cran: BEST | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-81688-5

Fungal diversity and community structure from coastal and barrier island beaches in the United States Gulf of Mexico
Cited by: 14
Author(s): Allison K. Walker, Brent M. Robicheau
Software Mentions: 16
Published: over 3 years ago

10.1371/journal.pone.0231982

Rapid processing of neutral and angry expressions within ongoing facial stimulus streams: Is it all about isolated facial features?
Cited by: 2
Author(s): Antonio Schettino, Emanuele Porcu, Christopher Gundlach, Christian Keitel, Matthias Müller
Software Mentions: 16
Published: about 4 years ago

10.3389/fmicb.2015.00104

Long-term forest soil warming alters microbial communities in temperate forest soils
Cited by: 237
Author(s): Kristen M. DeAngelis, Grace Pold, Begüm D. Topçuoğlu, Linda T. A. van Diepen, Rebecca Varney, Jeffrey L. Blanchard, Jerry M. Melillo, Serita D. Frey
Software Mentions: 15
Published: over 9 years ago

10.1186/s12940-018-0417-7

Swimmer’s itch in Canada: a look at the past and a survey of the present to plan for the future
Cited by: 13
Author(s): Michelle A. Gordy, Tyler P. Cobb, Patrick C. Hanington
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pone.0237435

Translating episodic future thinking manipulations for clinical use: Development of a clinical control
Cited by: 6
Author(s): Jillian M. Rung, Leonard H. Epstein
Software Mentions: 7
Published: almost 4 years ago

10.1111/mec.13891

Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African <scp>HIV</scp>/<scp>AIDS</scp> cohort
Cited by: 51
Author(s): Mathieu Vanhove, Mathew A. Beale, Johanna Rhodes, Duncan Chanda, Shabir Lakhi, Geoffrey Kwenda, Síle F. Molloy, Natasha Karunaharan, Neil Stone, Thomas S. Harrison, Tihana Bicanic, Matthew C. Fisher
Software Mentions: 7
Published: over 7 years ago

10.1186/s13012-018-0715-z

Proceedings of the 4th Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2017: implementation mechanisms: what makes implementation work and why? part 2
Cited by: 1
Author(s): Bryan Garner, David Kaiser, Michael Bradshaw, Elizabeth Ball, Alyssa Katherine Toro, James H. Ford, Mark Zehner, Heather J. Gotham, Traci Rieckmann, Michael Chaple, Kate Speck, Denna Vandersloot, Mat Roosa, Steve Martino
Software Mentions: 7
Published: about 6 years ago

10.21203/rs.3.rs-726620/v1

Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation.
Cited by: 27
Author(s): Mericien Venzon, Lucie Bernard-Raichon, Jonathan Klein, Jordan Axelrad, Grant A. Hussey, Alexis Sullivan, Arnau Casanovas‐Massana, María G. Noval, Ana M. Valero-Jimenez, Juan Gago, Evan Wilder, Yale Impact Team, Akiko Iwasaki, Lorna E. Thorpe, Dan R. Littman, Meike Dittmann, Kenneth A. Stapleford, Bo Shopsin, Victor J. Torres, Albert Icksang Ko, Ken Cadwell, Jonas Schluter
Software Mentions: 6
Published: almost 3 years ago

10.3389/fmicb.2016.00372

A Combination of Biochar–Mineral Complexes and Compost Improves Soil Bacterial Processes, Soil Quality, and Plant Properties
Cited by: 62
Author(s): Jun Ye, Rui Zhang, Shaun Nielsen, Stephen Joseph, Danfeng Huang, Torsten Thomas
Software Mentions: 6
Published: about 8 years ago

10.1093/gigascience/gix049

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
Cited by: 114
Author(s): Sarah S.T. Mak, Shyam Gopalakrishnan, Christian Carøe, Chunyu Geng, Shanlin Liu, Mikkel‐Holger S. Sinding, Lukas F. K. Kuderna, Wenwei Zhang, Shujin Fu, Filipe Garrett Vieira, Mietje Germonpré, Hervé Bocherens, Sergey Fedorov, Bent Petersen, Thomas Sicheritz-Pontén, Tomás Marquès-Bonet, Guojie Zhang, Hui Jiang, M. Thomas P. Gilbert
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0218582

Agricultural impacts on streams near Nitrate Vulnerable Zones: A case study in the Ebro basin, Northern Spain
Cited by: 8
Author(s): Rubén Ladrera, Óscar Belmar, Rafael Tomás, Narcı́s Prat, Miguel Cañedo‐Argüelles
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2021.652623

Construction of Condition-Specific Gene Regulatory Network Using Kernel Canonical Correlation Analysis
Cited by: 2
Author(s): Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Wi Hoon Jung, Sun Kim
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pone.0078120

Effective Population Size, Genetic Variation, and Their Relevance for Conservation: The Bighorn Sheep in Tiburon Island and Comparisons with Managed Artiodactyls
Cited by: 20
Author(s): Jaime Gasca-Pineda, Ivonne Cassaigne, Ricardo Alonso, Luis E. Eguiarte
Software Mentions: 5
Published: over 10 years ago

10.3389/fmicb.2019.02143

The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil
Cited by: 37
Author(s): Benjamin Moreira‐Grez, Kang Tam, Adam T. Cross, Jean Wan Hong Yong, Deepak Kumaresan, Paul Nevill, Mark Farrell, Andrew S. Whiteley
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0048990

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
Cited by: 58
Author(s): Jonathan J. Fong, Jeremy M. Brown, Matthew K. Fujita, Bastien Boussau
Software Mentions: 5
Published: over 11 years ago

10.1186/1471-2105-12-S9-S4

Fast and accurate methods for phylogenomic analyses
Cited by: 34
Author(s): Jimmy C. Yang, Tandy Warnow
Software Mentions: 5
Published: over 12 years ago

10.7717/peerj.2064

Microfungal oasis in an oligotrophic desert: diversity patterns and community structure in three freshwater systems of Cuatro Ciénegas, Mexico
Cited by: 13
Author(s): Patricia Vélez, Jaime Gasca-Pineda, Edmundo Rosique-Gil, Luis E. Eguiarte, Laura Espinosa-Asuar, Valeria Souza
Software Mentions: 5
Published: almost 8 years ago

10.1186/s40168-017-0301-7

Environmental drivers of viral community composition in Antarctic soils identified by viromics
Cited by: 87
Author(s): Evelien M. Adriaenssens, Rolf Kramer, Marc W. Van Goethem, Thulani P. Makhalanyane, Ian D. Hogg, Don A. Cowan
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2019.00069

Subsurface Microbial Habitats in an Extreme Desert Mars-Analog Environment
Cited by: 37
Author(s): Kimberley Warren‐Rhodes, Kevin C. Lee, Stephen Archer, Nathalie A. Cabrol, Linda Ng-Boyle, David Wettergreen, K. Zacny, Stephen B. Pointing
Software Mentions: 4
Published: about 5 years ago

10.3897/BDJ.3.e5848

PESI - a taxonomic backbone for Europe
Cited by: 19
Author(s): Yde de Jong, Juliana H.M. Kouwenberg, Louis Boumans, Charles G. Hussey, Roger Hyam, Nicky Nicolson, Paul M. Kirk, Alan Paton, Ellinor Michel, Michael D. Guiry, Phillip S Boegh, Henrik Ærenlund Pedersen, Henrik Enghoff, Eckhard Von Raab-Straube, Anton Güntsch, Marc Geoffroy, Andreas Müller, Andreas Kohlbecker, Walter G. Berendsohn, Ward Appeltans, Christos Arvanitidis, B. Vanhoorne, Joram Declerck, L. Vandepitte, F. Hernández, Róisín Nash, Mark J. Costello, David Ouvrard, Pascale Bezard-Falgas, Thierry Bourgoin, Florian T. Wetzel, Falko Glöckler, Günther Korb, Caroline Ring, Gregor Hagedorn, Christoph L. Häuser, Nihat Aktaç, Ahmet Asan, Adorian Ardelean, Paulo A. V. Borges, Dhimiter Dhora, Hasmik Khachatryan, Michael Malicky, Shaig Ibrahimov, Alexander V. Tuzikov, Aaike De Wever, Snejana Moncheva, Nikolaï Spassov, Karel Chobot, Alexi Popov, Igor Boršić, Spyros Sfenthourakis, Urmas Kõljalg, Pertti Uotila, Olivier Gargominy, Jean‐Claude Dauvin, David Tarkhnishvili, Giorgi Chaladze, Michael Tuerkay, Anastasios Legakis, László Peregovits, Gestur Guðmundsson, Erling Ólafsson, Liam Lysaght, Bella S. Galil, Francesco María Raimondo, Gianniantonio Domina, Fabio Stoch, Alessandro Minelli, Voldermars Spungis, Eduardas Budrys, Sergej Olenin, Armand Turpel, Tania J. Walisch, Vladimir Krpach, Marie Therese Gambin, Laurenția Ungureanu, Gordan S. Karaman, R.M.J.C. Kleukers, Elisabeth Stur, Kaare Aagaard, Nils Valland, Toril Loennechen Moen, Wiesław Bogdanowicz, Piotr Tykarski, Jan Marcin Węsławski, Monika Kędra, António M. de Frias Martins, António Domingos Abreu, Ricardo Silva, С. Г. Медведев, Alexander Ryss, Smiljka Šimić, Karol Marhold, Eduard Stloukal, Davorin Tome, Marian A. Ramos, B. Valdés, Francisco José Pina, S. Kullander, Anders Telenius, Yves Gonseth, Pascal Tschudin, O. A. Sergeyeva, V. Vladymyrov, Volodymyr Rizun, Chris Raper, Dan Lear, Pavel Stoev, Lyubomir Penev, Ana Casino Rubio, Thierry Backeljau, Hannu Saarenmaa, S.A. Ulenberg
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0080641

Distinguishing between Incomplete Lineage Sorting and Genomic Introgressions: Complete Fixation of Allospecific Mitochondrial DNA in a Sexually Reproducing Fish (Cobitis; Teleostei), despite Clonal Reproduction of Hybrids
Cited by: 54
Author(s): Lukáš Choleva, Zuzana Musilová, Alena Kohoutova-Sediva, Jan Pačes, Petr Ráb, Karel Janko
Software Mentions: 4
Published: almost 10 years ago

10.1107/S1600576714022730

Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing inJBluIcebeamline control system
Cited by: 12
Author(s): Sudhir Babu Pothineni, Nagarajan Venugopalan, Craig M. Ogata, Mark Hilgart, С. А. Степанов, Ruslan Sanishvili, Michael E. Becker, Graeme Winter, Nicholas K. Sauter, Janet L. Smith, Robert F. Fischetti
Software Mentions: 4
Published: over 9 years ago

10.1186/s13326-018-0181-1

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature
Cited by: 32
Author(s): Mercedes Argüello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadić, Julie Klein, John Keane, Robert Stevens
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-020-59210-0

Species-specific genetic variation in response to deep-sea environmental variation amongst Vulnerable Marine Ecosystem indicator taxa
Cited by: 16
Author(s): Cong Zeng, Ashley A. Rowden, Malcolm R. Clark, Jonathan P. A. Gardner
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0139817

Dietary Intervention for Overweight and Obese Adults: Comparison of Low-Carbohydrate and Low-Fat Diets. A Meta-Analysis
Cited by: 161
Author(s): Jonathan Sackner‐Bernstein, David Kanter, Sanjay Kaul
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2016.00902

Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem
Cited by: 27
Author(s): Francisco Dini‐Andreote, Maria Julia de Lima Brossi, Jan Dirk van Elsas, Joana Falccao Salles
Software Mentions: 4
Published: almost 8 years ago

10.3389/fnagi.2021.733388

Aging Increases Cross-Modal Distraction by Unexpected Sounds: Controlling for Response Speed
Cited by: 0
Author(s): Alicia Leiva, Pilar Andrés, Fabrice B. R. Parmentier
Software Mentions: 4
Published: over 2 years ago

10.1007/s00125-020-05121-8

Early puberty and risk for type 2 diabetes in men
Cited by: 9
Author(s): Claes Ohlsson, Maria Bygdell, Maria Nethander, Jenny M. Kindblom
Software Mentions: 4
Published: about 4 years ago

10.1107/S090744491201863X

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography
Cited by: 36
Author(s): Sándor Brockhauser, Olof Svensson, Matthew W. Bowler, Max H. Nanao, E. Gordón, Ricardo M. F. Leal, А. Н. Попов, Matthew Gerring, A.A. McCarthy, Andrew Götz
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0155706

Using Bayesian Nonparametric Hidden Semi-Markov Models to Disentangle Affect Processes during Marital Interaction
Cited by: 6
Author(s): William A. Griffin, Xun Li
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-018-2029-1

Deep learning of mutation-gene-drug relations from the literature
Cited by: 36
Author(s): Kyubum Lee, Byounggun Kim, Yong-Hwa Choi, Sunkyu Kim, Weon Ho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan, Jaewoo Kang
Software Mentions: 4
Published: over 6 years ago

10.1107/S2059798319003528

How best to use photons
Cited by: 13
Author(s): Graeme Winter, Richard J. Gildea, Neil G. Paterson, John Beale, Markus Gerstel, Danny Axford, M. Vollmar, Katherine McAuley, R.L. Owen, Ralf Flaig, Alun Ashton, David R. Hall
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-16-S10-S3

ASTRID: Accurate Species TRees from Internode Distances
Cited by: 153
Author(s): Pranjal Vachaspati, Tandy Warnow
Software Mentions: 3
Published: over 8 years ago

10.7717/peerj.10809

Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs
Cited by: 11
Author(s): Lauren F. Messer, Mark V. Brown, Paul D. van Ruth, Mark Doubell, Justin R. Seymour
Software Mentions: 3
Published: about 3 years ago

10.1107/S2059798315013236

A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error
Cited by: 55
Author(s): Randy J. Read, Airlie J. McCoy
Software Mentions: 3
Published: about 8 years ago

10.1107/S0907444910029690

Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis
Cited by: 19
Author(s): Ekaterina Morgunova, Boris Illarionov, Sabine Saller, Aleksander Popov, Thota Sambaiah, Adelbert Bacher, Mary Cushman, Markus Fischer, Rudolf Ladenstein
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0072506

Evolutionary History of the Grey-Faced Sengi, Rhynchocyon udzungwensis, from Tanzania: A Molecular and Species Distribution Modelling Approach
Cited by: 8
Author(s): Lucinda P. Lawson, Cristiano Vernesi, Silvia Ricci, Francesco Rovero
Software Mentions: 3
Published: over 10 years ago

10.1007/s00253-018-9243-7

Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure
Cited by: 18
Author(s): Andrew M. Zealand, Renwei Mei, P. Papachristodoulou, Anthony Paul Roskilly, Wen Tso Liu, David W. Graham
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0007353

Phylogenetic Analysis of Seven WRKY Genes across the Palm Subtribe Attaleinae (Arecaceae) Identifies Syagrus as Sister Group of the Coconut
Cited by: 63
Author(s): Alan W. Meerow, Larry R. Noblick, James W. Borrone, Thomas L. P. Couvreur, Margarita Mauro-Herrera, William J. Hahn, David N. Kuhn, Kyoko Nakamura, Nora H. Oleas, Raymond J. Schnell
Software Mentions: 3
Published: over 14 years ago

10.1007/s00426-018-1092-6

Recognising and reacting to angry and happy facial expressions: a diffusion model analysis
Cited by: 10
Author(s): Jason Tipples
Software Mentions: 3
Published: over 5 years ago

10.1111/1751-7915.13438

Molecular microbial ecology of stable versus failing rice straw anaerobic digesters
Cited by: 8
Author(s): Andrew M. Zealand, Renwei Mei, Anthony Paul Roskilly, Wentso Liu, David W. Graham
Software Mentions: 3
Published: almost 5 years ago

10.1002/brb3.454

Deficits in Visual System Functional Connectivity after Blast‐Related Mild <scp>TBI</scp> are Associated with Injury Severity and Executive Dysfunction
Cited by: 30
Author(s): Casey S. Gilmore, Jazmin Camchong, Nicholas D. Davenport, Nathaniel W. Nelson, Randy H. Kardon, Kelvin O. Lim, Scott R. Sponheim
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0228214

Multi-region assessment of pharmaceutical exposures and predicted effects in USA wadeable urban-gradient streams
Cited by: 33
Author(s): Paul M. Bradley, Celeste A. Journey, Daniel T. Button, Daren M. Carlisle, Bradley J. Huffman, Sharon L. Qi, Kristin M. Romanok, Peter C. Van Metre
Software Mentions: 3
Published: over 4 years ago

10.1186/s12862-019-1534-9

The effect of alignment uncertainty, substitution models and priors in building and dating the mammal tree of life
Cited by: 9
Author(s): Yan Du, Shaoyuan Wu, Scott V. Edwards, Liang Liu
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms19030916

Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations
Cited by: 2
Author(s): Long‐Can Mei, Yanping Zhou, Lizhe Zhu, Changlin Liu, Zhuo Wu, Fangkui Wang, Ge‐Fei Hao, Di Yu, Hong Yuan, Yanfang Cui
Software Mentions: 3
Published: about 6 years ago

10.1186/1471-2148-10-302

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Cited by: 562
Author(s): Liangliang Liu, Lili Yu, Scott V. Edwards
Software Mentions: 3
Published: over 14 years ago

10.3390/ijms21207683

Hydroxylation of Antitubercular Drug Candidate, SQ109, by Mycobacterial Cytochrome P450
Cited by: 12
Author(s): Sergey Bukhdruker, Tatsiana Varaksa, Irina Grabovec, Egor Marin, Polina Shabunya, Maria Kadukova, Sergei Grudinin, Anton Kavaleuski, Anastasiia Gusach, Andrei A. Gilep, Valentin Borshchevskiy, Natallia Strushkevich
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0234184

Evaluation of a nursing and midwifery exchange between rural and metropolitan hospitals: A mixed methods study
Cited by: 3
Author(s): Amy‐Louise Byrne, Clare Harvey, Diane Chamberlain, Adele Baldwin, Elspeth Wood
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-03356-x

Social odours covary with bacterial community in the anal secretions of wild meerkats
Cited by: 49
Author(s): Sarah Leclaire, Staffan Jacob, Lydia K. Greene, George R. Dubay, Christine M. Drea
Software Mentions: 3
Published: almost 7 years ago

10.3390/biomedicines9091197

Identification of CDK7 Inhibitors from Natural Sources Using Pharmacoinformatics and Molecular Dynamics Simulations
Cited by: 9
Author(s): Vikas Kumar, Shraddha Parate, Gunjan Thakur, Gihwan Lee, Hyeon Su Ro, Yong-Seong Kim, Hong Ja Kim, Myeong Ok Kim, Keun Woo Lee
Software Mentions: 3
Published: over 2 years ago

10.1186/s13062-016-0158-x

CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments
Cited by: 1
Author(s): Benjamin Hur, Sangsoo Lim, Han–Jung Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang, Sun Kim
Software Mentions: 3
Published: over 7 years ago

10.1098/rstb.2015.0335

Multilocus inference of species trees and DNA barcoding
Cited by: 62
Author(s): Diego Mallo, David Posada
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0056786

Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)
Cited by: 21
Author(s): Xiuguang Mao, Guimei He, Junpeng Zhang, Stephen J. Rossiter, Shuyi Zhang
Software Mentions: 3
Published: about 11 years ago

10.1186/s13321-021-00524-0

Ensemble completeness in conformer sampling: the case of small macrocycles
Cited by: 4
Author(s): Lea Seep, Anne Bonin, Katharina Meier, Holger Diedam, Andreas H. Göller
Software Mentions: 3
Published: almost 3 years ago

10.1038/s41598-020-60779-9

Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding
Cited by: 18
Author(s): Miwa Takahashi, Joseph D. DiBattista, Simon Jarman, Stephen Newman, Corey B. Wakefield, Euan S. Harvey, Michael Bunce
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0083496

Exploration of Virtual Candidates for Human HMG-CoA Reductase Inhibitors Using Pharmacophore Modeling and Molecular Dynamics Simulations
Cited by: 17
Author(s): Maeng-Hyun Son, Ayoung Baek, Sugunadevi Sakkiah, Chanin Park, John Strouboulis, Keun Woo Lee
Software Mentions: 3
Published: over 10 years ago

10.1186/s13040-020-00211-0

Deep learning methods improve linear B-cell epitope prediction
Cited by: 38
Author(s): Tao Liu, Kaiwen Shi, Wuju Li
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2458-14-871

Berlin evaluates school tobacco prevention - BEST prevention: study design and methodology
Cited by: 5
Author(s): Falk Müller‐Riemenschneider, Lilian Krist, Christin Bürger, Nanette Stroebele‐Benschop, Stephanie Roll, Nina Rieckmann, Jacqueline Müller‐Nordhorn, Stefan N. Willich
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2015.00746

Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils
Cited by: 19
Author(s): C. Ryan Penton, Derek St. Louis, Amanda Pham, James R. Cole, Liyou Wu, Yiqi Luo, E. A. G. Schuur, Jizhong Zhou, James M. Tiedje
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-8-268

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
Cited by: 138
Author(s): Michael J. Hickerson, Eli A. Stahl, Naoki Takebayashi
Software Mentions: 3
Published: almost 17 years ago

10.3389/fmicb.2015.01438

Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary
Cited by: 63
Author(s): Thomas C. Jeffries, Maria Luiza Schmitz Fontes, Donald D. Harrison, Virginie Van-Dongen-Vogels, Bradley D. Eyre, Peter J. Ralph, Justin R. Seymour
Software Mentions: 3
Published: over 8 years ago

10.1038/s42003-021-02532-0

Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn2+ ions
Cited by: 7
Author(s): Владислав А. Лушпа, Marina V. Goncharuk, Cong Lin, Arthur O. Zalevsky, Irina A. Talyzina, Aleksandra Luginina, Daniil Vakhrameev, M.B. Shevtsov, Sergey A. Goncharuk, Alexander S. Arseniev, Valentin Borshchevskiy, Xiaohui Wang, K.S. Mineev
Software Mentions: 3
Published: over 2 years ago

10.1107/S2059798319003991

Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient
Cited by: 5
Author(s): Turgay Kilic, A. Popov, Amelie Burk-Körner, A.D. Koromyslova, Harald zur Hausen, Timo Bund, Grant S. Hansman
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0032066

Molecular Systematics of the Deep-Sea Hydrothermal Vent Endemic Brachyuran Family Bythograeidae: A Comparison of Three Bayesian Species Tree Methods
Cited by: 27
Author(s): Mariana Mateos, Luis A. Hurtado, Carlos Santamaría, Vincent Leignel, Danièle Guinot
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2164-16-S10-S1

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
Cited by: 59
Author(s): Ruth Davidson, Pranjal Vachaspati, Siavash Mirarab, Tandy Warnow
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2164-15-S6-S11

BBCA: Improving the scalability of *BEAST using random binning
Cited by: 41
Author(s): Théo Zimmermann, Siavash Mirarab, Tandy Warnow
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-019-3222-6

BEST: a web server for brain expression Spatio-temporal pattern analysis
Cited by: 12
Author(s): Liyuan Guo, Wei Lin, Yidan Zhang, Wenhan Li, Jing Wang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-020-07319-x

A review of deep learning applications for genomic selection
Cited by: 101
Author(s): Osval A. Montesinos-L֯ópez, Abelardo Montesinos‐López, Paulino Pérez‐Rodríguez, José Alberto Barrón-López, Johannes W. R. Martini, Silvia Fajardo-Flores, Laura S. Gaytán-Lugo, Pedro C. Santana-Mancilla, J. Crossa
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-1335-8

Prioritizing biological pathways by recognizing context in time-series gene expression data
Cited by: 6
Author(s): Jusang Lee, Kyuri Jo, Sunwon Lee, Jaewoo Kang, Sun Kim
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0042167

The Influence of Coral Reef Benthic Condition on Associated Fish Assemblages
Cited by: 84
Author(s): Karen M. Chong‐Seng, Thomas D. Mannering, Morgan S. Pratchett, David R. Bellwood, Nicholas A. J. Graham
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2164-15-317

Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes
Cited by: 19
Author(s): Christian Dubos, Zsolt Kelemen, Álvaro Sebastián, Lorenz Bülow, Gunnar Huep, Wenjia Xu, Damaris Grain, Fabien Salsac, Cécile Brousse, Loïc Lepiniec, Bernd Weißhaar, Bruno Contreras‐Moreira, Reinhard Hehl
Software Mentions: 2
Published: about 10 years ago

10.1107/S1399004715017927

MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines
Cited by: 104
Author(s): U. Zander, Gleb Bourenkov, А. Н. Попов, Daniele de Sanctis, Olof Svensson, A.A. McCarthy, Ekaterina Round, Valentin Gordeliy, Christoph Mueller-Dieckmann, Gordon A. Leonard
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2148-14-67

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines
Cited by: 23
Author(s): Michael DeGiorgio, John Syring, Andrew J. Eckert, Aaron Liston, Richard Cronn, David B. Neale, Noah A. Rosenberg
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0216785

Variability in the functional composition of coral reef fish communities on submerged and emergent reefs in the central Great Barrier Reef, Australia
Cited by: 8
Author(s): Amanda Cooper, Chancey MacDonald, Thomas E. Roberts, Tom C. L. Bridge
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2148-11-291

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling
Cited by: 61
Author(s): David Gerard, H. Lisle Gibbs, Laura Kubatko
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2148-9-212

Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution
Cited by: 48
Author(s): Werner E. Mayer, M. Herrmann, Ralf J. Sommer
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0000145

Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis
Cited by: 8
Author(s): Eun Sung Park, Ju Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, J. Frederic Mushinski
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0136157

Impacts of Rotational Grazing on Soil Carbon in Native Grass-Based Pastures in Southern Australia
Cited by: 41
Author(s): Jonathan Sanderman, Reseigh Jodie, Michael Wurst, Young Mary-Anne, Jenet Austin
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0202339

But they move! Vicariance and dispersal in southern South America: Using two methods to reconstruct the biogeography of a clade of lizards endemic to South America
Cited by: 4
Author(s): Thomas N. Hibbard, María Soledad Andrade-Díaz, Juan Manuel Díaz Gómez
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0191156

Coral physiology and microbiome dynamics under combined warming and ocean acidification
Cited by: 106
Author(s): Andréa G. Grottoli, Paula Dalcin Martins, Michael J. Wilkins, Michael D. Johnston, Mark E. Warner, Wei Cai, Todd F. Melman, Kenneth D. Hoadley, D. Tye Pettay, Stephen Levas, Verena Schoepf
Software Mentions: 2
Published: over 6 years ago

10.1186/s12862-019-1439-7

An invariants-based method for efficient identification of hybrid species from large-scale genomic data
Cited by: 51
Author(s): Laura Kubatko, Julia Chifman
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0138271

Local and Regional Impacts of Pollution on Coral Reefs along the Thousand Islands North of the Megacity Jakarta, Indonesia
Cited by: 63
Author(s): Gunilla Baum, Hedi Indra Januar, Sebastian C. A. Ferse, Andreas Kunzmann
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2148-9-263

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data
Cited by: 36
Author(s): Ferran Palero, João S. Lopes, Pere Abelló, Enrique Macpherson, Marta Pascual, Mark A. Beaumont
Software Mentions: 2
Published: over 15 years ago

10.3390/md17030155

Correlation between Fatty Acid Profile and Anti-Inflammatory Activity in Common Australian Seafood by-Products
Cited by: 44
Author(s): Tarek B. Ahmad, David Rudd, Michael Kotiw, Лэй Лю, Kirsten Benkendorff
Software Mentions: 2
Published: about 5 years ago

10.1093/aobpla/plw019

Conflicting genomic signals affect phylogenetic inference in four species of North American pines
Cited by: 2
Author(s): Tomasz E. Koralewski, Mariana Mateos, Konstantin V. Krutovsky
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0039089

Coalescent Simulations Reveal Hybridization and Incomplete Lineage Sorting in Mediterranean Linaria
Cited by: 98
Author(s): José Luis Blanco‐Pastor, Pablo Vargas, Bernard E. Pfeil
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0097435

Human and Environmental Impacts on River Sediment Microbial Communities
Cited by: 105
Author(s): Sean M. Gibbons, Edwin P. Jones, Angelita Bearquiver, Frederick Blackwolf, Wayne Roundstone, Nicole M. Scott, Jeff Hooker, Robert Madsen, Maureen L. Coleman, Jack A. Gilbert
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0184146

Molecular prediction of lytic vs lysogenic states for Microcystis phage: Metatranscriptomic evidence of lysogeny during large bloom events
Cited by: 29
Author(s): Joshua M. A. Stough, Xiangming Tang, Lauren E. Krausfeldt, Morgan M. Steffen, Guang Gao, Gregory L. Boyer, Steven W. Wilhelm
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0082071

Effective Classification and Gene Expression Profiling for the Facioscapulohumeral Muscular Dystrophy
Cited by: 8
Author(s): Félix F. González-Navarro, Lluís A. Belanche-Muñoz, Karen A. Silva-Colón
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0190926

Drug drug interaction extraction from the literature using a recursive neural network
Cited by: 72
Author(s): Sangrak Lim, Kyubum Lee, Jaewoo Kang
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2148-12-171

Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data
Cited by: 78
Author(s): Ryan P. Lamers, Gowrishankar Muthukrishnan, Todd A. Castoe, Sergio Tafur, Alexander M. Cole, Christopher L. Parkinson
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0037544

Digits Lost or Gained? Evidence for Pedal Evolution in the Dwarf Salamander Complex (Eurycea, Plethodontidae)
Cited by: 11
Author(s): Trip Lamb, David A. Beamer
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12862-016-0649-5

Species boundaries in plant pathogenic fungi: a Colletotrichum case study
Cited by: 117
Author(s): Fang Liu, Mei Wang, Ulrike Damm, Pedro W. Crous, Lei Cai
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0209857

Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary
Cited by: 12
Author(s): Deepa Varkey, Sophie Mazard, Thomas C. Jeffries, David Hughes, Justin R. Seymour, Ian T. Paulsen, Martin Ostrowski
Software Mentions: 2
Published: over 5 years ago

10.1007/s13205-011-0037-1

Current methods in structural proteomics and its applications in biological sciences
Cited by: 20
Author(s): Babu A. Manjasetty, Konrad Büssow, Santosh Panjikar, A.P. Turnbull
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2148-9-150

On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?
Cited by: 53
Author(s): Christoph Bleidorn, Lars Podsiadłowski, Min Zhong, Igor Eeckhaut, Stefanie Hartmann, Kenneth M. Halanych, Ralph Tiedemann
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0004495

Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach with Variable Selection
Cited by: 9
Author(s): Ming Hu, Zhaohui S. Qin
Software Mentions: 2
Published: over 15 years ago

10.1002/mrm.28563

Phase unwrapping with a rapid opensource minimum spanning tree algorithm (ROMEO)
Cited by: 33
Author(s): Barbara Dymerska, Korbinian Eckstein, Beáta Bachratá, Bernard Siow, S. Trattnig, Karin Shmueli, Simon Daniel Robinson
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0059954

Benthic-Pelagic Coupling: Effects on Nematode Communities along Southern European Continental Margins
Cited by: 25
Author(s): Ellen Pape, Daniel O. B. Jones, Elena Manini, Tania Nara Bezerra, Ann Vanreusel
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0086632

The Discovery of phiAGATE, A Novel Phage Infecting Bacillus pumilus, Leads to New Insights into the Phylogeny of the Subfamily Spounavirinae
Cited by: 30
Author(s): Jakub Barylski, Grzegorz Nowicki, Anna Goździcka-Józefiak
Software Mentions: 2
Published: over 10 years ago

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