doi stringlengths 14 25 | title stringlengths 6 470 | authors stringlengths 5 600 | author_corresponding stringlengths 2 49 ⌀ | author_corresponding_institution stringlengths 1 160 ⌀ | date stringlengths 10 10 | version int64 0 25 | type stringclasses 8
values | license stringclasses 9
values | category stringclasses 58
values | jatsxml stringlengths 66 77 | abstract stringlengths 9 65.5k ⌀ | published stringlengths 12 59 ⌀ | server stringclasses 1
value |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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.... | null | biorxiv |
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... | null | biorxiv |
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 | 2013-12-16 | 1 | New Results | cc_by_nd | Plant Biology | https://www.biorxiv.org/content/early/2013/12/16/001438.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... | null | biorxiv |
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... | null | biorxiv |
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 | 2013-11-26 | 1 | New Results | cc_by_nc_nd | Plant Biology | https://www.biorxiv.org/content/early/2013/11/26/000950.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 |
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 |
10.1101/000943 | Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans | Frederick B. Shipley;Christopher M. Clark;Mark J. Alkema;Andrew M. Leifer; | Andrew M. Leifer | Princeton University | 2013-11-27 | 1 | New Results | cc_by_nc | Neuroscience | https://www.biorxiv.org/content/early/2013/11/27/000943.source.xml | Editor:\n\nA fundamental goal of systems neuroscience is to probe the dynamics of neural activity that generate behavior. Here we present an instrument to simultaneously manipulate and monitor neural activity and behavior in the freely moving nematode Caenorhabditis elegans. We use the instrument to directly observe th... | 10.3389/fncir.2014.00028 | biorxiv |
10.1101/000943 | Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans | Frederick B. Shipley;Christopher M. Clark;Mark J. Alkema;Andrew M. Leifer; | Andrew M. Leifer | Princeton University | 2013-12-01 | 2 | New Results | cc_by_nc | Neuroscience | https://www.biorxiv.org/content/early/2013/12/01/000943.source.xml | Editor:\n\nA fundamental goal of systems neuroscience is to probe the dynamics of neural activity that generate behavior. Here we present an instrument to simultaneously manipulate and monitor neural activity and behavior in the freely moving nematode Caenorhabditis elegans. We use the instrument to directly observe th... | 10.3389/fncir.2014.00028 | biorxiv |
10.1101/000943 | Simultaneous optogenetic manipulation and calcium imaging in freely moving C. elegans | Frederick B. Shipley;Christopher M. Clark;Mark J. Alkema;Andrew M. Leifer; | Andrew M. Leifer | Princeton University | 2014-04-02 | 3 | New Results | cc_by_nc | Neuroscience | https://www.biorxiv.org/content/early/2014/04/02/000943.source.xml | Editor:\n\nA fundamental goal of systems neuroscience is to probe the dynamics of neural activity that generate behavior. Here we present an instrument to simultaneously manipulate and monitor neural activity and behavior in the freely moving nematode Caenorhabditis elegans. We use the instrument to directly observe th... | 10.3389/fncir.2014.00028 | biorxiv |
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... | null | biorxiv |
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 ... | null | biorxiv |
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 |
10.1101/001214 | Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics | Adam H Marblestone;Evan R Daugharthy;Reza Kalhor;Ian D Peikon;Justus M Kebschull;Seth L Shipman;Yuriy Mishchenko;Je Hyuk Lee;David A Dalrymple;Bradley M Zamft;Konrad P Kording;Edward S Boyden;Anthony M Zador;George M Church; | Adam H Marblestone | Harvard University | 2013-12-10 | 1 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/12/10/001214.source.xml | We analyze the scaling and cost-performance characteristics of current and projected connectomics approaches, with reference to the potential implications of recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at the scale of whole mammalian brains are considered:... | null | biorxiv |
10.1101/001214 | Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics | Adam H Marblestone;Evan R Daugharthy;Reza Kalhor;Ian D Peikon;Justus M Kebschull;Seth L Shipman;Yuriy Mishchenko;Je Hyuk Lee;David A Dalrymple;Bradley M Zamft;Konrad P Kording;Edward S Boyden;Anthony M Zador;George M Church; | Adam H Marblestone | Harvard University | 2013-12-13 | 2 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/12/13/001214.source.xml | We analyze the scaling and cost-performance characteristics of current and projected connectomics approaches, with reference to the potential implications of recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at the scale of whole mammalian brains are considered:... | null | biorxiv |
10.1101/001214 | Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics | Adam H Marblestone;Evan R Daugharthy;Reza Kalhor;Ian D Peikon;Justus M Kebschull;Seth L Shipman;Yuriy Mishchenko;Je Hyuk Lee;David A Dalrymple;Bradley M Zamft;Konrad P Kording;Edward S Boyden;Anthony M Zador;George M Church; | Adam H Marblestone | Harvard University | 2013-12-16 | 3 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/12/16/001214.source.xml | We analyze the scaling and cost-performance characteristics of current and projected connectomics approaches, with reference to the potential implications of recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at the scale of whole mammalian brains are considered:... | null | biorxiv |
10.1101/001214 | Conneconomics: The Economics of Dense, Large-Scale, High-Resolution Neural Connectomics | Adam H Marblestone;Evan R Daugharthy;Reza Kalhor;Ian D Peikon;Justus M Kebschull;Seth L Shipman;Yuriy Mishchenko;Je Hyuk Lee;David A Dalrymple;Bradley M Zamft;Konrad P Kording;Edward S Boyden;Anthony M Zador;George M Church; | Adam H Marblestone | Harvard University | 2014-04-21 | 4 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2014/04/21/001214.source.xml | We analyze the scaling and cost-performance characteristics of current and projected connectomics approaches, with reference to the potential implications of recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at the scale of whole mammalian brains are considered:... | null | biorxiv |
10.1101/000968 | Functional connectivity networks with and without global signal correction | Satoru Hayasaka; | Satoru Hayasaka | Wake Forest School of Medicine | 2013-11-26 | 1 | New Results | cc_by_nc_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/11/26/000968.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 |
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 |
10.1101/001586 | Embodied cognition, embodied regulation, and the Data Rate Theorem | Rodrick Wallace; | Rodrick Wallace | New York State Psychiatric Institute | 2013-12-23 | 1 | New Results | cc_by_nd | Neuroscience | https://www.biorxiv.org/content/early/2013/12/23/001586.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 |
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 |
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 |
10.1101/000224 | Water and the biology of *prions* and plaques | Graham K Steel;Phillippa M Wiggins;n/a n/a; | Graham K Steel | null | 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 |
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. ... | null | biorxiv |
10.1101/000869 | Virulence in a Pseudomonas syringae Strain with a Small Repertoire of Predicted Effectors | Kevin L Hockett;Marc T Nishimura;Erick Karlsrud;Kevin Dougherty;David A Baltrus; | David A Baltrus | University of Arizona | 2013-11-23 | 1 | New Results | cc_no | Microbiology | https://www.biorxiv.org/content/early/2013/11/23/000869.source.xml | Both type III effector proteins and non-ribosomal peptide toxins play important roles for Pseudomonas syringae pathogenicity in host plants, but whether and how these virulence pathways interact to promote infection remains unclear. Genomic evidence from one clade of P. syringae suggests a tradeoff between the total nu... | null | biorxiv |
10.1101/000869 | Virulence in a Pseudomonas syringae Strain with a Small Repertoire of Predicted Effectors | Kevin L Hockett;Marc T Nishimura;Erick Karlsrud;Kevin Dougherty;David A Baltrus; | David A Baltrus | University of Arizona | 2014-04-21 | 2 | New Results | cc_no | Microbiology | https://www.biorxiv.org/content/early/2014/04/21/000869.source.xml | Both type III effector proteins and non-ribosomal peptide toxins play important roles for Pseudomonas syringae pathogenicity in host plants, but whether and how these virulence pathways interact to promote infection remains unclear. Genomic evidence from one clade of P. syringae suggests a tradeoff between the total nu... | null | biorxiv |
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 |
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 |
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... | null | biorxiv |
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... | null | biorxiv |
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... | null | biorxiv |
10.1101/000935 | The-LHON-Enigma: explaining the behaviour of Leber&#146;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 ... | null | biorxiv |
10.1101/000042 | Routes for breaching and protecting genetic privacy | Yaniv Erlich;Arvind Narayanan; | Yaniv Erlich | Whitehead Institute | 2013-11-07 | 1 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/07/000042.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 |
10.1101/000042 | Routes for breaching and protecting genetic privacy | Yaniv Erlich;Arvind Narayanan; | Yaniv Erlich | Whitehead Institute | 2013-11-11 | 2 | New Results | cc_by | Genomics | https://www.biorxiv.org/content/early/2013/11/11/000042.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 |
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 |
10.1101/000802 | Generation of high-resolution a priori Y-chromosome phylogenies using &#147;next-generation&#148; 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. | 2013-11-22 | 1 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/11/22/000802.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... | null | biorxiv |
10.1101/000802 | Generation of high-resolution a priori Y-chromosome phylogenies using &#147;next-generation&#148; 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. | 2013-11-22 | 2 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/11/22/000802.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... | null | biorxiv |
10.1101/000802 | Generation of high-resolution a priori Y-chromosome phylogenies using &#147;next-generation&#148; 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. | 2013-11-24 | 3 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/11/24/000802.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... | null | biorxiv |
10.1101/000802 | Generation of high-resolution a priori Y-chromosome phylogenies using &#147;next-generation&#148; 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. | 2013-12-12 | 4 | New Results | cc_no | Genomics | https://www.biorxiv.org/content/early/2013/12/12/000802.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... | null | biorxiv |
10.1101/000802 | Generation of high-resolution a priori Y-chromosome phylogenies using &#147;next-generation&#148; 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... | null | biorxiv |
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 |
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 |
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 |
10.1101/000026 | A Population Genetic Signature of Polygenic Local Adaptation | Jeremy J Berg;Graham Coop; | Graham Coop | University of California, Davis | 2013-11-07 | 1 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2013/11/07/000026.source.xml | Adaptation in response to selection on polygenic phenotypes occurs via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed knowledge about the specific loci underlying polygenic traits has begun to emerge from gen... | 10.1371/journal.pgen.1004412 | biorxiv |
10.1101/000026 | A Population Genetic Signature of Polygenic Local Adaptation | Jeremy J Berg;Graham Coop; | Graham Coop | University of California, Davis | 2014-09-08 | 2 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2014/09/08/000026.source.xml | Adaptation in response to selection on polygenic phenotypes occurs via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed knowledge about the specific loci underlying polygenic traits has begun to emerge from gen... | 10.1371/journal.pgen.1004412 | biorxiv |
10.1101/000257 | Matchmaker, Matchmaker, Make Me a Match: Migration of Populations via Marriages in the Past | Sang Hoon Lee;Robyn Ffrancon;Daniel M. Abrams;Beom Jun Kim;Mason A. Porter; | Sang Hoon Lee | Sungkyunkwan University | 2013-11-12 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2013/11/12/000257.source.xml | The study of human mobility is both of fundamental importance and of great potential value. For example, it can be leveraged to facilitate efficient city planning and improve prevention strategies when faced with epidemics. The newfound wealth of rich sources of data--including banknote flows, mobile phone records, and... | 10.1103/PhysRevX.4.041009 | biorxiv |
10.1101/000257 | Matchmaker, Matchmaker, Make Me a Match: Migration of Populations via Marriages in the Past | Sang Hoon Lee;Robyn Ffrancon;Daniel M. Abrams;Beom Jun Kim;Mason A. Porter; | Sang Hoon Lee | Sungkyunkwan University | 2014-05-27 | 2 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/05/27/000257.source.xml | The study of human mobility is both of fundamental importance and of great potential value. For example, it can be leveraged to facilitate efficient city planning and improve prevention strategies when faced with epidemics. The newfound wealth of rich sources of data--including banknote flows, mobile phone records, and... | 10.1103/PhysRevX.4.041009 | biorxiv |
10.1101/000257 | Matchmaker, Matchmaker, Make Me a Match: Migration of Populations via Marriages in the Past | Sang Hoon Lee;Robyn Ffrancon;Daniel M. Abrams;Beom Jun Kim;Mason A. Porter; | Sang Hoon Lee | Sungkyunkwan University | 2014-08-16 | 3 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/08/16/000257.source.xml | The study of human mobility is both of fundamental importance and of great potential value. For example, it can be leveraged to facilitate efficient city planning and improve prevention strategies when faced with epidemics. The newfound wealth of rich sources of data--including banknote flows, mobile phone records, and... | 10.1103/PhysRevX.4.041009 | biorxiv |
10.1101/000257 | Matchmaker, Matchmaker, Make Me a Match: Migration of Populations via Marriages in the Past | Sang Hoon Lee;Robyn Ffrancon;Daniel M. Abrams;Beom Jun Kim;Mason A. Porter; | Sang Hoon Lee | Sungkyunkwan University | 2014-10-16 | 4 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/10/16/000257.source.xml | The study of human mobility is both of fundamental importance and of great potential value. For example, it can be leveraged to facilitate efficient city planning and improve prevention strategies when faced with epidemics. The newfound wealth of rich sources of data--including banknote flows, mobile phone records, and... | 10.1103/PhysRevX.4.041009 | biorxiv |
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 |
10.1101/000687 | Human genetics and clinical aspects of neurodevelopmental disorders | Gholson J Lyon;Jason O'Rawe; | Gholson J Lyon | CSHL | 2013-11-18 | 1 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2013/11/18/000687.source.xml | Introduction Introduction Clinical classifications and the... De novo mutations, germline... Rare and compensatory mutations Current ability / approaches Prenatal diagnosis,... Implications for acceptance,... Conclusions References \"our incomplete studies do not permit actual classification; but it is better to leave ... | null | biorxiv |
10.1101/000687 | Human genetics and clinical aspects of neurodevelopmental disorders | Gholson J Lyon;Jason O'Rawe; | Gholson J Lyon | CSHL | 2014-02-20 | 2 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2014/02/20/000687.source.xml | Introduction Introduction Clinical classifications and the... De novo mutations, germline... Rare and compensatory mutations Current ability / approaches Prenatal diagnosis,... Implications for acceptance,... Conclusions References \"our incomplete studies do not permit actual classification; but it is better to leave ... | null | biorxiv |
10.1101/000687 | Human genetics and clinical aspects of neurodevelopmental disorders | Gholson J Lyon;Jason O'Rawe; | Gholson J Lyon | CSHL | 2014-06-22 | 3 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2014/06/22/000687.source.xml | Introduction Introduction Clinical classifications and the... De novo mutations, germline... Rare and compensatory mutations Current ability / approaches Prenatal diagnosis,... Implications for acceptance,... Conclusions References \"our incomplete studies do not permit actual classification; but it is better to leave ... | null | biorxiv |
10.1101/000687 | Human genetics and clinical aspects of neurodevelopmental disorders | Gholson J Lyon;Jason O'Rawe; | Gholson J Lyon | CSHL | 2014-10-06 | 4 | New Results | cc_by | Genetics | https://www.biorxiv.org/content/early/2014/10/06/000687.source.xml | Introduction Introduction Clinical classifications and the... De novo mutations, germline... Rare and compensatory mutations Current ability / approaches Prenatal diagnosis,... Implications for acceptance,... Conclusions References \"our incomplete studies do not permit actual classification; but it is better to leave ... | null | biorxiv |
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 |
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 |
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... | null | biorxiv |
10.1101/001453 | Selection signatures in worldwide Sheep populations | Maria-Ines Fariello;Bertrand Servin;Gwenola Tosser-Klopp;Rachelle Rupp;Carole Moreno;International Sheep Genomics Consortium n.a.;Magali San Cristobal;simon boitard; | simon boitard | INRA | 2013-12-17 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2013/12/17/001453.source.xml | The diversity of populations in domestic species offer great opportunities to study genome response to selection. The recently published Sheep Hapmap dataset is a great example of characterization of the world wide genetic diversity in the Sheep. In this study, we re-analyzed the Sheep Hapmap dataset to identify select... | 10.1371/journal.pone.0103813 | biorxiv |
10.1101/001453 | Selection signatures in worldwide Sheep populations | Maria-Ines Fariello;Bertrand Servin;Gwenola Tosser-Klopp;Rachelle Rupp;Carole Moreno;International Sheep Genomics Consortium n.a.;Magali San Cristobal;simon boitard; | simon boitard | INRA | 2014-04-11 | 2 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/04/11/001453.source.xml | The diversity of populations in domestic species offer great opportunities to study genome response to selection. The recently published Sheep Hapmap dataset is a great example of characterization of the world wide genetic diversity in the Sheep. In this study, we re-analyzed the Sheep Hapmap dataset to identify select... | 10.1371/journal.pone.0103813 | biorxiv |
10.1101/001552 | Ancient human genomes suggest three ancestral populations for present-day Europeans | Iosif Lazaridis;Nick Patterson;Alissa Mittnik;Gabriel Renaud;Swapan Mallick;Karola Kirsanow;Peter H. Sudmant;Joshua G. Schraiber;Sergi Castellano;Mark Lipson;Bonnie Berger;Christos Economou;Ruth Bollongino;Qiaomei Fu;Kirsten Bos;Susanne Nordenfelt;Heng Li;Cesare de Filippo;Kay Prüfer;Susanna Sawyer;Cosimo Posth;Wolfgan... | Johannes Krause | Institute for Archaeological Sciences, University of Tübingen | 2013-12-23 | 1 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2013/12/23/001552.source.xml | We sequenced genomes from a [~]7,000 year old early farmer from Stuttgart in Germany, an [~]8,000 year old hunter-gatherer from Luxembourg, and seven [~]8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great m... | 10.1038/nature13673 | biorxiv |
10.1101/001552 | Ancient human genomes suggest three ancestral populations for present-day Europeans | Iosif Lazaridis;Nick Patterson;Alissa Mittnik;Gabriel Renaud;Swapan Mallick;Karola Kirsanow;Peter H. Sudmant;Joshua G. Schraiber;Sergi Castellano;Mark Lipson;Bonnie Berger;Christos Economou;Ruth Bollongino;Qiaomei Fu;Kirsten Bos;Susanne Nordenfelt;Heng Li;Cesare de Filippo;Kay Prüfer;Susanna Sawyer;Cosimo Posth;Wolfgan... | Johannes Krause | Institute for Archaeological Sciences, University of Tübingen | 2014-04-02 | 2 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/04/02/001552.source.xml | We sequenced genomes from a [~]7,000 year old early farmer from Stuttgart in Germany, an [~]8,000 year old hunter-gatherer from Luxembourg, and seven [~]8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great m... | 10.1038/nature13673 | biorxiv |
10.1101/001552 | Ancient human genomes suggest three ancestral populations for present-day Europeans | Iosif Lazaridis;Nick Patterson;Alissa Mittnik;Gabriel Renaud;Swapan Mallick;Karola Kirsanow;Peter H. Sudmant;Joshua G. Schraiber;Sergi Castellano;Mark Lipson;Bonnie Berger;Christos Economou;Ruth Bollongino;Qiaomei Fu;Kirsten Bos;Susanne Nordenfelt;Heng Li;Cesare de Filippo;Kay Prüfer;Susanna Sawyer;Cosimo Posth;Wolfgan... | Johannes Krause | Institute for Archaeological Sciences, University of Tübingen | 2014-04-02 | 3 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/04/02/001552.source.xml | We sequenced genomes from a [~]7,000 year old early farmer from Stuttgart in Germany, an [~]8,000 year old hunter-gatherer from Luxembourg, and seven [~]8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great m... | 10.1038/nature13673 | biorxiv |
10.1101/001552 | Ancient human genomes suggest three ancestral populations for present-day Europeans | Iosif Lazaridis;Nick Patterson;Alissa Mittnik;Gabriel Renaud;Swapan Mallick;Karola Kirsanow;Peter H. Sudmant;Joshua G. Schraiber;Sergi Castellano;Mark Lipson;Bonnie Berger;Christos Economou;Ruth Bollongino;Qiaomei Fu;Kirsten Bos;Susanne Nordenfelt;Heng Li;Cesare de Filippo;Kay Prüfer;Susanna Sawyer;Cosimo Posth;Wolfgan... | Johannes Krause | Institute for Archaeological Sciences, University of Tübingen | 2014-04-05 | 4 | New Results | cc_by_nc_nd | Genetics | https://www.biorxiv.org/content/early/2014/04/05/001552.source.xml | We sequenced genomes from a [~]7,000 year old early farmer from Stuttgart in Germany, an [~]8,000 year old hunter-gatherer from Luxembourg, and seven [~]8,000 year old hunter-gatherers from southern Sweden. We analyzed these data together with other ancient genomes and 2,345 contemporary humans to show that the great m... | 10.1038/nature13673 | biorxiv |
10.1101/001347 | Evaluating the use of ABBA-BABA statistics to locate introgressed loci | Simon H. Martin;John W. Davey;Chris D. Jiggins; | Simon H. Martin | University of Cambridge | 2013-12-11 | 1 | New Results | cc_by | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/11/001347.source.xml | Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Pattersons D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structur... | 10.1093/molbev/msu269 | biorxiv |
10.1101/001347 | Evaluating the use of ABBA-BABA statistics to locate introgressed loci | Simon H. Martin;John W. Davey;Chris D. Jiggins; | Simon H. Martin | University of Cambridge | 2014-06-02 | 2 | New Results | cc_by | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/06/02/001347.source.xml | Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Pattersons D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structur... | 10.1093/molbev/msu269 | biorxiv |
10.1101/001347 | Evaluating the use of ABBA-BABA statistics to locate introgressed loci | Simon H. Martin;John W. Davey;Chris D. Jiggins; | Simon H. Martin | University of Cambridge | 2014-08-20 | 3 | New Results | cc_by | Evolutionary Biology | https://www.biorxiv.org/content/early/2014/08/20/001347.source.xml | Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Pattersons D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structur... | 10.1093/molbev/msu269 | biorxiv |
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 |
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 | 2013-12-13 | 1 | New Results | cc_no | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/13/001289.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 |
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 |
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 ... | null | biorxiv |
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--... | null | biorxiv |
10.1101/001529 | Revisiting the effect of population size on cumulative cultural evolution | Ryan Baldini; | Ryan Baldini | UC Davis | 2013-12-21 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/21/001529.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 |
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 |
10.1101/001172 | Species Delimitation using Genome-Wide SNP Data | Adam Leache;Matthew Fujita;Vladimir Minin;Remco Bouckaert; | Adam Leache | University of Washington | 2013-12-05 | 1 | New Results | cc_by_nc_nd | Evolutionary Biology | https://www.biorxiv.org/content/early/2013/12/05/001172.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 |
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 |
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... | null | biorxiv |
10.1101/000760 | Linking indices for biodiversity monitoring to extinction risk theory | Michael A. McCarthy;Alana L. Moore;Jochen Krauss;John W Morgan;Christopher F. Clements; | Michael A. McCarthy | The University of Melbourne | 2013-11-21 | 1 | New Results | cc_no | Ecology | https://www.biorxiv.org/content/early/2013/11/21/000760.source.xml | Biodiversity indices often combine data from different species when used in monitoring programs. Heuristic properties can suggest preferred indices, but we lack objective ways to discriminate between indices with similar heuristics. Biodiversity indices can be evaluated by determining how well they reflect management o... | 10.1111/cobi.12308 | biorxiv |
10.1101/000760 | Linking indices for biodiversity monitoring to extinction risk theory | Michael A. McCarthy;Alana L. Moore;Jochen Krauss;John W Morgan;Christopher F. Clements; | Michael A. McCarthy | The University of Melbourne | 2014-02-07 | 2 | New Results | cc_no | Ecology | https://www.biorxiv.org/content/early/2014/02/07/000760.source.xml | Biodiversity indices often combine data from different species when used in monitoring programs. Heuristic properties can suggest preferred indices, but we lack objective ways to discriminate between indices with similar heuristics. Biodiversity indices can be evaluated by determining how well they reflect management o... | 10.1111/cobi.12308 | biorxiv |
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 |
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 |
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 ... | null | biorxiv |
10.1101/001255 | Broad-scale spatial patterns of canopy cover and pond morphology affect the structure of a Neotropical amphibian metacommunity | Diogo B. Provete;Thiago Gonçalves-Souza;Michel Garey;Itamar A. Martins;Denise Rossa-Feres; | Diogo B. Provete | Universidade Federal de Goiás | 2013-12-10 | 1 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2013/12/10/001255.source.xml | Spatial and environmental processes influence species composition at distinct scales. Previous studies suggested that the landscape-scale distribution of larval anurans is influenced by environmental gradients related to adult breeding site selection, such as pond canopy cover, but not water chemistry. However, the com... | 10.1007/s10750-014-1870-0 | biorxiv |
10.1101/001255 | Broad-scale spatial patterns of canopy cover and pond morphology affect the structure of a Neotropical amphibian metacommunity | Diogo B. Provete;Thiago Gonçalves-Souza;Michel Garey;Itamar A. Martins;Denise Rossa-Feres; | Diogo B. Provete | Universidade Federal de Goiás | 2014-04-09 | 2 | New Results | cc_by_nc_nd | Ecology | https://www.biorxiv.org/content/early/2014/04/09/001255.source.xml | Spatial and environmental processes influence species composition at distinct scales. Previous studies suggested that the landscape-scale distribution of larval anurans is influenced by environmental gradients related to adult breeding site selection, such as pond canopy cover, but not water chemistry. However, the com... | 10.1007/s10750-014-1870-0 | biorxiv |
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 |
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 |
10.1101/001677 | Beyond species: why ecological interaction networks vary through space and time | Timothée Poisot;Daniel B Stouffer;Dominique Gravel; | Timothée Poisot | Université du Québec à Rimouski | 2014-01-03 | 1 | New Results | cc_by_nd | Ecology | https://www.biorxiv.org/content/early/2014/01/03/001677.source.xml | Community ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological ... | 10.1111/oik.01719 | biorxiv |
10.1101/001677 | Beyond species: why ecological interaction networks vary through space and time | Timothée Poisot;Daniel B Stouffer;Dominique Gravel; | Timothée Poisot | Université du Québec à Rimouski | 2014-01-04 | 2 | New Results | cc_by_nd | Ecology | https://www.biorxiv.org/content/early/2014/01/04/001677.source.xml | Community ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological ... | 10.1111/oik.01719 | biorxiv |
10.1101/001677 | Beyond species: why ecological interaction networks vary through space and time | Timothée Poisot;Daniel B Stouffer;Dominique Gravel; | Timothée Poisot | Université du Québec à Rimouski | 2014-04-11 | 3 | New Results | cc_by_nd | Ecology | https://www.biorxiv.org/content/early/2014/04/11/001677.source.xml | Community ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological ... | 10.1111/oik.01719 | biorxiv |
10.1101/001677 | Beyond species: why ecological interaction networks vary through space and time | Timothée Poisot;Daniel B Stouffer;Dominique Gravel; | Timothée Poisot | Université du Québec à Rimouski | 2014-07-21 | 4 | New Results | cc_by | Ecology | https://www.biorxiv.org/content/early/2014/07/21/001677.source.xml | Community ecology is tasked with the considerable challenge of predicting the structure, and properties, of emerging ecosystems. It requires the ability to understand how and why species interact, as this will allow the development of mechanism-based predictive models, and as such to better characterize how ecological ... | 10.1111/oik.01719 | biorxiv |
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 |
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... | null | biorxiv |
10.1101/000653 | An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells | David A Turner;Jamie Trott;Penelope Hayward;Pau Rué;Alfonso Martinez Arias; | Alfonso Martinez Arias | Department of Genetics. University of Cambridge. Cambridge CB2 3EH. UK. | 2013-11-18 | 1 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2013/11/18/000653.source.xml | Embryonic Stem cells derived from the epiblast tissue of the mammalian blastocyst, retain the capability to differentiate into any adult cell type and are able to self-renew indefinitely under appropriate culture conditions. Despite the large amount of knowledge that we have accumulated to date about the regulation and... | 10.1242/bio.20148409 | biorxiv |
10.1101/000653 | An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells | David A Turner;Jamie Trott;Penelope Hayward;Pau Rué;Alfonso Martinez Arias; | Alfonso Martinez Arias | Department of Genetics. University of Cambridge. Cambridge CB2 3EH. UK. | 2013-11-21 | 2 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2013/11/21/000653.source.xml | Embryonic Stem cells derived from the epiblast tissue of the mammalian blastocyst, retain the capability to differentiate into any adult cell type and are able to self-renew indefinitely under appropriate culture conditions. Despite the large amount of knowledge that we have accumulated to date about the regulation and... | 10.1242/bio.20148409 | biorxiv |
10.1101/000653 | An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells | David A Turner;Jamie Trott;Penelope Hayward;Pau Rué;Alfonso Martinez Arias; | Alfonso Martinez Arias | Department of Genetics. University of Cambridge. Cambridge CB2 3EH. UK. | 2014-01-30 | 3 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2014/01/30/000653.source.xml | Embryonic Stem cells derived from the epiblast tissue of the mammalian blastocyst, retain the capability to differentiate into any adult cell type and are able to self-renew indefinitely under appropriate culture conditions. Despite the large amount of knowledge that we have accumulated to date about the regulation and... | 10.1242/bio.20148409 | biorxiv |
10.1101/000653 | An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells | David A Turner;Jamie Trott;Penelope Hayward;Pau Rué;Alfonso Martinez Arias; | Alfonso Martinez Arias | Department of Genetics. University of Cambridge. Cambridge CB2 3EH. UK. | 2014-01-30 | 4 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2014/01/30/000653.source.xml | Embryonic Stem cells derived from the epiblast tissue of the mammalian blastocyst, retain the capability to differentiate into any adult cell type and are able to self-renew indefinitely under appropriate culture conditions. Despite the large amount of knowledge that we have accumulated to date about the regulation and... | 10.1242/bio.20148409 | biorxiv |
10.1101/000653 | An interplay between extracellular signalling and the dynamics of the exit from pluripotency drives cell fate decisions in mouse ES cells | David A Turner;Jamie Trott;Penelope Hayward;Pau Rué;Alfonso Martinez Arias; | Alfonso Martinez Arias | Department of Genetics. University of Cambridge. Cambridge CB2 3EH. UK. | 2014-06-30 | 5 | New Results | cc_by | Developmental Biology | https://www.biorxiv.org/content/early/2014/06/30/000653.source.xml | Embryonic Stem cells derived from the epiblast tissue of the mammalian blastocyst, retain the capability to differentiate into any adult cell type and are able to self-renew indefinitely under appropriate culture conditions. Despite the large amount of knowledge that we have accumulated to date about the regulation and... | 10.1242/bio.20148409 | biorxiv |
10.1101/001685 | Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones | Stefan Siebert;Freya E. Goetz;Samuel H. Church;Pathikrit Bhattacharyya;Felipe Zapata;Steven H.D. Haddock;Casey W. Dunn; | Stefan Siebert | Brown University | 2014-01-06 | 1 | New Results | cc_by_nc_nd | Developmental Biology | https://www.biorxiv.org/content/early/2014/01/06/001685.source.xml | BackgroundSiphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies) Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-... | 10.1186/s13227-015-0018-2 | biorxiv |
10.1101/001685 | Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones | Stefan Siebert;Freya E. Goetz;Samuel H. Church;Pathikrit Bhattacharyya;Felipe Zapata;Steven H.D. Haddock;Casey W. Dunn; | Stefan Siebert | Brown University | 2015-03-16 | 2 | New Results | cc_by_nc_nd | Developmental Biology | https://www.biorxiv.org/content/early/2015/03/16/001685.source.xml | BackgroundSiphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies) Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-... | 10.1186/s13227-015-0018-2 | biorxiv |
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... | null | biorxiv |
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 | 2013-12-29 | 1 | New Results | cc_no | Cell Biology | https://www.biorxiv.org/content/early/2013/12/29/001602.source.xml | Proteasome inhibition elicits an evolutionarily conserved response wherein proteasome subunit mRNAs are upregulated, resulting in recovery of proteasome activity. We previously demonstrated that the transcription factor Nrf1 mediates this homeostatic response in mammalian cells. We show here that Nrf1 is initially tran... | 10.7554/eLife.01856.001 | biorxiv |
10.1101/001602 | 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 | 2013-12-30 | 2 | New Results | cc_no | Cell Biology | https://www.biorxiv.org/content/early/2013/12/30/001602.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 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.