cran: ROCR | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1004553

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response
Cited by: 18
Author(s): Robin van der Lee, Feng Qian, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen
Software Mentions: 3
Published: about 9 years ago

10.1007/s41048-016-0033-4

MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets
Cited by: 9
Author(s): Xilin Xu, Aiping Wu, Xinlei Zhang, Mingming Su, Taijiao Jiang, Zheming Yuan
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pcbi.1000300

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery
Cited by: 55
Author(s): Schraga Schwartz, Nurit Gal-Mark, Nir Kfir, Oren Ram, Eddo Kim, Gil Ast
Software Mentions: 3
Published: over 15 years ago

10.3390/biomedicines8050114

RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens
Cited by: 20
Author(s): Maxim Sorokin, Kirill Ignatev, Elena Poddubskaya, Uliana Vladimirova, Нуршат Гайфуллин, Dmitriy Lantsov, Andrew Garazha, Daria Allina, Maria Suntsova, Victoria Barbara, Anton Buzdin
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-018-0575-z

A urine-based DNA methylation assay, ProCUrE, to identify clinically significant prostate cancer
Cited by: 25
Author(s): Fang Zhao, Ekaterina Olkhov‐Mitsel, Shivani Kamdar, Renu Jeyapala, Julia Garcia, Rachel Hurst, Marcelino Yazbek Hanna, Robert Mills, Alexandra V. Tuzova, Eve O’Reilly, Sarah Kelly, Christopher S. Cooper, Daniel Brewer, Antoinette S. Perry, Jeremy Clark, Neil Fleshner, Bharati Bapat
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers11081157

A Novel Type of Blood Biomarker: Distinct Changes of Cytokine-Induced STAT Phosphorylation in Blood T Cells Between Colorectal Cancer Patients and Healthy Individuals
Cited by: 14
Author(s): Jae Won Yun, Sejoon Lee, Hye Mi Kim, Sejong Chun, Edgar G. Engleman, Hee Cheol Kim, Eun Suk Kang
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.159

BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways
Cited by: 11
Author(s): Charles Warden, Noriko Kanaya, Shiuan Chen, Yuan Yun
Software Mentions: 3
Published: about 11 years ago

10.3389/fvets.2018.00229

Evaluation of the Performance of the IDvet IFN-Gamma Test for Diagnosis of Bovine Tuberculosis in Spain
Cited by: 12
Author(s): María Luisa de la Cruz, Adam J. Branscum, Jesus Nacar, Enrique Pages, Pilar Pozo, Andrés Perez, Anna Grau, José Luis Sáez, Lucía de Juan, Rosa Díaz, Olga Mínguez, Julio Álvarez
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0243772

Phenotypical antimicrobial resistance data of clinical and non-clinical Escherichia coli from poultry in Germany between 2014 and 2017
Cited by: 8
Author(s): Octavio Mesa-Varona, Heike Kaspar, Mirjam Grobbel, Bernd‐Alois Tenhagen
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-11-S9-S6

Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
Cited by: 21
Author(s): Alexander A. Morgan, Purvesh Khatri, Richard H. Jones, Minnie M. Sarwal, Atul J. Butte
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.ppat.1006425

Aberrant plasma IL-7 and soluble IL-7 receptor levels indicate impaired T-cell response to IL-7 in human tuberculosis
Cited by: 32
Author(s): Christian Lundtoft, Anthony Afum-Adjei Awuah, Jens Rimpler, Kirstin Harling, Norman Nausch, Malte Kohns, Ernest Adankwah, Franziska Lang, Laura Olbrich, Ertan Mayatepek, Ellis Owusu‐Dabo, Marc Jacobsen
Software Mentions: 3
Published: over 7 years ago

10.1155/2021/6667201

Predicting Ovarian/Breast Cancer Pathogenic Risks of Human BRCA1 Gene Variants of Unknown Significance
Cited by: 0
Author(s): Hui-Heng Lin, Hongxing Xu, Hongbo Hu, Zhu Ma, Jie Zhou, Qingyun Liang
Software Mentions: 3
Published: over 3 years ago

10.1186/s40169-019-0245-6

Network vulnerability‐based and knowledge‐guided identification of microRNA biomarkers indicating platinum resistance in high‐grade serous ovarian cancer
Cited by: 23
Author(s): Xin Qi, Chunjiang Yu, Yi Wang, Yuxin Lin, Bairong Shen
Software Mentions: 3
Published: about 5 years ago

10.3389/fonc.2020.544330

Blood Cell DNA Methylation of Aging-Related Ubiquitination Gene DZIP3 Can Predict the Onset of Early Stage Colorectal Cancer
Cited by: 6
Author(s): Quan Yuan, Feng Liang, Deqing Wu, Xueqing Yao, Zhihuang Hu, Yuexing Zhu, Ying Chen, Aoli Wu, Da-nian Tang, Bingyang Huang, Ruifeng Xu, Zejian Lyu, Qian Yan, Li Luo, Zhengzhi Ning, Yong Li, Jianghui Xiong
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13062-016-0151-4

modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks
Cited by: 1
Author(s): Neetu Sain, Debasisa Mohanty
Software Mentions: 3
Published: about 8 years ago

10.7717/peerj.6304

Prioritizing bona fide bacterial small RNAs with machine learning classifiers
Cited by: 6
Author(s): Erik JJ Eppenhof, Lourdes Peña‐Castillo
Software Mentions: 3
Published: almost 6 years ago

10.1186/s13018-021-02201-2

Bioinformatics analysis of miRNA and mRNA expression profiles to reveal the key miRNAs and genes in osteoarthritis
Cited by: 13
Author(s): Peiyan Huang, Junguo Wu, Jun Gu, Tie-qi Zhang, Lingfeng Li, Siqun Wang, Ming-Hai Wang
Software Mentions: 3
Published: almost 4 years ago

10.1002/ece3.1743

Bioacoustics for species management: two case studies with a Hawaiian forest bird
Cited by: 19
Author(s): Esther Sebastián‐González, Joshua Pang‐Ching, José Marcos Barbosa, Patrick J. Hart
Software Mentions: 2
Published: about 9 years ago

10.18632/aging.102645

Concomitant memantine and Lactobacillus plantarum treatment attenuates cognitive impairments in APP/PS1 mice
Cited by: 65
Author(s): Qiujun Wang, Yue’e Shen, Xin Wang, Shuang Fu, Xin Zhang, Yina Zhang, Ruitao Wang
Software Mentions: 2
Published: almost 5 years ago

10.1002/acn3.50965

Transmembrane protease serine 5: a novel Schwann cell plasma marker for CMT1A
Cited by: 24
Author(s): Hongge Wang, Matt Davison, Kathryn Wang, Tai-he Xia, Martin Kramer, Katherine M. Call, Jun Luo, Xingyao Wu, Riccardo Zuccarino, Chelsea Bacon, Yunhong Bai, John J. Moran, Laurie Gutmann, Shawna Feely, Tiffany Grider, Alexander M. Rossor, John Svaren, Michael E. Shy
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12859-017-1637-5

Drug repositioning for enzyme modulator based on human metabolite-likeness
Cited by: 10
Author(s): Yoon Hyeok Lee, Hojae Choi, Seongyong Park, Boah Lee, Gwan‐Su Yi
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-14-155

Greedy feature selection for glycan chromatography data with the generalized Dirichlet distribution
Cited by: 4
Author(s): Marie Galligan, Radka Saldova, Matthew P. Campbell, Pauline M. Rudd, Brendan Murphy
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-9-381

MetWAMer: eukaryotic translation initiation site prediction
Cited by: 14
Author(s): Michael E. Sparks, Volker Brendel
Software Mentions: 2
Published: about 16 years ago

10.1186/1471-2105-13-44

Grading amino acid properties increased accuracies of single point mutation on protein stability prediction
Cited by: 12
Author(s): Jianguo Liu, Xianjiang Kang
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-11-603

Content-based microarray search using differential expression profiles
Cited by: 39
Author(s): J Engreitz, Alexander A. Morgan, Joel T. Dudley, Rong Chen, Rahul Thathoo, Russ B. Altman, Atul J. Butte
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2105-13-89

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art
Cited by: 75
Author(s): Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser EL-Manzalawy, Drena Dobbs, Vasant Honavar
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-10-129

Improving classification in protein structure databases using text mining
Cited by: 14
Author(s): Antonis Koussounadis, Oliver Redfern, David T. Jones
Software Mentions: 2
Published: over 15 years ago

10.1186/s12859-016-0948-2

Structure-based Markov random field model for representing evolutionary constraints on functional sites
Cited by: 6
Author(s): Chanseok Jeong, Dongsup Kim
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-13-309

An assessment on epitope prediction methods for protozoa genomes
Cited by: 21
Author(s): Daniela de Melo Resende, Antônio Mauro Rezende, Nesley J D Oliveira, Izabella Cristina Andrade Batista, Rodrigo Corrêa-Oliveira, Alexandre Barbosa Reis, Jerônimo C. Ruiz
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2105-9-S12-S20

Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies
Cited by: 16
Author(s): Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Tao Lin, Yixue Li, Zhiwei Cao
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12885-020-07620-8

Analysis of the expression and potential molecular mechanism of interleukin-1 receptor antagonist (IL1RN) in papillary thyroid cancer via bioinformatics methods
Cited by: 4
Author(s): Zhenyu Xie, Xin Li, Yuzhen He, Song Wu, Shiyue Wang, Jing Sun, Yuchen He, Yu Lun, Shijie Xin, Jian Zhang
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2261-11-2

Incidence of cardiovascular events after kidney transplantation and cardiovascular risk scores: study protocol
Cited by: 30
Author(s): Salvador Pita-Fernández, Sonia Pértega-Díaz, Francisco Valdés-Cañedo, Rocío Seijo-Bestilleiro, Teresa Seoane-Pillado, Constantino Fernández-Rivera, Ángel Alonso-Hernández, Dolores Lorenzo-Aguiar, Beatriz López‐Calviño, Andrés López-Muñiz
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-13-630

A histone arginine methylation localizes to nucleosomes in satellite II and III DNA sequences in the human genome
Cited by: 10
Author(s): Daniel Capurso, Hao Xiong, Mark R. Segal
Software Mentions: 2
Published: about 12 years ago

10.1186/s12879-020-05194-1

Use of resuscitation promoting factors to screen for tuberculosis infection in household-exposed children in The Gambia
Cited by: 1
Author(s): Welmoed van Loon, Marie P Gomez, Dawda Jobe, Kees L. M. C. Franken, Tom H. M. Ottenhoff, M. Coninx, Luc Kestens, Jayne S. Sutherland, Beate Kampmann, Leopold D. Tientcheu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12879-020-05116-1

A blood RNA transcript signature for TB exposure in household contacts
Cited by: 10
Author(s): Philip Kam Weng Kwan, Balamurugan Periaswamy, Paola Flórez de Sessions, Wei Lin, James S. Molton, Claire M. Naftalin, Ahmad Nazri Mohamed Naim, Martin L. Hibberd, Nicholas I. Paton
Software Mentions: 2
Published: over 4 years ago

10.1186/s12879-020-05350-7

Prediction of treatment failure and compliance in patients with tuberculosis
Cited by: 20
Author(s): Hyeon‐Kyoung Koo, Jinsoo Min, Hyung Woo Kim, Joosun Lee, Ju Sang Kim, Jae Seuk Park, Sung-Soon Lee
Software Mentions: 2
Published: about 4 years ago

10.1186/s12920-015-0158-1

Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner
Cited by: 34
Author(s): Yoshiyuki Hizukuri, Ryusuke Sawada, Yoshihiro Yamanishi
Software Mentions: 2
Published: almost 9 years ago

10.1186/1755-8794-5-13

Novel biomarker combination improves the diagnosis of serious bacterial infections in Malawian children
Cited by: 19
Author(s): Adam Irwin, Fiona Marriage, Limangeni Mankhambo, Graham Jeffers, Ruwanthi Kolamunnage-Donà, Malcolm Guiver, Brigitte Denis, Elizabeth Molyneux, Malcolm E. Molyneux, Philip J. Day, Enitan D. Carrol
Software Mentions: 2
Published: over 12 years ago

10.1186/1755-8794-3-4

Genome-wide methylation and expression profiling identifies promoter characteristics affecting demethylation-induced gene up-regulation in melanoma
Cited by: 19
Author(s): Jill C. Rubinstein, Nam Tran, Shuangge Ma, Ruth Halaban, Michael Krauthammer
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2180-13-76

Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi
Cited by: 86
Author(s): Anne‐Cécile Normand, Christophe Cassagne, Stéphane Ranque, Coralie L’Ollivier, Patrick Fourquet, Sam Roesems, Marijke Hendrickx, Renaud Piarroux
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2415-11-6

Evaluation of a combined index of optic nerve structure and function for glaucoma diagnosis
Cited by: 21
Author(s): Michael V. Boland, Harry A. Quigley
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12917-015-0612-5

Development and validation of an indirect ELISA as a confirmatory test for surveillance of infectious bovine rhinotracheitis in vaccinated herds
Cited by: 14
Author(s): Luigi Bertolotti, Elvira Muratore, Chiara Nogarol, Claudio Caruso, Laura Lucchese, Margherita Profiti, Laura Anfossi, Loretta Masoero, S. Nardelli, Sergio Rosati
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13040-021-00264-9

Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children
Cited by: 3
Author(s): Nicholas Giangreco, Nicholas P. Tatonetti
Software Mentions: 2
Published: over 3 years ago

10.1186/1756-0381-7-14

A simple structure-based model for the prediction of HIV-1 co-receptor tropism
Cited by: 27
Author(s): Dominik Heider, J. Nikolaj Dybowski, Christoph Wilms, Daniel Hoffmann
Software Mentions: 2
Published: over 10 years ago

10.1186/1756-0381-4-16

Interpol: An R package for preprocessing of protein sequences
Cited by: 19
Author(s): Dominik Heider, Daniel Hoffmann
Software Mentions: 2
Published: over 13 years ago

10.1093/bioinformatics/btx515

In silico identification of rescue sites by double force scanning
Cited by: 10
Author(s): Matteo Tiberti, Alessandro Pandini, Franca Fraternali, Arianna Fornili
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btw518

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
Cited by: 23
Author(s): Nicole E. Wheeler, Lars Barquist, Robert A. Kingsley, Paul P. Gardner
Software Mentions: 2
Published: over 8 years ago

10.1093/bioinformatics/bty754

Understanding and predicting disease relationships through similarity fusion
Cited by: 14
Author(s): Erin Oerton, Ian N. Roberts, Patrick Lewis, Tim Guilliams
Software Mentions: 2
Published: about 6 years ago

10.1155/2021/6650966

MicroRNA Biomarkers of High-Grade Cervical Intraepithelial Neoplasia in Liquid Biopsy
Cited by: 9
Author(s): Rhafaela Lima Causin, Luciane S. da Silva, Adriane Feijó Evangelista, Letícia Ferro Leal, Karen Cristina Borba Souza, Danielle Pessôa‐Pereira, Graziela M. Matsushita, Rui Manuel Reis, José Humberto Tavares Guerreiro Fregnani, Márcia Maria Chiquitelli Marques
Software Mentions: 2
Published: over 3 years ago

10.1186/bcr2192

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer
Cited by: 117
Author(s): Fabien Reyal, Martin H. van Vliet, Nicola J. Armstrong, Hugo M. Horlings, Karin E. de Visser, M Kok, Andrew E. Teschendorff, Stella Mook, Laura van ’t Veer, Carlos Caldas, Rémy Salmon, Marc J. van de Vijver, Lodewyk F.A. Wessels
Software Mentions: 2
Published: about 16 years ago

10.1186/bcr3110

Breast cancer risk prediction and individualised screening based on common genetic variation and breast density measurement
Cited by: 106
Author(s): Hatef Darabi, Kamila Czene, Wanting Zhao, Jianjun Li, Per Hall, Keith Humphreys
Software Mentions: 2
Published: almost 13 years ago

10.1186/s40168-020-00912-y

Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery
Cited by: 30
Author(s): Wei Wu, Suraphan Panyod, Po-Yu Liu, Chieh Chang Chen, Hsien‐Li Kao, Hsiao-Li Chuang, Ying Hsien Chen, Hsin Bai Zou, Han Chun Kuo, Ching‐Hua Kuo, Ben-Yang Liao, Tina H.T. Chiu, Chi Hsiang Chung, Angela Yu-Chen Lin, Yi‐Chia Lee, Sen Lin Tang, Jin Town Wang, Yu Wei Wu, Cheng Chih Hsu, Lee‐Yan Sheen, Alexander N. Orekhov, Ming Shiang Wu
Software Mentions: 2
Published: about 4 years ago

10.3390/microorganisms8030450

Liver Transudate, a Potential Alternative to Detect Anti-Hepatitis E Virus Antibodies in Pigs and Wild Boars (Sus scrofa)
Cited by: 4
Author(s): Alejandro Rodríguez Navarro, Carmen Bárcena, Pilar Pozo, Alberto Díez-Guerrier, Irene Martínez, Coral Polo, Clara María Duque, David Rodríguez‐Lázaro, J. Goyache, N. Garcı́a
Software Mentions: 2
Published: over 4 years ago

10.3390/microorganisms9040678

Comparison of Phenotypical Antimicrobial Resistance between Clinical and Non-Clinical E. coli Isolates from Broilers, Turkeys and Calves in Four European Countries
Cited by: 4
Author(s): Octavio Mesa-Varona, Rodolphe Mader, Martina Velasova, Jean‐Yves Madec, Sophie A. Granier, Agnès Perrin-Guyomard, Madelaine Norström, Heike Kaspar, Mirjam Grobbel, Éric Jouy, Muna F. Anjum, Bernd‐Alois Tenhagen
Software Mentions: 2
Published: over 3 years ago

10.1093/molbev/mst221

A Guide for the Design of Evolve and Resequencing Studies
Cited by: 137
Author(s): Robert Kofler, Christian Schlötterer
Software Mentions: 2
Published: about 11 years ago

10.1186/s13071-016-1399-3

Modelling hotspots of the two dominant Rift Valley fever vectors (Aedes vexans and Culex poicilipes) in Barkédji, Sénégal
Cited by: 12
Author(s): Cheikh Talla, Diawo Diallo, Ibrahima Dia, Yamar Bâ, Jacques André Ndione, Andrew P. Morse, Aliou Diop, Mawlouth Diallo
Software Mentions: 2
Published: over 8 years ago

10.1186/s13071-017-2369-0

Dogs as victims of their own worms: Serodiagnosis of canine alveolar echinococcosis
Cited by: 12
Author(s): Claude Frey, Nelson Marreros, Stefanie Renneker, Leah Schmidt, Heinz Sager, Brigitte Hentrich, S Milesi, Bruno Gottstein
Software Mentions: 2
Published: about 7 years ago

10.3389/pore.2021.1609784

Integrative Analysis of DNA Methylation and Gene Expression Profiles Identifies Colorectal Cancer-Related Diagnostic Biomarkers
Cited by: 4
Author(s): Mingyue Xu, Lijun Yuan, Yan Wang, Shuo Chen, Lin Zhang, Xipeng Zhang
Software Mentions: 2
Published: over 3 years ago

10.7717/peerj.4274

Habitat use in south-west European skinks (genusChalcides)
Cited by: 4
Author(s): Daniel Escoriza, Guillem Pascual, Alberto Sánchez‐Vialas
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pcbi.1004418

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
Cited by: 27
Author(s): Zing Tsung-Yeh Tsai, Shin-Han Shiu, Huai Kuang Tsai
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1002798

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State
Cited by: 40
Author(s): Bartek Wilczyński, Ya Hsin Liu, Zhen Xuan Yeo, Eileen E. M. Furlong
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pcbi.1002256

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers
Cited by: 9
Author(s): Andrew Tae-Jun Kwon, Alice Chou, David J. Arenillas, Wyeth W. Wasserman
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1002646

Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context
Cited by: 53
Author(s): Artyom A. Alekseyenko, Joshua W. K. Ho, Shouyong Peng, Marnie E. Gelbart, Michael Y. Tolstorukov, Annette Plachetka, Peter V. Kharchenko, Youngsook L. Jung, Andrey A. Gorchakov, Erica Larschan, Tingting Gu, Aki Minoda, Nicole C. Riddle, Yuri B. Schwartz, Sarah C. R. Elgin, Gary H. Karpen, Vincenzo Pirrotta, Mitzi I. Kuroda, Peter J. Park
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pmed.1003489

A combination of urinary biomarker panel and PancRISK score for earlier detection of pancreatic cancer: A case–control study
Cited by: 23
Author(s): Silvana Debernardi, Harrison O’Brien, Asma S. Algahmdi, Núria Malats, Grant D. Stewart, Marija Plješa-Ercegovac, Eithne Costello, William Greenhalf, Ahmed S. Saad, Rhiannon Roberts, Alexander Ney, Stephen P. Pereira, Hemant M. Kocher, Stephen W. Duffy, Oleg Blyuss, Tatjana Crnogorac‐Jurčević
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0189641

Diagnostic markers for the detection of ovarian cancer in BRCA1 mutation carriers
Cited by: 8
Author(s): Daphne Gschwantler‐Kaulich, Sigrid Weingartshofer, Christine Rappaport-Fürhauser, Robert Zeilinger, Dietmar Pils, Daniela Muhr, Elena Ioana Braicu, Marie-Therese Kastner, Yen Y. Tan, Lorenz Semmler, Jalid Sehouli, Christian F. Singer
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0156624

Sex Differences in Serum Markers of Major Depressive Disorder in the Netherlands Study of Depression and Anxiety (NESDA)
Cited by: 53
Author(s): Jordan M. Ramsey, Jason D. Cooper, Mariska Bot, Paul C. Guest, Femke Lamers, Cynthia Shannon Weickert, Brenda W. J. H. Penninx, Sabine Bahn
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0139685

Application of LogitBoost Classifier for Traceability Using SNP Chip Data
Cited by: 13
Author(s): Kwondo Kim, Minseok Seo, Hao Kang, Seoae Cho, Heebal Kim, Kang Seok Seo
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0002830

Protection Induced by Plasmodium falciparum MSP142 Is Strain-Specific, Antigen and Adjuvant Dependent, and Correlates with Antibody Responses
Cited by: 71
Author(s): Jeffrey A. Lyon, Evelina Angov, Michael P. Fay, JoAnn S. Sullivan, Autumn S. Girourd, Sally Robinson, Elke S. Bergmann‐Leitner, Elizabeth H. Duncan, Christian A. Darko, William E. Collins, Carole A. Long, John W. Barnwell
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0104558

The Development of the Pediatric NAFLD Fibrosis Score (PNFS) to Predict the Presence of Advanced Fibrosis in Children with Nonalcoholic Fatty Liver Disease
Cited by: 64
Author(s): Naim Alkhouri, Sana Mansoor, Paola Giammaria, Daniela Liccardo, Rocío López, Valério Nobili
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0041337

Regime Shifts and Weakened Environmental Gradients in Open Oak and Pine Ecosystems
Cited by: 44
Author(s): Brice B. Hanberry, Dan Dey, Hong S. He
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0061709

Winning and Losing Tree Species of Reassembly in Minnesota’s Mixed and Broadleaf Forests
Cited by: 23
Author(s): Brice B. Hanberry, Brian J. Palik, Hong S. He
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0061327

Prospecting for Novel Plant-Derived Molecules of Rauvolfia serpentina as Inhibitors of Aldose Reductase, a Potent Drug Target for Diabetes and Its Complications
Cited by: 46
Author(s): Shivalika Pathania, Vinay Randhawa, Ganesh Bagler
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0054325

Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways
Cited by: 13
Author(s): Vijaykumar Yogesh Muley, Akash Ranjan
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0132327

Analysis of Deregulated microRNAs and Their Target Genes in Gastric Cancer
Cited by: 37
Author(s): Simonas Juzėnas, Violeta Šaltenienė, Juozas Kupčinskas, Alexander Link, Gediminas Kiudelis, Laimas Jonaitis, Sonata Jarmalaitė, Limas Kupčinskas, Peter Malfertheiner, Jurgita Skiecevičienė
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0013735

A Pilot Study of Circulating miRNAs as Potential Biomarkers of Early Stage Breast Cancer
Cited by: 349
Author(s): Hua Zhao, Jie Shen, Leonard Medico, Dan Wang, Christine B. Ambrosone, Song Liu
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0225721

Analysis of the characteristics of chemotherapy-resistant renal cell carcinomas based on global transcriptional analysis of their tissues and cell lines
Cited by: 0
Author(s): Takahiro Isono, Masafumi Suzaki
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0228772

A fluorescent plasmonic biochip assay for multiplex screening of diagnostic serum antibody targets in human Lyme disease
Cited by: 17
Author(s): Eunice Chou, Erica Lasek‐Nesselquist, Benjamin Taubner, Arturo Pilar, Ernest Guignon, William D. Page, Yi Pin Lin, Nathaniel C. Cady
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0191047

Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility
Cited by: 37
Author(s): Simon Graspeuntner, Michael K. Bohlmann, Kathrin Gillmann, Runa Speer, Sven Kuenzel, Heike Mark, Friederike Hoellen, Reinhard Lettau, G. Griesinger, Inke R. König, John F. Baines, Jan Rupp
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0017238

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods
Cited by: 401
Author(s): Chao Chen, Kay Grennan, Judith A. Badner, Dandan Zhang, Elliot S. Gershon, Li Jin, Chun Yu Liu
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0143199

Reliably Detecting Clinically Important Variants Requires Both Combined Variant Calls and Optimized Filtering Strategies
Cited by: 39
Author(s): Matthew A. Field, Vicky Cho, Thomas D. Andrews, Christopher C. Goodnow
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0234130

Evaluation of multi-antigen serological screening for active tuberculosis among people living with HIV
Cited by: 9
Author(s): Devan Jaganath, Jayant V. Rajan, Christina Yoon, Resmi Ravindran, Alfred Andama, Lucy Asege, Sandra Mwebe, Jane Katende, Martha Nakaye, Fred C. Semitala, Imran Khan, Adithya Cattamanchi
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0007387

V3 Loop Sequence Space Analysis Suggests Different Evolutionary Patterns of CCR5- and CXCR4-Tropic HIV
Cited by: 13
Author(s): Katarzyna Bożek, Alexander Thielen, Saleta Sierra, Rolf Kaiser, Thomas Lengauer
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0256606

Frontiers in assessing septic systems vulnerability in coastal Georgia, USA: Modeling approach and management implications
Cited by: 3
Author(s): Nahal Hoghooghi, J. Scott Pippin, Brian K. Meyer, John B. Hodges, Brian P. Bledsoe
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0044486

Pseudoabsence Generation Strategies for Species Distribution Models
Cited by: 33
Author(s): Brice B. Hanberry, Hong S. He, Brian J. Palik
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0243138

Early life ecology of the invasive lionfish (Pterois spp.) in the western Atlantic
Cited by: 1
Author(s): Jason Mostowy, Estrella Malca, Leif K. Rasmuson, Lourdes Vásquez–Yeomans, Trika Gerard, Eloy Sosa Cordero, Laura Carrillo, John T. Lamkin
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0161452

Estimation of Position Specific Energy as a Feature of Protein Residues from Sequence Alone for Structural Classification
Cited by: 14
Author(s): Sumaiya Iqbal, Tamjidul Hoque
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0176653

Year-round spatiotemporal distribution of harbour porpoises within and around the Maryland wind energy area
Cited by: 20
Author(s): Jessica E. Wingfield, Michael H. P. O’Brien, Vyacheslav Lyubchich, Jason J. Roberts, Patrick N. Halpin, Aaron N. Rice, Helen Bailey
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0038904

Predicting Progression of IgA Nephropathy: New Clinical Progression Risk Score
Cited by: 104
Author(s): Jingyuan Xie, Krzysztof Kiryluk, Weiming Wang, Zhaohui Wang, Shanmai Guo, Ping Shen, Hong Ren, Xiaoxia Pan, Xiaonong Chen, Wen Zhang, Xiao Li, Hao Shi, Yifu Li, Ali G. Gharavi, Nan Chen
Software Mentions: 2
Published: over 12 years ago

10.3390/cancers12020353

Plasma Next Generation Sequencing and Droplet Digital-qPCR-Based Quantification of Circulating Cell-Free RNA for Noninvasive Early Detection of Cancer
Cited by: 22
Author(s): Martin Metzenmacher, Renáta Váraljai, Balázs Hegedűs, Igor Cima, Jan Förster, Alexander Schramm, Björn Scheffler, Peter A. Horn, Christoph A. Klein, Tibor Szarvas, Henning Reis, Nicola Bielefeld, Alexander Roesch, Clemens Aigner, Volker Kunzmann, Marcel Wiesweg, Jens T. Siveke, Martin Schüler, Smiths Lueong
Software Mentions: 2
Published: almost 5 years ago

10.3390/cancers12092654

Analysis of Bone Scans in Various Tumor Entities Using a Deep-Learning-Based Artificial Neural Network Algorithm—Evaluation of Diagnostic Performance
Cited by: 18
Author(s): Jan Wuestemann, Sebastian Hupfeld, Dennis Kupitz, Philipp Genseke, Simone Schenke, Maciej Pech, Michael C. Kreißl, Oliver S. Großer
Software Mentions: 2
Published: about 4 years ago

10.3390/cells8070719

Inflammatory Bowel Disease Types Differ in Markers of Inflammation, Gut Barrier and in Specific Anti-Bacterial Response
Cited by: 31
Author(s): Štěpán Coufal, Natalie Galanová, Lukáš Bajer, Zuzana Gajdárová, Dagmar Schierová, Zuzana Jirásková Zákostelská, Klara Kostovcikova, Zuzana Jackova, Zuzana Stehlíková, Pavel Drastich, Helena Tlaskalová‐Hogenová, Miloslav Kverka
Software Mentions: 2
Published: over 5 years ago

10.1155/2014/639751

A Comprehensive In Silico Analysis of the Functional and Structural Impact of Nonsynonymous SNPs in the ABCA1 Transporter Gene
Cited by: 12
Author(s): Francisco R. Marín-Martín, Cristina Soler‐Rivas, Roberto Martín‐Hernández, Arantxa Rodrı́guez-Casado
Software Mentions: 2
Published: over 10 years ago

10.1186/s12014-019-9251-3

Predictive proteomic signatures for response of pancreatic cancer patients receiving chemotherapy
Cited by: 15
Author(s): Hong Peng, Ru Chen, Teresa A. Brentnall, Jimmy K. Eng, Vincent J. Picozzi, Sheng Pan
Software Mentions: 2
Published: over 5 years ago

10.1155/2017/7847531

Correcting Classifiers for Sample Selection Bias in Two-Phase Case-Control Studies
Cited by: 8
Author(s): Norbert Krautenbacher, Fabian J. Theis, Christiane Fuchs
Software Mentions: 2
Published: almost 8 years ago

10.1007/s00125-017-4325-0

Early metabolic markers identify potential targets for the prevention of type 2 diabetes
Cited by: 92
Author(s): Peddinti Gopalacharyulu, Jeff E. Cobb, Loïc Yengo, Philippe Froguel, Jasmina Kravić, Beverley Balkau, Tiinamaija Tuomi, Tero Aittokallio, Leif Groop
Software Mentions: 2
Published: over 7 years ago

10.1186/s40478-020-00984-9

Molecular identification of CNS NB-FOXR2, CNS EFT-CIC, CNS HGNET-MN1 and CNS HGNET-BCOR pediatric brain tumors using tumor-specific signature genes
Cited by: 26
Author(s): Maria Łastowska, Joanna Trubicka, Anna Sobocińska, Bartosz Wojtaś, Magdalena Niemira, Anna Szałkowska, Adam Krętowski, Agnieszka Karkucińska-Więckowska, Magdalena Kaleta, Maria Ejmont, Marta Perek-Polnik, Bożenna Dembowska–Bagińska, Wiesława Grajkowska, Ewa Matyja
Software Mentions: 2
Published: over 4 years ago

10.1002/ece3.7166

Reproductive interference hampers species coexistence despite conspecific sperm precedence
Cited by: 5
Author(s): Ryosuke Iritani, Suzuki Noriyuki
Software Mentions: 2
Published: almost 4 years ago

10.1002/ece3.2696

Species distribution models predict temporal but not spatial variation in forest growth
Cited by: 31
Author(s): Ernst van der Maaten, Andreas Hamann, Marieke van der Maaten‐Theunissen, A.R. Bergsma, G.M. Hengeveld, R.J.A. van Lammeren, Frits Mohren, Gert‐Jan Nabuurs, R.L. Terhürne, Frank J. Sterck
Software Mentions: 2
Published: over 7 years ago

10.14252/foodsafetyfscj.D-20-00004

Quantitative Release Assessment of mcr-mediated Colistin-resistant Escherichia Coli from Japanese Pigs
Cited by: 6
Author(s): Kohei Makita, Yoshiyuki Fujimoto, Nami Sugahara, Takeshi Miyama, Masaru Usui, Tetsuo Asai, Michihiro Kawanishi, Manao Ozawa, Yutaka Tsutsumi
Software Mentions: 2
Published: almost 5 years ago

10.3389/fchem.2019.00402

GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism
Cited by: 56
Author(s): Christina de Bruyn Kops, Conrad Stork, Martin Šícho, Nikolay Kochev, Daniel Svozil, Nina Jeliazkova, Johannes Kirchmair
Software Mentions: 2
Published: over 5 years ago

Projects: cran: ROCR

Papers Mentioning ROCR 596