 138 |
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 | 141 |
10.1101/001610 | Black rhinoceros demography should be stage, not age, based. | Peter R Law;Wayne L Linklater; | Peter R Law | na | 2013-12-30 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2013/12/30/001610.source.xml | Biologically meaningful and standardized definitions of life stages are essential for demographic studies, especially for endangered and intensively managed species such as rhinoceros. Focusing on the black rhinoceros Diceros bicornis, we argue that standardized biological definitions of calf, subadult, and adult, rath... | 10.1111/aje.12148 | biorxiv | 145 |
10.1101/001537 | Assessing the Use of Antiviral Treatment to Control Influenza | Sarah C Kramer;Shweta Bansal; | Shweta Bansal | Georgetown University; National Institutes of Health | 2013-12-26 | 1 | New Results | cc_no | Ecology | https://www.biorxiv.org/content/early/2013/12/26/001537.source.xml | Vaccines are the cornerstone of influenza control policy, but can suffer from several drawbacks. Seasonal influenza vaccines are prone to production problems and low efficacies, while pandemic vaccines are unlikely to be available in time to slow a rapidly spreading global outbreak. Antiviral therapy was found to be be... | 10.1017/S0950268814002520 | biorxiv | 146 |
10.1101/001172 | Species Delimitation using Genome-Wide SNP Data | Adam Leache;Matthew Fujita;Vladimir Minin;Remco Bouckaert; | Adam Leache | University of Washington | 2014-01-04 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/01/04/001172.source.xml | The multi-species coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian species delimitation methods typically require brute force integration over gene trees via Ma... | 10.1093/sysbio/syu018 | biorxiv | 147 |
10.1101/001529 | Revisiting the effect of population size on cumulative cultural evolution | Ryan Baldini; | Ryan Baldini | UC Davis | 2013-12-31 | 2 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/31/001529.source.xml | Henrich (2004) argued that larger populations can better maintain complex technologies because they contain more highly skilled people whom others can imitate. His original model, however, did not distinguish the effects of population size from population density or network size; a learners social network included the ... | 10.1163/15685373-12342153 | biorxiv | 148 |
10.1101/001636 | Hippocampal Motifs | Zahra Aghajan;Lavanya Acharya;Jesse Cushman;Cliff Vuong;Jason Moore;Mayank Mehta; | Mayank Mehta | UCLA | 2013-12-31 | 1 | New Results | cc_no | Neuroscience | https://www.biorxiv.org/content/early/2013/12/31/001636.source.xml | Dorsal Hippocampal neurons provide an allocentric map of space1, characterized by three key properties. First, their firing is spatially selective1-3, termed a rate code. Second, as animals traverse through place fields, neurons sustain elevated firing rates for long periods, however this has received little attention.... | 10.1038/nn.3884 | biorxiv | 149 |
10.1101/001586 | Embodied cognition, embodied regulation, and the Data Rate Theorem | Rodrick Wallace; | Rodrick Wallace | New York State Psychiatric Institute | 2014-01-13 | 2 | New Results | cc_by_nd | Neuroscience | https://www.biorxiv.org/content/early/2014/01/13/001586.source.xml | The Data Rate Theorem carries deep implications for theories of embodied cognition, extensions providing a spectrum of necessary conditions dynamic statistical models useful in empirical studies. A large deviations argument, however, implies that the regulation and stabilization of such systems is itself an interpenetr... | 10.1016/j.bica.2014.02.003 | biorxiv | 150 |
10.1101/000950 | An XA21-Associated Kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors | Xuewei Chen;Shimin Zuo;Benjamin Schwessinger;Mawsheng Chern;Patrick Canlas;Deling Ruan;Arsalan Daudi;Xiaogang Zhang;Jing Wang;Christopher Petzold;Joshua Heazlewood;Pamela C Ronald; | Pamela C Ronald | Department of Plant Pathology and the Genome Center, University of California, Davis, California 956 | 2013-12-25 | 2 | New Results | cc_by_nc_nd | Plant Biology | https://www.biorxiv.org/content/early/2013/12/25/000950.source.xml | The rice XA21 immune receptor kinase and the structurally related XA3 receptor, confer immunity to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight. Here we report the isolation of OsSERK2 (rice somatic embryogenesis receptor kinase 2) and demonstrate that OsSERK2 positively regulates immu... | 10.1093/mp/ssu003 | biorxiv | 151 |
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 | 152 |
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 | 153 |
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 | 156 |
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... | NA | biorxiv | 158 |
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 | 159 |
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 | 165 |
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 | 167 |
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 | 169 |
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 ... | NA | biorxiv | 172 |
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 | 173 |
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 | 174 |
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bioRxiv Paper Metadata Dataset
This dataset includes metadata of all papers (297,902) from bioRxiv between November 16, 2013, and March 17, 2025. To access the full text, please visit the official website by searching the paper title or DOI: https://www.biorxiv.org/ , or retrieve the paper using the official API: https://api.biorxiv.org/ .
Dataset Fields
- doi: Digital Object Identifier.
- title: Paper title.
- authors: List of authors.
- author_corresponding: Corresponding author.
- author_corresponding_institution: Corresponding author's institution.
- date: Publication date.
- version: Version information.
- type: Paper type.
- license: License information.
- category: Subject category.
- jatsxml: Content in JATS XML format.
- abstract: Abstract.
- published: Publication status.
- server: Server information.
- index_level_0: Index.
Usage
You can load the dataset using the following code:
import pandas as pd
# Log in using huggingface-cli to access this dataset
df = pd.read_parquet("hf://datasets/jackkuo/bioRxiv_meta/combined_biorxiv_data.parquet")
Update Log
- 2025-03-16: Dataset updated; future updates will occur monthly.
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