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Petabase-scale sequence alignment catalyses viral discovery

Abstract

Not specified

Authors: Robert C. Edgar, Jeff Taylor, Tomer Altman, Pierre Barbera, Dmitry Meleshko, Victor Lin, Dan Lohr, Gherman Novakovsky, Basem Al-Shayeb, Jillian F. Banfield, Anton Korobeynikov, Rayan Chikhi, Artem Babaian

Date Published: 10th Aug 2020

Publication Type: Journal

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

Abstract

Not specified

Authors: Alexey Kozlov, Joao Alves, Alexandros Stamatakis, David Posada

Date Published: 2nd Aug 2020

Publication Type: Journal

Photometric detection of internal gravity waves in upper main-sequence stars

Abstract (Expand)

Context. Massive stars are predicted to excite internal gravity waves (IGWs) by turbulent core convection and from turbulent pressure fluctuations in their near-surface layers. These IGWs are extremely … efficient at transporting angular momentum and chemical species within stellar interiors, but they remain largely unconstrained observationally. Aims. We aim to characterise the photometric detection of IGWs across a large number of O and early-B stars in the Hertzsprung–Russell diagram, and explain the ubiquitous detection of stochastic variability in the photospheres of massive stars. Methods. We combined high-precision time-series photometry from the NASA Transiting Exoplanet Survey Satellite with high-resolution ground-based spectroscopy of 70 stars with spectral types O and B to probe the relationship between the photometric signatures of IGWs and parameters such as spectroscopic mass, luminosity, and macroturbulence. Results. A relationship is found between the location of a star in the spectroscopic Hertzsprung–Russell diagram and the amplitudes and frequencies of stochastic photometric variability in the light curves of massive stars. Furthermore, the properties of the stochastic variability are statistically correlated with macroturbulent velocity broadening in the spectral lines of massive stars. Conclusions. The common ensemble morphology for the stochastic low-frequency variability detected in space photometry and its relationship to macroturbulence is strong evidence for IGWs in massive stars, since these types of waves are unique in providing the dominant tangential velocity field required to explain the observed spectroscopy.

Authors: D. M. Bowman, S. Burssens, S. Simón-Díaz, P. V. F. Edelmann, T. M. Rogers, L. Horst, F. K. Röpke, C. Aerts

Date Published: 1st Aug 2020

Publication Type: Journal

SBML Level 3: an extensible format for the exchange and reuse of biological models

Abstract

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Authors: Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

Date Published: 1st Aug 2020

Publication Type: Journal

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry

Abstract

Not specified

Authors: Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz

Date Published: 27th Jul 2020

Publication Type: Journal

Towards standardization guidelines for in silico approaches in personalized medicine

Abstract (Expand)

Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind … its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.

Authors: Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath

Date Published: 24th Jul 2020

Publication Type: Journal

PSIXAS : A Psi4 plugin for efficient simulations of X‐ray absorption spectra based on the transition‐potential and Δ‐Kohn–Sham method

Abstract (Expand)

Near edge X‐ray absorption fine structure (NEXAFS) spectra and their pump‐probe extension (PP‐NEXAFS) offer insights into valence‐ and core‐excited states. We present PSIXAS, a recent implementation … for simulating NEXAFS and PP‐NEXAFS spectra by means of the transition‐potential and the Δ‐Kohn–Sham method. The approach is implemented in form of a software plugin for the Psi4 code, which provides access to a wide selection of basis sets as well as density functionals. We briefly outline the theoretical foundation and the key aspects of the plugin. Then, we use the plugin to simulate PP‐NEXAFS spectra of thymine, a system already investigated by others and us. It is found that larger, extended basis sets are needed to obtain more accurate absolute resonance positions. We further demonstrate that, in contrast to ordinary NEXAFS simulations, where the choice of the density functional plays a minor role for the shape of the spectrum, for PP‐NEXAFS simulations the choice of the density functional is important. Especially hybrid functionals (which could not be used straightforwardly before to simulate PP‐NEXAFS spectra) and their amount of “Hartree‐Fock like” exact exchange affects relative resonance positions in the spectrum.

Authors: Christopher Ehlert, Tillmann Klamroth

Date Published: 15th Jul 2020

Publication Type: Journal

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