Ecosyste.ms: Papers

10.1186/1471-2105-10-364

multiplierz: an extensible API based desktop environment for proteomics data analysis
Cited by: 63
Author(s): Jignesh R. Parikh, Manor Askenazi, Scott B. Ficarro, Tanya Cashorali, James T. Webber, Nathaniel C. Blank, Yi Zhang, Jarrod A. Marto
Software Mentions: 6
Published: about 15 years ago

10.1186/s12859-020-03718-9

binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions
Cited by: 2
Author(s): Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, L. Wilson, Hao Helen Zhang, Yves A. Lussier
Software Mentions: 5
Published: about 4 years ago

10.1186/s13012-020-00985-1

Proceedings from the 12th Annual Conference on the Science of Dissemination and Implementation
Cited by: 2
Author(s):
Software Mentions: 4
Published: over 4 years ago

10.1186/s13059-021-02289-z

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis
Cited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-017-00170-3

Robust Analysis of Fluxes in Genome-Scale Metabolic Pathways
Cited by: 17
Author(s): Michael R MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0226370

Effects of SCUBA bubbles on counts of roving piscivores in a large remote marine protected area
Cited by: 1
Author(s): Keolohilani H. Lopes, Ivor D. Williams, Randall K. Kosaki, Andrew K. Gray, Jason C. Leonard
Software Mentions: 2
Published: almost 5 years ago

10.1155/2014/232419

Spontaneous Ad Hoc Mobile Cloud Computing Network
Cited by: 23
Author(s): Raquel Lacuesta, Jaime Lloret, Sandra Sendra, Lourdes Peñalver
Software Mentions: 2
Published: almost 11 years ago

10.1186/1745-6150-6-38

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
Cited by: 380
Author(s): Kira S. Makarova, L. Aravind, Yuri I. Wolf, Eugene V. Koonin
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pgen.1008967

Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development
Cited by: 8
Author(s): Katherine I Farley-Barnes, Engin Deniz, Maya M Overton, Mustafa K. Khokha, Susan J. Baserga
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0233846

Growth differentiation factor-15 slows the growth of murine prostate cancer by stimulating tumor immunity
Cited by: 14
Author(s): Yasmin Husaini, Vicky Wang-Wei Tsai, Rakesh Manandhar, Hong Ping Zhang, Ka Ki Michelle Lee-Ng, Hélène Lebhar, Christopher Marquis, David A. Brown, Samuel N. Breit
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1009583

RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit
Cited by: 6
Author(s): Emilie L. Cerezo, Thibault Houlès, Oriane Lié, Marie-Kerguelen Sarthou, Charlotte Audoynaud, Geneviève Lavoie, Maral Halladjian, Sylvain Cantaloube, Carine Froment, Odile Burlet‐Schiltz, Y. Henry, Philippe P. Roux, Anthony K. Henras, Yves Roméo
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1005018

The Ribosome Biogenesis Factor Nol11 Is Required for Optimal rDNA Transcription and Craniofacial Development in Xenopus
Cited by: 36
Author(s): John N. Griffin, Samuel B. Sondalle, Florencia Del Viso, Susan J. Baserga, Mustafa K. Khokha
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0079604

Monitoring Herbivorous Fishes as Indicators of Coral Reef Resilience in American Samoa
Cited by: 50
Author(s): Adel Heenan, Ivor D. Williams
Software Mentions: 2
Published: about 11 years ago

10.1186/1472-6807-9-72

Prediction of calcium-binding sites by combining loop-modeling with machine learning
Cited by: 23
Author(s): Tianyun Liu, Russ B. Altman
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0235567

Severe-intensity constant-work-rate cycling indicates that ramp incremental cycling underestimates ⩒o2max in a heterogeneous cohort of sedentary individuals
Cited by: 7
Author(s): Avigdor D. Arad, Kaitlyn Bishop, Deena Adimoolam, Jeanine Albu, Fred J. DiMenna
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0046089

Has Alberta Oil Sands Development Altered Delivery of Polycyclic Aromatic Compounds to the Peace-Athabasca Delta?
Cited by: 72
Author(s): Roland I. Hall, Brent B. Wolfe, Johan A. Wiklund, Thomas W. D. Edwards, Andrea J. Farwell, D. George Dixon
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0114135

Combating Obesity through Healthy Eating Behavior: A Call for System Dynamics Optimization
Cited by: 23
Author(s): Norhaslinda Zainal Abidin, Mustafa Mamat, Brian Dangerfield, Jafri Zulkepli, Md. Azizul Baten, Antoni Wibowo
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0181008

Assessment of peak oxygen uptake during handcycling: Test-retest reliability and comparison of a ramp-incremented and perceptually-regulated exercise test
Cited by: 10
Author(s): Michael J. Hutchinson, Thomas A.W. Paulson, Roger G. Eston, Victoria L. Goosey-Tolfrey
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0061974

Quantifying Climatological Ranges and Anomalies for Pacific Coral Reef Ecosystems
Cited by: 85
Author(s): Jamison M. Gove, Gareth J. Williams, Margaret A. McManus, Scott F. Heron, Stuart A. Sandin, Oliver J. Vetter, David G. Foley
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0241118

Feasibility of using surgical implantation methods for acoustically tagging alewife (Alosa pseudoharengus) with V5 acoustic transmitters
Cited by: 7
Author(s): Elizabetha Tsitrin, Montana F. McLean, Arthur Gibson, David C. Hardie, Michael J. W. Stokesbury
Software Mentions: 1
Published: almost 4 years ago

10.1155/2013/632893

Multiantibody Strategies for HIV
Cited by: 7
Author(s): Andrew Hiatt, Larry Zeitlin, Kevin J. Whaley
Software Mentions: 1
Published: almost 12 years ago

10.1093/conphys/cow031

Physiological stress response, reflex impairment and delayed mortality of white sturgeon<i>Acipenser transmontanus</i>exposed to simulated fisheries stressors
Cited by: 31
Author(s): Montana F. McLean, Kyle C. Hanson, Steven J. Cooke, Scott G. Hinch, David A. Patterson, Taylor L. Nettles, Matt K. Litvak, Glenn T. Crossin
Software Mentions: 1
Published: over 8 years ago

10.1093/conphys/cox027

Chill out: physiological responses to winter ice-angling in two temperate freshwater fishes
Cited by: 16
Author(s): Michael J. Louison, Caleb T. Hasler, Graham D. Raby, Cory D. Suski, Jeffrey A. Stein
Software Mentions: 1
Published: almost 8 years ago

10.1186/cc13830

Mechanical ventilation drives pneumococcal pneumonia into lung injury and sepsis in mice: protection by adrenomedullin
Cited by: 61
Author(s): Holger Müller-Redetzky, Daniel Will, Katharina Hellwig, Wolfgang Kummer, Thomas Tschernig, Uwe Pfeil, Renate Paddenberg, Michael D. Menger, Olivia Kershaw, Achim D. Gruber, Norbert Weißmann, Stefan Hippenstiel, Norbert Suttorp, Martin Witzenrath
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.dib.2020.105308

Watershed, climate, and stable isotope data (oxygen-18 and deuterium) for 50 boreal lakes in the oil sands region, northeastern Alberta, Canada, 2002–2017
Cited by: 3
Author(s): J. J. Gibson, Yaolin Yi, S. J. Birks
Software Mentions: 1
Published: over 4 years ago

10.1093/database/bax067

RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions
Cited by: 2
Author(s): Nadav Topaz, Nazia Mojib, Aroon T. Chande, Julia Kubanek, I. King Jordan
Software Mentions: 1
Published: almost 8 years ago

10.1186/1742-7622-6-4

Assessment of methods for prediction of human West Nile virus (WNV) disease from WNV-infected dead birds
Cited by: 7
Author(s): A.K. Veksler, Millicent Eidson, Igor G. Žurbenko
Software Mentions: 1
Published: over 15 years ago

10.1007/s10661-020-8067-y

Use of pre-industrial baselines to monitor anthropogenic enrichment of metals concentrations in recently deposited sediment of floodplain lakes in the Peace-Athabasca Delta (Alberta, Canada)
Cited by: 15
Author(s): Tanner J. Owca, Mitchell L. Kay, Jelle A. Faber, Casey R. Remmer, Nelson Zabel, Johan A. Wiklund, Brent B. Wolfe, Roland I. Hall
Software Mentions: 1
Published: almost 5 years ago

10.3389/fnins.2016.00482

Analog Memristive Synapse in Spiking Networks Implementing Unsupervised Learning
Cited by: 129
Author(s): Erika Covi, Stefano Brivio, Alexantrou Serb, Themis Prodromakis, M. Fanciulli, S. Spiga
Software Mentions: 1
Published: about 8 years ago

10.3389/fpls.2020.00748

Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance
Cited by: 36
Author(s): Dhiraj Kumar, Animesh Kumar, Vinod Chhokar, O. P. Gangwar, Subhash Bhardwaj, M. Sivasamy, S. V. Sai Prasad, T. L. Prakasha, Hanif Khan, R. P. Singh, Pradeep Sharma, Sonia Sheoran, Mir Asif Iquebal, Sarika Jaiswal, U. B. Angadi, Gyanendra Pratap Singh, Anil Rai, Gyanendra Pratap Singh, Dinesh Kumar, Ruchi Tiwari
Software Mentions: 1
Published: over 4 years ago

10.1074/jbc.M115.688218

Receptor Activity-modifying Proteins 2 and 3 Generate Adrenomedullin Receptor Subtypes with Distinct Molecular Properties
Cited by: 35
Author(s): Harriet A. Watkins, Madhuri Chakravarthy, Rekhati S. Abhayawardana, Joseph J. Gingell, Michael L. Garelja, Meenakshi Pardamwar, James McElhinney, Alex Lathbridge, Arran Constantine, Paul W. R. Harris, Tsz Ying Yuen, Margaret A. Brimble, James Barwell, David R. Poyner, Michael J. Woolley, Alex C. Conner, Augen A. Pioszak, Christopher A. Reynolds, Debbie L. Hay
Software Mentions: 1
Published: over 8 years ago

10.1186/1749-8090-9-40

Case report: atypical fungal obstruction of the left ventricular assist device outflow cannula
Cited by: 10
Author(s): Jiří Malý, Ondřej Szárszoi, Zora Dorazilová, Josef Bešík, Martin Pokorný, Tomáš Kotulák, Ivan Netuka
Software Mentions: 1
Published: over 10 years ago

10.1017/cts.2020.536

An innovative program to provide methodological mentoring and to foster the development of robust research teams for K awardees: RAMP Mentors
Cited by: 2
Author(s): Laura J. Rasmussen‐Torvik, Lauren Daniels, Keith Herzog, Emily J. Traw, Michael F. Fleming, Richard M. Pope, Donald M Lloyd-Jones, Leah J. Welty
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-019-53902-y

Relative contributions to vergence eye movements of two binocular cues for motion-in-depth
Cited by: 5
Author(s): Martin Giesel, Alexandra Yakovleva, Marina Bloj, Alex Wade, Anthony M. Norcia, Julie M. Harris
Software Mentions: 1
Published: almost 5 years ago

10.3390/s17112525

A Middleware Solution for Wireless IoT Applications in Sparse Smart Cities
Cited by: 15
Author(s): Paolo Bellavista, Carlo Giannelli, Stefano Lanzone, Giulio Riberto, Cesare Stefanelli, Mauro Tortonesi
Software Mentions: 1
Published: about 7 years ago

10.3390/s19173810

Localization of Two Sound Sources Based on Compressed Matched Field Processing with a Short Hydrophone Array in the Deep Ocean
Cited by: 5
Author(s): Ran Cao, Kunde Yang, Qi Yang, Peng Chen, Quan Sun, Rui Xue
Software Mentions: 1
Published: about 5 years ago

10.3390/toxins12040215

A Humanized Monoclonal Antibody Cocktail to Prevent Pulmonary Ricin Intoxication
Cited by: 11
Author(s): Yinghui Rong, Michael Pauly, Adrian Guthals, Henry Pham, Dylan Ehrbar, Larry Zeitlin, Nicholas J. Mantis
Software Mentions: 1
Published: over 4 years ago

10.3390/ijerph16142523

Demonstration of a Low-Cost Multi-Pollutant Network to Quantify Intra-Urban Spatial Variations in Air Pollutant Source Impacts and to Evaluate Environmental Justice
Cited by: 34
Author(s): Rebecca Tanzer, Carl Malings, Aliaksei Hauryliuk, R. Subramanian, Albert A. Presto
Software Mentions: 1
Published: over 5 years ago

10.3390/ijerph17114157

Adaptation and Validation of the Scale of Types of Users in Gamification with the Spanish Adolescent Population
Cited by: 12
Author(s): Ana Manzano León, Pablo Camacho-Lazarraga, Miguel A. Guerrero-Puerta, Laura Guerrero Puerta, Antonio Alías, Rubén Trigueros, José Manuel Aguilar-Parra
Software Mentions: 1
Published: over 4 years ago

10.3390/ijerph17145180

Water Sorption by Different Types of Filter Media Used for Particulate Matter Collection Under Varying Temperature and Humidity Conditions
Cited by: 6
Author(s): Kamila Widziewicz-Rzońca, Malwina Tytła
Software Mentions: 1
Published: over 4 years ago

10.1186/s13722-019-0154-4

Rural access to MAT in Pennsylvania (RAMP): a hybrid implementation study protocol for medication assisted treatment adoption among rural primary care providers
Cited by: 11
Author(s): Gerald Cochran, Evan S. Cole, Jack Warwick, Julie M. Donohue, Adam J. Gordon, Walid F. Gellad, Todd Bear, David Kelley, Ellen DiDomenico, Jan Pringle
Software Mentions: 1
Published: over 5 years ago

10.3390/ijerph18126195

Effect of Online Training during the COVID-19 Quarantine on the Aerobic Capacity of Youth Soccer Players
Cited by: 7
Author(s): Paweł Kalinowski, Jakub Myszkowski, Jakub Marynowicz
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-7-278

Automated functional classification of experimental and predicted protein structures
Cited by: 5
Author(s): Kai Wang, Ram Samudrala
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2148-9-199

Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea
Cited by: 16
Author(s): Aaron D. Goldman, John A. Leigh, Ram Samudrala
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2296-15-8

Prevalence of complications among Chinese diabetic patients in urban primary care clinics: a cross-sectional study
Cited by: 30
Author(s): Kenny Kung, Kai Ming Chow, Elaine Hui, Maurice P. Leung, Shuk Yun Leung, Cheuk‐Chun Szeto, Augustine Lam, Philip Kam-Tao Li
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12875-015-0291-0

Evaluation of the quality of care of a multi-disciplinary Risk Factor Assessment and Management Programme for Hypertension (RAMP-HT)
Cited by: 7
Author(s): Esther Yee Tak Yu, Eric Yuk Fai Wan, Karina Hiu Yen Chan, Carlos King Ho Wong, R. W. M. Kwok, Daniel Yee Tak Fong, Cindy Lo Kuen Lam
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2229-13-43

Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens
Cited by: 15
Author(s): Ahmed J. Afzal, Ali Srour, Abhishek Goil, Sheeja Vasudaven, Tianyun Liu, Ram Samudrala, Navneet Dogra, Punit Kohli, Ayan Malakar, David A. Lightfoot
Software Mentions: 1
Published: over 11 years ago

10.1186/1472-6807-8-24

Improving the accuracy of template-based predictions by mixing and matching between initial models
Cited by: 12
Author(s): Tianyun Liu, Michal Guerquin, Ram Samudrala
Software Mentions: 1
Published: over 16 years ago

10.1186/1472-6807-13-S1-S9

Unbiased, scalable sampling of protein loop conformations from probabilistic priors
Cited by: 7
Author(s): Yajia Zhang, Kris Hauser
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12917-015-0494-6

Therapeutic effect of polysaccharide fraction of Atractylodis macrocephalae Koidz. in bovine subclinical mastitis
Cited by: 16
Author(s): Wei Xu, Ran Guan, Yisong Lu, Xiaoyan Su, Yebin Xu, Aifang Du, Songhua Hu
Software Mentions: 1
Published: over 9 years ago

10.1186/s12933-014-0127-6

Effects of the Multidisciplinary Risk Assessment and Management Program for Patients with Diabetes Mellitus (RAMP-DM) on biomedical outcomes, observed cardiovascular events and cardiovascular risks in primary care: a longitudinal comparative study
Cited by: 34
Author(s): Fangfang Jiao, Colman Siu Cheung Fung, Carlos King Ho Wong, Yuk-Fai Wan, Daisy Dai, R. W. M. Kwok, Cindy Lo Kuen Lam
Software Mentions: 1
Published: over 10 years ago

10.1186/s12933-015-0267-3

Long-term effects of the multidisciplinary risk assessment and management program for patients with diabetes mellitus (RAMP-DM): a population-based cohort study
Cited by: 38
Author(s): Fangfang Jiao, Colman Siu Cheung Fung, Yuk-Fai Wan, Sarah M. McGhee, Carlos King Ho Wong, Daisy Dai, R. W. M. Kwok, Cindy Lo Kuen Lam
Software Mentions: 1
Published: over 9 years ago

10.1007/s11306-012-0438-0

Metabolic profiling in Caenorhabditis elegans provides an unbiased approach to investigations of dosage dependent lead toxicity
Cited by: 10
Author(s): Gita Sudama, Junyi Zhang, Jenefir D. Isbister, James D. Willett
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pbio.3000279

Reversible association with motor proteins (RAMP): A streptavidin-based method to manipulate organelle positioning
Cited by: 20
Author(s): Carlos M. Guardia, Raffaella De Pace, Aritra Sen, Amra Sarić, Michal Jarník, David A. Kolin, Ambarish Kunwar, Juan S. Bonifacino
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pcbi.1000181

Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information
Cited by: 37
Author(s): Kai Wang, Jeremy A. Horst, Gong Cheng, David C. Nickle, Ram Samudrala
Software Mentions: 1
Published: about 16 years ago