Ecosyste.ms: Papers

10.1186/s12864-016-3387-6

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
Cited by: 64
Author(s): Charalampos Lazaris, Stephen M. Kelly, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 28
Published: almost 8 years ago

10.1371/journal.pntd.0009252

Optimising predictive modelling of Ross River virus using meteorological variables
Cited by: 4
Author(s): Iain S. Koolhof, Simon M. Firestone, SS Bettiol, Michael A. Charleston, Katherine B Gibney, Peter J. Neville, Andrew Jardine, Scott Carver
Software Mentions: 23
Published: over 3 years ago

10.3390/ijerph17114132

Data-Driven Modeling and the Influence of Objective Function Selection on Model Performance in Limited Data Regions
Cited by: 4
Author(s): Thelma Dede Baddoo, Zhijia Li, Yiqing Guan, Kenneth Rodolphe Chabi Boni, Isaac Kwesi Nooni
Software Mentions: 21
Published: over 4 years ago

10.1186/s12864-017-4353-7

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
Cited by: 72
Author(s): Ali Sharifi-Zarchi, Daniela Gerovska, Kenjiro Adachi, Mehdi Totonchi, Hamid Pezeshk, Ryan J. Taft, Hans R. Schöler, Hamidreza Chitsaz, Mehdi Sadeghi, Hossein Baharvand, Marcos J. Araúzo-Bravo
Software Mentions: 21
Published: almost 7 years ago

10.1002/eap.1898

Spatiotemporal prediction of wildfire size extremes with Bayesian finite sample maxima
Cited by: 40
Author(s): Maxwell B. Joseph, Matthew W. Rossi, Nathan Mietkiewicz, Adam L. Mahood, Megan E. Cattau, Lise A. St. Denis, R. Chelsea Nagy, Virginia Iglesias, John T. Abatzoglou, Jennifer K. Balch
Software Mentions: 17
Published: over 5 years ago

10.1186/s13007-018-0376-6

PhenoFly Planning Tool: flight planning for high-resolution optical remote sensing with unmanned areal systems
Cited by: 43
Author(s): Lukas Roth, Andreas Hund, Helge Aasen
Software Mentions: 15
Published: almost 6 years ago

10.1186/s12859-021-03970-7

stochprofML: stochastic profiling using maximum likelihood estimation in R
Cited by: 3
Author(s): Lisa Amrhein, Christiane Fuchs
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0212956

Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation
Cited by: 24
Author(s): Colin Lischik, Leonie Adelmann, Joachim Wittbrodt
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pone.0250817

#MaskOn! #MaskOff! Digital polarization of mask-wearing in the United States during COVID-19
Cited by: 48
Author(s): Jun Lang, Wesley W. Erickson, Zhuo Jing–Schmidt
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pone.0152098

Combining Soil Databases for Topsoil Organic Carbon Mapping in Europe
Cited by: 37
Author(s): Ece Aksoy, Yusuf Yiğini, Luca Montanarella
Software Mentions: 12
Published: over 8 years ago

10.1186/s40462-019-0175-3

Exploration during early life: distribution, habitat and orientation preferences in juvenile king penguins
Cited by: 14
Author(s): Florian Orgeret, Clara Péron, Manfred R. Enstipp, Karine Delord, Henri Weimerskirch, CA Bost
Software Mentions: 10
Published: about 5 years ago

10.1186/s12864-021-07493-6

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome
Cited by: 19
Author(s): Richard Edwards, Matthew A. Field, James M. Ferguson, Olga Dudchenko, Jens Keilwagen, Benjamin D. Rosen, Gary S. Johnson, Edward S. Rice, La Deanna Hillier, Jillian M. Hammond, Samuel G. Towarnicki, Arina D. Omer, Ruqayya Khan, Ksenia Skvortsova, Ozren Bogdanović, Robert A. Zammit, E Aiden, Wesley C. Warren, J. William O. Ballard
Software Mentions: 10
Published: over 3 years ago

10.1093/gbe/evz003

Repeated Evolution Versus Common Ancestry: Sex Chromosome Evolution in the Haplochromine Cichlid<i>Pseudocrenilabrus philander</i>
Cited by: 25
Author(s): Astrid Böhne, Alexandra Anh‐Thu Weber, Jelena Rajkov, Michael Rechsteiner, Andrin Riss, Bernhard Egger, Walter Salzburger
Software Mentions: 10
Published: almost 6 years ago

10.3390/ijerph18168271

Cluster Analysis of Urban Acoustic Environments on Barcelona Sensor Network Data
Cited by: 10
Author(s): Antonio Pita, Francisco Javier Iglesias Rodríguez, Juan M. Navarro
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-017-09382-z

New approaches to high-resolution mapping of marine vertical structures
Cited by: 43
Author(s): Katleen Robert, Veerle A.I. Huvenne, Aggeliki Georgiopoulou, Daniel O. B. Jones, Leigh Marsh, Gareth Carter, Leo Chaumillon
Software Mentions: 9
Published: over 7 years ago

10.1098/rsos.172177

The evolutionary history of polycotylid plesiosaurians
Cited by: 27
Author(s): Valentin Fischer, Roger Benson, Patrick S. Druckenmiller, Hilary F. Ketchum, Nathalie Bardet
Software Mentions: 9
Published: over 6 years ago

10.1093/cid/ciz060

Global Review of the Age Distribution of Rotavirus Disease in Children Aged &lt;5 Years Before the Introduction of Rotavirus Vaccination
Cited by: 35
Author(s): Mateusz Hasso-Agopsowicz, Chandresh N Ladva, Benjamin A. Lopman, Colin Sanderson, Adam L. Cohen, Jacqueline E. Tate, Ximena Riveros, Ana María Henao-Restrepo, Andrew Clark, Míriam Alkorta, Christina Atchison, Salem Banajeh, Sylvia Becker‐Dreps, Mohammed Benhafid, Nita Bhandari, Ladaporn Bodhidatta, Tessa Braeckman, Josephine Bwogi, Rita de Cássia Compagnoli Carmona, Gustavo Cilla, Ingrid L. Contreras-Roldan, Barbara S. Coulson, Nigel A. Cunliffe, Ron Dagan, N. Givon, Juan Ignacio Degiuseppe, Shaveta Dhiman, Zhang Dian, Jenna Diaz, Shubha Ranjan Dutta, Triveni Krishnan, Byomkesh Manna, Stephanie Fletcher-Lartey, Chuanxi Fu, D. Gendrel, Khalifa Sifaw Ghenghesh, G. Gonzalez Mago, Simona De Grazia, Keith Grimwood, Michelle Groome, Md. Ahshanul Haque, Ulrich Heininger, Eric R. Houpt, Miren Iturriza‐Gómara, Daniel Hungerford, Claudia Jarquín, John P. McCracken, I. L. Contreras, Celia Cordón-Rosales, Petra Kaiser-Labusch, Gagandeep Kang, Sumit Kar, Nicholas M. Kiulia, Karen L. Kotloff, Renat Latipov, Alexandre da Costa Linhares, Mathie Lorrot, Marcelo Gastón Mandile, Christine Mast, M. A. Mathew, F. Matinon-Torres, Jelle Matthijnssens, Z. Mladenova, Marina Monini, Milagrosa Montes, Ainara Arana, Mohammad Motamedifar, Akram Najafi, Tell Nelson, James Nokes, Francine Ntoumi, Kei Numazaki, Ciara E. O’Reilly, Theresa J. Ochoa, Nicola Page, Anne‐Laure Page, Céline Langendorf, Alexander T. Podkolzin, Caroline Quach, Maria Lúcia Rácz, Alexis de Rougemont, Guillermo M. Ruíz-Palacios, Samir K. Saha, Samir K. Saha, Syed Moinuddin Satter, L. Soares, Subijanto Marto Sudarmo, Katsumi Shigemura, Toshihiko Shirakawa, Alpha Fardah Athiyyah, Beckie Nnenna Tagbo, Phillip I. Tarr, Eileen J. Klein, Donna M. Denno, Ann Turner, Ezeonwu Bertilla Uzoma, R. R. Vatosoa, Ernest Apondi Wandera, Mary E. Wikswo, Daniel C. Payne, Huang Yhu-Chering, Tetsushi Yoshikawa, Ken Sugata, Qianqian Yuan, Liang LiYing, Khalequ Zaman, Xiaofang Zhou, S. X. Zhang, Wei Xu, Fatima Serhan, Tomoka Nakamura, Sébastien Antoni, Mary Agócs, Jillian Murray, Thomas Cherian, Jason M. Mwenda, Goitom Weldegebriel, Joseph Nsiari-Muzeyi Biey, Dah Cheikh, Nadia Teleb, Hossam Abdel Rahman, Hinda Ahmed, Danni Daniels, Dovile Videbaek, Annemarie Wasley, Simarjit Singh, Lúcia de Oliveira, Gloria Rey-Benito, N. Jennifer Sanwogou, Jayantha Liyanage, Pushpa Ranjan Wijesinghe, Batmunkh Nyambat, Varja Grabovac, Kimberley Fox, Fem Julia Paladin, Nicholas Henschke
Software Mentions: 8
Published: almost 6 years ago

10.3390/cancers13102432

Computational Treatment Simulations to Assess the Need for Personalized Tamoxifen Dosing in Breast Cancer Patients of Different Biogeographical Groups
Cited by: 1
Author(s): Anna Mueller‐Schoell, Robin Michelet, Lena Klopp‐Schulze, Madelé van Dyk, Thomas E. Mürdter, Matthias Schwab, Markus Joerger, Wilhelm Huisinga, Gerd Mikus, Charlotte Kloft
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-021-88349-7

Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander
Cited by: 4
Author(s): Guillermo Velo‐Antón, André Lourenço, Pedro Galán, Alfredo G. Nicieza, Pedro Tarroso
Software Mentions: 7
Published: over 3 years ago

10.3390/ani9110973

The Development of a Hoof Conformation Assessment for Use in Dairy Goats
Cited by: 5
Author(s): Laura Deeming, Ngaio J. Beausoleil, Kevin J. Stafford, James R. Webster, Maryann Staincliffe, Gosia Zobel
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.5669

From the cage to the wild: introductions of Psittaciformes to Puerto Rico
Cited by: 10
Author(s): Wilfredo Falcón, Raymond L. Tremblay
Software Mentions: 6
Published: about 6 years ago

10.3390/ph14020115

Simulation-Based Assessment of the Impact of Non-Adherence on Endoxifen Target Attainment in Different Tamoxifen Dosing Strategies
Cited by: 4
Author(s): Anna Mueller‐Schoell, Lena Klopp‐Schulze, Robin Michelet, Madelé van Dyk, Thomas E. Mürdter, Matthias Schwab, Markus Joerger, Wilhelm Huisinga, Gerd Mikus, Charlotte Kloft
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0174623

Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit
Cited by: 57
Author(s): Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, R. Harald Baayen
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0183149

Low validity of Google Trends for behavioral forecasting of national suicide rates
Cited by: 76
Author(s): Ulrich S. Tran, Rita Andel, Thomas Niederkrotenthaler, Benedikt Till, Vladeta Ajdacic-Gross, Martin Voracek
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0143309

Spatial Patterns in Water Quality Changes during Dredging in Tropical Environments
Cited by: 48
Author(s): Rebecca Fisher, Clair Stark, Peter V. Ridd, Ross Jones
Software Mentions: 6
Published: almost 9 years ago

10.1038/gim.2015.156

VisCap: inference and visualization of germ-line copy-number variants from targeted clinical sequencing data
Cited by: 58
Author(s): Trevor J. Pugh, Sami S. Amr, Mark J. Bowser, Sivakumar Gowrisankar, Elizabeth Hynes, Lisa Mahanta, Heidi L. Rehm, Birgit Funke, Matthew S. Lebo
Software Mentions: 6
Published: over 8 years ago

10.2196/12843

Rapid Analysis of Diagnostic and Antimicrobial Patterns in R (RadaR): Interactive Open-Source Software App for Infection Management and Antimicrobial Stewardship
Cited by: 13
Author(s): Christian F. Luz, Matthijs S. Berends, Jan-Willem H. Dik, Mariëtte Lokate, Céline Pulcini, Corinna Glasner, Bhanu Sinha
Software Mentions: 5
Published: over 5 years ago

10.3389/fvets.2021.699352

The Impact of Socioeconomic Factors on Knowledge, Attitudes, and Practices of Dog Owners on Dog Rabies Control in Thailand
Cited by: 6
Author(s): Sith Premashthira, Sarin Suwanpakdee, Weerapong Thanapongtharm, Onpawee Sagarasaeranee, Weerakorn Thichumpa, Chayanin Sararat, Anuwat Wiratsudakul
Software Mentions: 5
Published: over 3 years ago

10.3389/fphar.2019.00005

Exposure of Infants to Isoniazid via Breast Milk After Maternal Drug Intake of Recommended Doses Is Clinically Insignificant Irrespective of Metaboliser Status. A Physiologically-Based Pharmacokinetic (PBPK) Modelling Approach to Estimate Drug Exposure of Infants via Breast-Feeding
Cited by: 12
Author(s): Estella Dora Germaine Garessus, Hans Mielke, Ursula Gundert‐Remy
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2010-11-3-r29

Genome-wide functional analysis of human 5' untranslated region introns
Cited by: 69
Author(s): Can Cenik, Adnan Derti, Joseph Mellor, Gabriel F. Berriz, Frederick P. Roth
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pone.0137112

Temporal Patterns in Seawater Quality from Dredging in Tropical Environments
Cited by: 53
Author(s): Ross Jones, Rebecca Fisher, Clair Stark, Peter V. Ridd
Software Mentions: 4
Published: about 9 years ago

10.1186/s13071-021-04780-9

Spatio-temporal modelling of Culicoides Latreille (Diptera: Ceratopogonidae) populations on Reunion Island (Indian Ocean)
Cited by: 0
Author(s): Yannick Grimaud, Annelise Tran, Samuel Benkimoun, Floriane Boucher, Olivier Esnault, Catherine Cêtre-Sossah, Éric Cardinale, Claire Garros, Hélène Guis
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.02254-20

CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
Cited by: 27
Author(s): Wen Li, Parmit K. Singh, Gregory A. Sowd, Gregory J. Bedwell, Sungwoo Jang, Vasudevan Achuthan, Amarachi V. Oleru, Doris Wong, Hind J. Fadel, Kyeongeun Lee, Vineet N. KewalRamani, Eric M. Poeschla, Alon Herschhorn, Alan Engelman
Software Mentions: 4
Published: about 4 years ago

10.3390/v12040478

Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses
Cited by: 42
Author(s): Michele Della Bartola, Stephen Byrne, Ewen Mullins
Software Mentions: 4
Published: over 4 years ago

10.1186/s12889-019-7521-7

Methods for detecting seasonal influenza epidemics using a school absenteeism surveillance system
Cited by: 9
Author(s): Madeline A. Ward, Anu Stanley, Lorna E. Deeth, Rob Deardon, Zeny Feng, Lise A. Trotz-Williams
Software Mentions: 4
Published: about 5 years ago

10.1038/srep23858

Ambient air pollution, weather changes and outpatient visits for allergic conjunctivitis: A retrospective registry study
Cited by: 60
Author(s): Jiaxu Hong, Taoling Zhong, Huili Li, Jianming Xu, Xiaofang Ye, Zhanglei Mu, Yi Lü, Alireza Mashaghi, Ying Zhou, Mengxi Tan, Qiyuan Li, Xinghuai Sun, Zuguo Liu, Jianjiang Xu
Software Mentions: 3
Published: over 8 years ago

10.1534/g3.115.017665

Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis
Cited by: 26
Author(s): Nicholas Haase, Timothy Beissinger, Candice N. Hirsch, Brieanne Vaillancourt, Shweta Deshpande, Kerrie Barry, C. Robin Buell, Shawn M. Kaeppler, Natalia de León
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.08527

Protein biogenesis machinery is a driver of replicative aging in yeast
Cited by: 149
Author(s): Georges E. Janssens, Anne C Meinema, Javier González, Justina C. Wolters, Alexander Schmidt, Victor Guryev, Rainer Bischoff, Ernst Wit, Liesbeth M. Veenhoff, Matthias Heinemann
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.21715

Spinal microcircuits comprising dI3 interneurons are necessary for motor functional recovery following spinal cord transection
Cited by: 41
Author(s): Tuan V. Bui, Nicolas Stifani, Turgay Akay, Robert M. Brownstone
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0010588

Rhinovirus Genome Evolution during Experimental Human Infection
Cited by: 50
Author(s): Samuel Cordey, Thomas Junier, Daniel Gerlach, Francesca Gobbini, Laurent Farinelli, Evgeny M. Zdobnov, Birgit Winther, Caroline Tapparel, Laurent Kaiser
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0164938

Metabolic Cost of the Activation of Immune Response in the Fish-Eating Myotis (Myotis vivesi): The Effects of Inflammation and the Acute Phase Response
Cited by: 32
Author(s): Aída Otálora‐Ardila, José Juan Flores‐Martínez, Kenneth C. Welch
Software Mentions: 2
Published: about 8 years ago

10.1038/s41398-017-0084-4

Testing frameworks for personalizing bipolar disorder
Cited by: 15
Author(s): Amy L. Cochran, André Schultz, Melvin G. McInnis, Daniel B. Forger
Software Mentions: 2
Published: almost 7 years ago

10.1534/g3.116.029231

mRNA-Associated Processes and Their Influence on Exon-Intron Structure in <i>Drosophila melanogaster</i>
Cited by: 6
Author(s): Gildas Lepennetier, Francesco Catania
Software Mentions: 2
Published: over 8 years ago

10.1093/geroni/igab014

Testing the Feasibility of Virtual Reality With Older Adults With Cognitive Impairments and Their Family Members Who Live at a Distance
Cited by: 10
Author(s): Tamara D. Afifi, Nancy L. Collins, Kyle Rand, Ken Fujiwara, Allison P. Mazur, Chris Otmar, Norah E. Dunbar, Kathryn Harrison, Rebecca G. Logsdon
Software Mentions: 2
Published: over 3 years ago