pypi: language | Projects | Ecosyste.ms: Papers

10.7717/peerj.2836

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
Cited by: 273
Author(s): Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel
Software Mentions: 20
Published: over 7 years ago

10.3390/cancers12040948

Reconstruction of Ewing Sarcoma Developmental Context from Mass-Scale Transcriptomics Reveals Characteristics of EWSR1-FLI1 Permissibility
Cited by: 23
Author(s): Henry E. Miller, Aparna Gorthi, Nicklas Bassani, Liesl A. Lawrence, Brian S. Iskra, Alexander J.R. Bishop
Software Mentions: 19
Published: about 4 years ago

10.7717/peerj.9539

The importance of open science for biological assessment of aquatic environments
Cited by: 15
Author(s): Marcus W. Beck, Casey C. O’Hara, Julia S. Stewart Lowndes, Raphael D. Mazor, Susanna Theroux, David J. Gillett, Belize Lane, Gregory Gearheart
Software Mentions: 17
Published: almost 4 years ago

10.3389/fimmu.2017.00445

Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations
Cited by: 15
Author(s): Michael T. Zimmermann, Richard B. Kennedy, Diane E. Grill, Ann L. Oberg, Krista M. Goergen, Inna G. Ovsyannikova, Iana H. Haralambieva, Gregory A. Poland
Software Mentions: 16
Published: about 7 years ago

10.3390/insects10100321

Evaluation of NEON Data to Model Spatio-Temporal Tick Dynamics in Florida
Cited by: 5
Author(s): Geraldine Klarenberg, Samantha M. Wisely
Software Mentions: 14
Published: over 4 years ago

10.2196/mental.9946

Predicting Caller Type From a Mental Health and Well-Being Helpline: Analysis of Call Log Data
Cited by: 9
Author(s): Alexander Grigorash, Siobhan O’Neill, Raymond Bond, Colette Ramsey, Chérie Armour, Maurice Mulvenna
Software Mentions: 13
Published: almost 6 years ago

10.1038/s41598-018-21217-z

Spatially-explicit valuation of coastal wetlands for cyclone mitigation in Australia and China
Cited by: 32
Author(s): Xiaoguang Ouyang, Joe Lee, Rod M. Connolly, Martin J. Kainz
Software Mentions: 13
Published: over 6 years ago

10.1371/journal.pone.0178783

Pharmacokinetics of caspofungin acetate to guide optimal dosing in cats
Cited by: 8
Author(s): Jana Leshinsky, Andrew J. McLachlan, David J. R. Foster, Ross Norris, Vanessa R. Barrs
Software Mentions: 13
Published: almost 7 years ago

10.1186/s13023-020-01520-7

Identification of risk features for complication in Gaucher’s disease patients: a machine learning analysis of the Spanish registry of Gaucher disease
Cited by: 11
Author(s): Marcio Andrade‐Campos, Laura López de Frutos, Jorge J. Cebolla, Irene Serrano-Gonzalo, Blanca Medrano-Engay, Mercedes Roca-Espiau, Beatriz Gomez-Barrera, Jorge Pérez-Heredia, D. Íñiguez, Pilar Giraldo
Software Mentions: 13
Published: over 3 years ago

10.1186/s13321-015-0094-2

RRegrs: an R package for computer-aided model selection with multiple regression models
Cited by: 40
Author(s): Georgia Tsiliki, Cristian R. Munteanu, José A. Seoane, Carlos Fernández-Lozano, Haralambos Sarimveis, Egon Willighagen
Software Mentions: 10
Published: over 8 years ago

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: almost 12 years ago

10.3390/ijms22042214

How Are the Flower Structure and Nectar Composition of the Generalistic Orchid Neottia ovata Adapted to a Wide Range of Pollinators?
Cited by: 8
Author(s): Emilia Brzosko, Andrzej Bajguz, Magdalena Chmur, Justyna Burzyńska, Edyta Jermakowicz, Paweł Mirski, Piotr Zieliński
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0216485

Understanding heterogeneous tumor microenvironment in metastatic melanoma
Cited by: 31
Author(s): Yiyi Yan, Alexey A. Leontovich, Michael J. Gerdes, Keyur Desai, Jinhong Dong, Anup Sood, Alberto Santamaría-Pang, Aaron S. Mansfield, Chrystal Chadwick, Rong Zhang, Wendy K. Nevala, Thomas J. Flotte, Fiona Ginty, Svetomir N. Markovic
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0212248

Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti
Cited by: 17
Author(s): Ruvini V. Lelwala, Pasi K. Korhonen, Neil D. Young, Jason B. Scott, Peter K. Ades, Robin B. Gasser, P. W. J. Taylor
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0133581

Spatial Scales of Genetic Structure in Free-Standing and Strangler Figs (Ficus, Moraceae) Inhabiting Neotropical Forests
Cited by: 12
Author(s): Katrin Heer, Elisabeth K. V. Kalko, Larissa Albrecht, Roosevelt García‐Villacorta, Felix C. Staeps, Edward Allen Herre, Christopher W. Dick
Software Mentions: 8
Published: almost 9 years ago

10.3390/healthcare8020111

A Comparative Analysis of Breast Cancer Detection and Diagnosis Using Data Visualization and Machine Learning Applications
Cited by: 64
Author(s): Muhammet Fatih Ak
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0196865

Predicting potential drug-drug interactions on topological and semantic similarity features using statistical learning
Cited by: 89
Author(s): Andrej Kastrin, Polonca Ferk, Brane Leskošek
Software Mentions: 8
Published: about 6 years ago

10.3389/fphys.2017.00917

Uncertainty Quantification Reveals the Importance of Data Variability and Experimental Design Considerations for in Silico Proarrhythmia Risk Assessment
Cited by: 66
Author(s): Kelly C. Chang, Sara Dutta, Gary R. Mirams, Kylie A. Beattie, Jiansong Sheng, Phu N. Tran, Min Wu, Wendy Wu, Thomas Colatsky, David G. Strauss, Zhihua Li
Software Mentions: 7
Published: over 6 years ago

10.1107/S0907444913007051

OpenStructure: an integrated software framework for computational structural biology
Cited by: 82
Author(s): Marco Biasini, Tobias Schmidt, Stefan Bienert, Valerio Mariani, Gabriel Studer, Juergen Haas, Niklaus Johner, Andreas Schenk, Ansgar Philippsen, Torsten Schwede
Software Mentions: 7
Published: about 11 years ago

10.1007/s13304-020-00883-7

Factors predicting survival in patients with locally advanced pancreatic cancer undergoing pancreatectomy with arterial resection
Cited by: 11
Author(s): Niccolò Napoli, Emanuele Federico Kauffmann, Concetta Cacace, Francesca Menonna, Davide Caramella, Carla Cappelli, Daniela Campani, Andrea Cacciato Insilla, Enrico Vasile, Caterina Vivaldi, Lorenzo Fornaro, G Amorese, Fabio Vistoli, Ugo Boggi
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.49874

Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria
Cited by: 114
Author(s): Ceereena Ubaida‐Mohien, Alexey E. Lyashkov, Marta González-Freire, Ravi Tharakan, Michelle Shardell, Ruin Moaddel, Richard D. Semba, Chee W. Chia, Myriam Gorospe, Ranjan Sen, Luigi Ferrucci
Software Mentions: 7
Published: over 4 years ago

10.1186/s12874-021-01319-5

Development and validation of a risk index to predict kidney graft survival: the kidney transplant risk index
Cited by: 7
Author(s): Sameera Senanayake, Sanjeewa Kularatna, Helen Healy, Nicholas Graves, Keshwar Baboolal, Matthew P. Sypek, Adrian Barnett
Software Mentions: 7
Published: almost 3 years ago

10.1186/s12885-018-4345-2

The impact of pharmacokinetic gene profiles across human cancers
Cited by: 3
Author(s): Michael T. Zimmermann, Terry M. Therneau, Jean Pierre A. Kocher
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0097678

Evaluation of Toxicogenomics Approaches for Assessing the Risk of Nongenotoxic Carcinogenicity in Rat Liver
Cited by: 16
Author(s): Johannes Eichner, Clemens Wrzodek, Michael Roemer, Heidrun Ellinger‐Ziegelbauer, Andreas Zell
Software Mentions: 7
Published: about 10 years ago

10.1186/s12915-020-00910-4

Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites
Cited by: 24
Author(s): Marco F. Schmidt, Tiago Maié, Edgar Dahl, Ivan G. Costa, Wolfgang Wagner
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0189084

Charting the transcriptional landscape of cells of renin lineage following podocyte depletion
Cited by: 1
Author(s): Alastair McClelland, Julia Lichtnekert, Diana G. Eng, Jeffrey W. Pippin, Kenneth W. Gross, Sina A. Gharib, Stuart J. Shankland
Software Mentions: 7
Published: over 6 years ago

10.3390/plants8070224

Phenotypic and Genetic Variation of an Interspecific Centaurium Hybrid (Gentianaceae) and Its Parental Species
Cited by: 4
Author(s): Tijana Banjanac, Sanja Đurović, Mihailo Jelić, Milan Dragićević, Danijela Mišić, Marijana Škorić, Jelena Živković, Branislav Šiler
Software Mentions: 7
Published: almost 5 years ago

10.1002/ece3.923

On the evolution of omnivory in a community context
Cited by: 24
Author(s): Alex M Chubaty, O. Brian, R. Will Stein, D. R. Gillespie, Lee M. Henry, Conan Phelan, Eiríkur Pálsson, Franz W. Simon, Bernard D. Roitberg
Software Mentions: 6
Published: over 10 years ago

10.3389/fimmu.2021.726747

Identifying Immune Cell Infiltration and Effective Diagnostic Biomarkers in Rheumatoid Arthritis by Bioinformatics Analysis
Cited by: 45
Author(s): Sheng Zhou, Hongmei Lü, Min Xiong
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pone.0071090

Glocal Clinical Registries: Pacemaker Registry Design and Implementation for Global and Local Integration – Methodology and Case Study
Cited by: 29
Author(s): Kátia Regina da Silva, Roberto Costa, Elizabeth Sartori Crevelari, Marianna Sobral Lacerda, Caio Marcos de Moraes Albertini, Martino Martinelli Filho, José Eduardo Santana, João Ricardo Nickenig Vissoci, Ricardo Pietrobon, Jacson Venâncio de Barros
Software Mentions: 6
Published: almost 11 years ago

10.1002/cam4.4161

Integrated pan‐cancer of AURKA expression and drug sensitivity analysis reveals increased expression of AURKA is responsible for drug resistance
Cited by: 12
Author(s): Noushin Miralaei, Ahmad Majd, Kamran Ghaedi, Maryam Peymani, Masoomeh Safaei
Software Mentions: 6
Published: almost 3 years ago

10.1371/journal.pntd.0005246

The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni
Cited by: 39
Author(s): Kathrin K. Geyer, Umar Niazi, David Timothy Duval, Céline Cosseau, Chad Tomlinson, Iain W. Chalmers, Martin Swain, David Cutress, Utibe Bickham-Wright, Sabrina E. Munshi, Christoph Grunau, Timothy P. Yoshino, Karl F. Hoffmann
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0077776

Extension of Life Span by Impaired Glucose Metabolism in Caenorhabditis elegans Is Accompanied by Structural Rearrangements of the Transcriptomic Network
Cited by: 20
Author(s): Stefan Priebe, Uwe Menzel, Kim Zarse, Marco Groth, Matthias Platzer, Michael Ristow, Reinhard Guthke
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0073938

A Toxicogenomic Approach for the Prediction of Murine Hepatocarcinogenesis Using Ensemble Feature Selection
Cited by: 16
Author(s): Johannes Eichner, Nadine Kossler, Clemens Wrzodek, Arno Kalkuhl, Dorthe Bach Toft, Nina Ostenfeldt, V. Espley Richard, Andreas Zell
Software Mentions: 6
Published: over 10 years ago

10.1186/s13071-019-3524-6

Metazoan parasite infracommunities of the dusky flounder (Syacium papillosum) as bioindicators of environmental conditions in the continental shelf of the Yucatan Peninsula, Mexico
Cited by: 30
Author(s): Víctor M. Vidal‐Martínez, Iván Velázquez‐Abunader, Oscar Arturo Centeno-Chalé, Ana Luisa May-Tec, Lilia C. Soler-Jiménez, Daniel Pech, Ismael Mariño‐Tapia, Cecilia Enríquez, Omar Zapata-Pérez, Jorge Herrera-Silveira, David Iván Hernández-Mena, Sharon Z. Herzka, Uriel Ordóñez-López, M. Leopoldina Aguirre-Macedo
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0241848

Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle)
Cited by: 3
Author(s): Hyo Jun Lee, Young Jin Chung, Sungbong Jang, Dongil Seo, Hak Kyo Lee, Duhak Yoon, Dajeong Lim, Seung Hwan Lee
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0152034

System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination
Cited by: 45
Author(s): Michael T. Zimmermann, Ann L. Oberg, Diane E. Grill, Inna G. Ovsyannikova, Iana H. Haralambieva, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 6
Published: about 8 years ago

10.1186/1471-2105-14-351

On the amyloid datasets used for training PAFIG how (not) to extend the experimental dataset of hexapeptides
Cited by: 10
Author(s): Małgorzata Kotulska, Olgierd Unold
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0245157

A comparison of machine learning models versus clinical evaluation for mortality prediction in patients with sepsis
Cited by: 38
Author(s): William P T M van Doorn, Patricia M. Stassen, Hella F. Borggreve, Maaike J. Schalkwijk, Judith Stoffers, Otto Bekers, Steven J.R. Meex
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0180215

Possible mechanisms of pollination failure in hybrid carrot seed and implications for industry in a changing climate
Cited by: 18
Author(s): Melissa Broussard, Flore Mas, Brad G. Howlett, David E. Pattemore, Jason M. Tylianakis
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12979-020-00182-0

Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22
Cited by: 11
Author(s): Arttu Autio, Tapio Nevalainen, Binisha H. Mishra, Marja Jylhä, Heini Flinck, Mikko Hurme
Software Mentions: 5
Published: about 4 years ago

10.1172/jci.insight.146196

Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis
Cited by: 9
Author(s): Carolin Czauderna, Alicia Poplawski, Colm J. O’Rourke, Darko Castven, Benjamín Pérez-Aguilar, Diana Becker, Markus M. Nöthen, Margarete Odenthal, W Amer, M Schmiel, Uta Drebber, Harald Binder, Dirk A. Ridder, Mario Schindeldecker, Beate K. Straub, Peter R. Galle, Jesper B. Andersen, Snorri S. Thorgeirsson, Young Nyun Park, Jens U. Marquardt
Software Mentions: 5
Published: over 2 years ago

10.1111/gcb.15118

Climate change causes critical transitions and irreversible alterations of mountain forests
Cited by: 91
Author(s): Katharina Albrich, Werner Rammer, Rupert Seidl
Software Mentions: 5
Published: about 4 years ago

10.1186/s12967-018-1707-0

Evaluation of the prognostic value of paraoxonase 1 in the recurrence and metastasis of hepatocellular carcinoma and establishment of a liver-specific predictive model of survival
Cited by: 18
Author(s): Zhenzhen Yu, Qifeng Ou, Chongxi Fan, Jiong Bi, Wen Li, Jiachi Ma, Rongchang Wang, Xiaohui Huang
Software Mentions: 5
Published: over 5 years ago

10.7150/jca.42736

TOP2A Promotes Tumorigenesis of High-grade Serous Ovarian Cancer by Regulating the TGF-β/Smad Pathway
Cited by: 23
Author(s): Yan Gao, Hongyu Zhao, Meng Ren, Qi Chen, Jie Li, Zhefeng Li, Chenghong Yin, Wentao Yue
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2018.00973

A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains
Cited by: 15
Author(s): Xiangchen Li, Wenjun Tong, Lina Wang, Siddiq Ur Rahman, Gehong Wei, Shiheng Tao
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0244439

The peptide symporter SLC15a4 is essential for the development of systemic lupus erythematosus in murine models
Cited by: 14
Author(s): Arna Katewa, Eric Suto, Jessica Hui, Jose Heredia, Jie Liang, Jason A. Hackney, Keith R. Anderson, Tuija Alcantar, Natasha Bacarro, Debra Dunlap, Jeffrey Eastham, Andrés Paler-Martı́nez, Xin Y. Rairdan, Zora Modrušan, Wyne P. Lee, Cary D. Austin, Daniel Lafkas, Nico Ghilardi
Software Mentions: 5
Published: over 3 years ago

10.1186/s13029-019-0071-7

eUTOPIA: solUTion for Omics data PreprocessIng and Analysis
Cited by: 34
Author(s): Veer Singh Marwah, Giovanni Scala, Pia Anneli Sofia Kinaret, Angela Serra, Harri Alenius, Vittorio Fortino, Dario Greco
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0174212

The relationship between least-cost and resistance distance
Cited by: 38
Author(s): Robby R. Marrotte, Jeff Bowman
Software Mentions: 5
Published: about 7 years ago

10.1152/ajpendo.00473.2013

Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice
Cited by: 289
Author(s): Meritxell Rosell, Myrsini Kaforou, Andrea Frontini, Anthony Okolo, Yi‐Wah Chan, Evanthia Nikolopoulou, Steven Millership, Matthew Fenech, David A. MacIntyre, J. Turner, Jonathan D. Moore, E. K. Blackburn, William J. Gullick, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pgen.1006667

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans
Cited by: 85
Author(s): Eve W. L. Chow, Shelly Applen Clancey, R. Blake Billmyre, Anna Floyd Averette, Joshua A. Granek, Piotr A. Mieczkowski, María E. Cárdenas, Joseph Heitman
Software Mentions: 5
Published: about 7 years ago

10.3390/ijms21207720

A Bioinformatic Pipeline Places STAT5A as a miR-650 Target in Poorly Differentiated Aggressive Breast Cancer
Cited by: 1
Author(s): Eric López-Huerta, Ezequiel M. Fuentes‐Pananá
Software Mentions: 5
Published: over 3 years ago

10.1038/sdata.2018.218

Small non-coding RNA expression in mouse nephrogenic mesenchymal progenitors
Cited by: 4
Author(s): Yu Leng Phua, Andrew Clugston, Kevin Hong Chen, Dennis Kostka, Jacqueline Ho
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.8717

Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains
Cited by: 10
Author(s): Michelle Su, James T. Lyles, Robert A. Petit, Jessica Peterson, Michelle Hargita, Huaqiao Tang, Claudia Solís-Lemus, Cassandra L. Quave, Timothy D. Read
Software Mentions: 5
Published: about 4 years ago

10.3390/biom10060845

The Effect of the Photoperiod on the Fatty Acid Profile and Weight in Hatchery-Reared Underyearlings and Yearlings of Atlantic Salmon Salmo salar L.
Cited by: 13
Author(s): Н. Н. Немова, З. А. Нефедова, С. Н. Пеккоева, Viktor P. Voronin, N. S. Shulgina, М. В. Чурова, С. А. Мурзина
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-015-2096-x

The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh
Cited by: 19
Author(s): James Boocock, David Chagné, Tony R. Merriman, Michael A. Black
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0236165

Diversity and structure of soil microbiota of the Jinsha earthen relic
Cited by: 4
Author(s): Sheng Yang, Linfeng Wu, Bin Wu, Yizheng Zhang, Haiyan Wang, Xuemei Tan
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcell.2020.608044

Loss of G-Protein Pathway Suppressor 2 Promotes Tumor Growth Through Activation of AKT Signaling
Cited by: 10
Author(s): Stefanie Chan, Emma Smith, Yuan Gao, Julian Kwan, Benjamin Blum, Andrew Tilston-Lünel, Isabella Turcinovic, Xaralabos Varelas, Maria Dafne Cardamone, Stefano Monti, Andrew Emili, Valentina Perissi
Software Mentions: 5
Published: over 3 years ago

10.21203/rs.3.rs-25643/v1

Identification of new drug treatments to combat COVID19: A signature-based approach using iLINCS
Cited by: 5
Author(s): Sinead M. O’Donovan, Hunter M. Eby, Nicholas Henkel, Justin Creeden, Ali Sajid Imami, Sophie Asah, Xiaolu Zhang, Xiaojun Wu, Rawan Alnafisah, R Travis Taylor, James Reigle, Alexander W. Thorman, Behrouz Shamsaei, Jarek Meller, Robert E. McCullumsmith
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0203672

Integrating the skin and blood transcriptomes and serum proteome in hidradenitis suppurativa reveals complement dysregulation and a plasma cell signature
Cited by: 65
Author(s): Lauren Hoffman, Lewis Tomalin, Gregory S. Schultz, Michael D. Howell, Niroshana Anandasabapathy, Afsáneh Alavi, Mayte Suárez‐Fariñas, Michelle A. Lowes
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.7841

Evaluating remote sensing datasets and machine learning algorithms for mapping plantations and successional forests in Phnom Kulen National Park of Cambodia
Cited by: 8
Author(s): Minerva Singh, Damian Evans, Jean-Baptiste Chevance, Boun Suy Tan, Nicholas Wiggins, Leaksmy Kong, Sakada Sakhoeun
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-017-1708-7

Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
Cited by: 322
Author(s): Aziz Khan, Anthony Mathelier
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13104-016-2209-x

Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success
Cited by: 14
Author(s): Emily Humble, Michael A. S. Thorne, Jaume Forcada, Joseph I. Hoffman
Software Mentions: 4
Published: over 7 years ago

10.3390/genes11121503

Seascape Genomics of the Sugar Kelp Saccharina latissima along the North Eastern Atlantic Latitudinal Gradient
Cited by: 14
Author(s): Jaromir Guzinski, Paolo Ruggeri, Marion Ballenghien, Stéphane Mauger, Bertrand Jacquemin, Chloé Jollivet, Jérôme Coudret, Lucie Jaugeon, Christophe Destombe, Myriam Valéro
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0049230

Seasonal Response of Grasslands to Climate Change on the Tibetan Plateau
Cited by: 55
Author(s): Haiying Yu, Jianchu Xu, Erick Okuto, Eike Luedeling
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-020-74564-1

ScatLay: utilizing transcriptome-wide noise for identifying and visualizing differentially expressed genes
Cited by: 5
Author(s): Thuy Tien Bui, Daniel Lee, Kumar Selvarajoo
Software Mentions: 4
Published: over 3 years ago

10.3389/fonc.2020.00846

LPAR1, Correlated With Immune Infiltrates, Is a Potential Prognostic Biomarker in Prostate Cancer
Cited by: 50
Author(s): Jingqi Shi, Duyin Jiang, Shuya Yang, Xiyang Zhang, Jing Wang, Yang Liu, Yuanjie Sun, You Lu, Kun Yang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12870-018-1611-z

Phytohormone treatment induces generation of cryptic peptides with antimicrobial activity in the Moss Physcomitrella patens
Cited by: 25
Author(s): Igor Fesenko, Regina Azarkina, Ilya Kirov, Andrei Kniazev, Anna Filippova, Ekaterina N. Grafskaia, В. Н. Лазарев, Victor G. Zgoda, Ivan Butenko, Olga Bukato, Irina Lyapina, Dmitry Nazarenko, S. N. Elansky, Anna Mamaeva, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0102091

Pesticide Methoxychlor Promotes the Epigenetic Transgenerational Inheritance of Adult-Onset Disease through the Female Germline
Cited by: 191
Author(s): Mohan Manikkam, M. Muksitul Haque, Carlos Guerrero-Bosagna, Eric Nilsson, Michael K. Skinner
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12866-015-0351-6

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
Cited by: 365
Author(s): J. Paul Brooks, D.J. Edwards, Michael Harwich, Maria C. Rivera, Jennifer M. Fettweis, Myrna G. Serrano, Robert Reris, Nihar U. Sheth, Bernice Huang, Philippe H. Girerd, Jerome F. Strauss, Kimberly K. Jefferson, Gregory A. Buck
Software Mentions: 4
Published: about 9 years ago

10.3390/antibiotics6040038

Decreasing Inappropriate Use of Antibiotics in Primary Care in Four Countries in South America—Cluster Randomized Controlled Trial
Cited by: 8
Author(s): Inés Urbiztondo, Lars Bjerrum, Lidia Caballero, Marı́a Dolores Suárez, Monica Olinisky, Gloria Córdoba
Software Mentions: 4
Published: over 6 years ago

10.1186/s12967-020-02400-1

Collapsing the list of myocardial infarction-related differentially expressed genes into a diagnostic signature
Cited by: 11
Author(s): German Osmak, Natalia Baulina, Philipp Koshkin, О. О. Фаворова
Software Mentions: 4
Published: almost 4 years ago

10.3390/s16121980

Emotion-Bracelet: A Web Service for Expressing Emotions through an Electronic Interface
Cited by: 2
Author(s): Alicia Martínez, Hugo Estrada, Alejandra Molina, Manuel Mejia, Joaquín Pérez
Software Mentions: 4
Published: over 7 years ago

10.2196/mhealth.7820

Well-Being Tracking via Smartphone-Measured Activity and Sleep: Cohort Study
Cited by: 38
Author(s): Orianna DeMasi, Sidney Feygin, Aluma Dembo, Adrián Aguilera, Benjamin Recht
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-021-01784-0

A multi-ethnic genome-wide association study implicates collagen matrix integrity and cell differentiation pathways in keratoconus
Cited by: 36
Author(s): Alison J. Hardcastle, Petra Lišková, Yelena Bykhovskaya, Bennet J McComish, Alice E. Davidson, Chris F. Inglehearn, Xiaohui Li, Hélène Choquet, Mahmoud Habeeb, Sionne E. M. Lucas, Srujana Sahebjada, Nikolas Pontikos, Karla E. Rojas López, Anthony P Khawaja, Manir Ali, Ľubica Ďuďáková, Pavlína Skalická, Bart T. H. van Dooren, Annette J M Geerards, Christoph Haudum, Valeria Lo Faro, Abi Tenen, Mark James Simcoe, Karina Patasova, Darioush Yarrand, Jie Yin, Salina Siddiqui, Anthony J. Rice, Layal Abi Farraj, Yii Der Ida Chen, Jugnoo S Rahi, Ronald M. Krauss, Elizabeth Theusch, Jac Charlesworth, Loretta Szczotka-Flynn, Carmel Toomes, Magda A. Meester-Smoor, Andrea J. Richardson, Paul Mitchell, Kent D. Taylor, Ronald B. Melles, Anthony J. Aldave, Richard A. Mills, Ke Cao, Elsie Chan, Mark Daniell, Jie Jin Wang, Jerome I. Rotter, Alex W. Hewitt, Stuart MacGregor, Caroline C W Klaver, Wishal D. Ramdas, Jamie E Craig, Sudha K. Iyengar, David O’Brart, Eric Jorgenson, Paul N. Baird, Yaron S. Rabinowitz, Kathryn P. Burdon, Chris Hammond, Stephen Tuft, Pirro G. Hysi
Software Mentions: 4
Published: about 3 years ago

10.1186/s12859-019-2994-z

An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets
Cited by: 29
Author(s): Arezo Torang, Paraag Gupta, David J. Klinke
Software Mentions: 4
Published: over 4 years ago

10.1192/j.eurpsy.2020.17

Identification of newborns at risk for autism using electronic medical records and machine learning
Cited by: 21
Author(s): Rayees Rahman, Arad Kodesh, Stephen Z. Levine, Sven Sandin, Abraham Reichenberg, Avner Schlessinger
Software Mentions: 4
Published: over 4 years ago

10.3389/fnagi.2017.00013

MRI-Based Classification Models in Prediction of Mild Cognitive Impairment and Dementia in Late-Life Depression
Cited by: 62
Author(s): Aleksandra Lebedeva, Eric Westman, Tom Borza, Mona K. Beyer, Knut Engedal, Dag Aarsland, Geir Selbæk, Asta Håberg
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0047722

Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis
Cited by: 378
Author(s): Erin L. Gross, Clifford J. Beall, Stacey R. Kutsch, Noah D. Firestone, Eugene J. Leys, Ann L. Griffen
Software Mentions: 4
Published: over 11 years ago

10.1038/sdata.2018.147

Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Cited by: 2
Author(s): Philip L. Tzou, Soo-Yon Rhee, Sergei L. Kosakovsky Pond, Justen Manasa, Robert W. Shafer
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41597-019-0088-4

Transcriptome of dorsal root ganglia caudal to a spinal cord injury with modulated behavioral activity
Cited by: 7
Author(s): Julia H. Chariker, Cynthia Gomes, Fiona Brabazon, Kathryn A. Harman, Sujata Saraswat Ohri, David S.K. Magnuson, Scott R. Whittemore, Jeffrey C. Petruska, Eric C. Rouchka
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0102188

Large-Scale Structure of a Network of Co-Occurring MeSH Terms: Statistical Analysis of Macroscopic Properties
Cited by: 21
Author(s): Andrej Kastrin, Thomas C. Rindflesch, Dimitar Hristovski
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12859-018-2131-4

On the rank-distance median of 3 permutations
Cited by: 4
Author(s): Leonid Chindelevitch, João Paulo Pereira Zanetti, João Meidânis
Software Mentions: 4
Published: about 6 years ago

10.1042/BSR20201427

Mining novel cell glycolysis related gene markers that can predict the survival of colon adenocarcinoma patients
Cited by: 16
Author(s): Sihan Chen, Guodong Cao, Wei Wu, Yida Lu, Xueling He, Lei Yang, Ke Chen, Bo Chen, Maoming Xiong
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.ppat.1009732

Germinal Center T follicular helper (GC-Tfh) cell impairment in chronic HIV infection involves c-Maf signaling
Cited by: 2
Author(s): Marita Chakhtoura, Mike Fang, Rafael Cubas, Margaret O'Connor, Carmen N. Nichols, Brian Richardson, Aarthi Talla, Susan Moir, Mark J. Cameron, Virginie Tardif, Elias K. Haddad
Software Mentions: 4
Published: almost 3 years ago

10.1155/2020/3416807

Identification of Hub Genes as Biomarkers Correlated with the Proliferation and Prognosis in Lung Cancer: A Weighted Gene Co-Expression Network Analysis
Cited by: 2
Author(s): Xuting Xu, Limin Xu, Huilian Huang, Jing Li, Shunli Dong, Lili Jin, Zhiyong Ma, Liqin Li
Software Mentions: 4
Published: almost 4 years ago

10.1007/s13304-021-01079-3

Feasibility and safety of robotic-assisted total pancreatectomy: a pilot western series
Cited by: 5
Author(s): Emanuele Federico Kauffmann, Niccolò Napoli, Valerio Genovese, Michael Ginesini, Cesare Gianfaldoni, Fabio Vistoli, G Amorese, Ugo Boggi
Software Mentions: 4
Published: about 3 years ago

10.15252/msb.20209596

Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation
Cited by: 108
Author(s): Erika Kelmer Sacramento, Joanna Kirkpatrick, Mariateresa Mazzetto, Mario Baumgart, Aleksandar Bartolome, Simone Di Sanzo, Cinzia Caterino, Michele Sanguanini, Nikoletta Papaevgeniou, Maria Lefaki, Dorothee Childs, Sara Bagnoli, Eva Terzibasi Tozzini, Domenico Di Fraia, Natalie Romanov, Peter H. Sudmant, Wolfgang Huber, Niki Chondrogianni, Michele Vendruscolo, Alessandro Cellerino, Alessandro Ori
Software Mentions: 4
Published: almost 4 years ago

10.3390/plants9111589

Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana
Cited by: 11
Author(s): Dragana D Antonić, Angelina Subotić, Milan Dragićević, Danijel Pantelić, Snežana Milošević, Ana Simonović, Ivana Momčilović
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0146324

Marine Fouling Assemblages on Offshore Gas Platforms in the Southern North Sea: Effects of Depth and Distance from Shore on Biodiversity
Cited by: 54
Author(s): Tim van der Stap, Joop W.P. Coolen, H.J. Lindeboom
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2148-6-3

Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio
Cited by: 54
Author(s): Yan Boucher, Camilla Nesbø, Michael J. Joss, Andrew Robinson, Bridget C. Mabbutt, Michael R. Gillings, W. Ford Doolittle, H. W. Stokes
Software Mentions: 3
Published: over 18 years ago

10.1186/s12979-015-0038-8

Hormetic effect of rotenone in primary human fibroblasts
Cited by: 13
Author(s): Shiva Marthandan, Stefan Priebe, Marco Groth, Reinhard Guthke, Matthias Platzer, Peter Hemmerich, Stephan Diekmann
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0186742

Spatial relationships between above-ground biomass and bird species biodiversity in Palawan, Philippines
Cited by: 5
Author(s): Minerva Singh, Daniel A. Friess, Bruno Vilela, Jose Don T. De Alban, A. Monzón, Rizza Veridiano, Roven D. Tumaneng
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0257639

Examining the impact of a community-based exercise intervention on cardiorespiratory fitness, cardiovascular health, strength, flexibility and physical activity among adults living with HIV: A three-phased intervention study
Cited by: 9
Author(s): Kelly K O’Brien, Aileen M. Davis, Soo Chan Carusone, Lisa Avery, Ada Tang, Patricia Solomon, Rachel Aubry, Mehdi Zobeiry, Ivan Ilić, Zoran Pandovski, Ahmed M. Bayoumi
Software Mentions: 3
Published: over 2 years ago

10.1371/journal.pone.0254697

Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex
Cited by: 1
Author(s): Anne E. Roehrig, Kristina Klupsch, Juan Oses-Prieto, Selim Chaib, Stephen Henderson, Warren Emmett, Lucy C. Young, Silvia Šurinová, Andreas Blees, Anett Pfeiffer, Maha Tijani, Fabian Brunk, Nicole Hartig, Marta Muñoz-Alegre, Alexander Hergovich, Barbara Jennings, Alma L. Burlingame, Pablo Rodríguez‐Viciana
Software Mentions: 3
Published: over 2 years ago

10.1186/s12885-019-5801-3

A new pragmatic design for dose escalation in phase 1 clinical trials using an adaptive continual reassessment method
Cited by: 20
Author(s): Bernard V. North, Hemant M. Kocher, Peter Sasieni
Software Mentions: 3
Published: almost 5 years ago

10.1093/aobpla/plw060

Differential plant invasiveness is not always driven by host promiscuity with bacterial symbionts
Cited by: 14
Author(s): Metha M. Klock, Luke G. Barrett, Peter H. Thrall, Kyle E. Harms
Software Mentions: 3
Published: almost 9 years ago

10.3389/fphar.2020.602030

A Novel Text-Mining Approach for Retrieving Pharmacogenomics Associations From the Literature
Cited by: 3
Author(s): Maria‐Theodora Pandi, Peter J. van der Spek, Maria Koromina, George P. Patrinos
Software Mentions: 3
Published: over 3 years ago

10.18632/aging.103888

Revealing the targets and mechanisms of vitamin A in the treatment of COVID-19
Cited by: 55
Author(s): Rong Li, Ka Wu, Yu Liu, Liang Xiao, William Ka Fai Tse, Yang Lu, Keng Po Lai
Software Mentions: 3
Published: almost 4 years ago

10.1210/me.2013-1254

RIP140 Represses the “Brown-in-White” Adipocyte Program Including a Futile Cycle of Triacyclglycerol Breakdown and Synthesis
Cited by: 41
Author(s): Evangelos Kiskinis, Lemonia Chatzeli, Ed Curry, Myrsini Kaforou, Andrea Frontini, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 3
Published: about 10 years ago

Projects: pypi: language

Papers Mentioning language 427