10.1002/1878-0261.12134

Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma
Cited by: 21
Author(s): Merrina Anugraham, Francis Jacob, Arun Everest‐Dass, Andreas Schoetzau, Sheri Nixdorf, Neville F. Hacker, Daniel Fink, Viola Heinzelmann‐Schwarz, Nicolle H. Packer
Software Mentions: 11
Published: almost 9 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: about 5 years ago

10.3389/fonc.2021.683582

Novel Prognostic Biomarkers in Gastric Cancer: CGB5, MKNK2, and PAPPA2
Cited by: 6
Author(s): Min Qin, Zhihai Liang, Hao Qin, Yifang Huo, Qing Yang Steve Wu, Huiying Yang, Guodu Tang
Software Mentions: 11
Published: over 5 years ago

10.3389/fpsyg.2019.01529

Social Support and Emotional Intelligence as Protective Resources for Well-Being in Moroccan Adolescents
Cited by: 33
Author(s): Esther López-Zafra, Manuel M. Ramos‐Álvarez, Karima El Ghoudani, Octavio Luque-Reca, José María Augusto Landa, Benaissa Zarhbouch, Smail Alaoui, Daniel Cortés-Denia, Manuel Pulido-Martos
Software Mentions: 11
Published: about 7 years ago

10.1007/s40300-021-00213-w

Editorial, special issue on “Advances in Robust Statistics”
Cited by: 1
Author(s): Marco Riani, Mia Hubert
Software Mentions: 11
Published: about 5 years ago

10.3389/fmolb.2019.00025

Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Cited by: 22
Author(s): Dalibor Trapl, Izabela Horvacanin, Václav Mareška, Furkan Özçelik, Gözde Ünal, Vojtěch Spiwok
Software Mentions: 11
Published: over 7 years ago

10.1038/s42003-020-01166-y

Spatial patterns of microbial communities across surface waters of the Great Barrier Reef
Cited by: 28
Author(s): Pedro R. Frade, Bettina Glasl, Samuel A. Matthews, Camille Mellin, Ester Á. Serrão, Kennedy Wolfe, Peter J. Mumby, Nicole S. Webster, David G. Bourne
Software Mentions: 11
Published: about 6 years ago

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: about 5 years ago

10.1186/s12864-017-3819-y

RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samples
Cited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 9 years ago

10.1002/sim.8116

Correlation‐adjusted regression survival scores for high‐dimensional variable selection
Cited by: 10
Author(s): Thomas Welchowski, Verena Zuber, Matthias Schmid
Software Mentions: 11
Published: over 7 years ago

10.1186/s12935-020-01393-7

Small nucleolar RNAs signature (SNORS) identified clinical outcome and prognosis of bladder cancer (BLCA)
Cited by: 5
Author(s): Rui Cao, Bo Ma, Lushun Yuan, Gang Wang, Ye Tian
Software Mentions: 11
Published: about 6 years ago

10.1002/ece3.7881

Conversion of rainforest into oil palm and rubber plantations affects the functional composition of litter and soil Collembola
Cited by: 4
Author(s): Winda Ika Susanti, Tamara Bartels, Valentyna Krashevska, Rahayu Widyastuti, Louis Deharveng, Stefan Scheu, Anton M. Potapov
Software Mentions: 11
Published: about 5 years ago

10.1155/2009/201325

Analysis of Array-CGH Data Using the R and Bioconductor Software Suite
Cited by: 8
Author(s): Winfried Hofmann, Anja Weigmann, Marcel Tauscher, Britta Skawran, Tim Focken, R Buurman, Luzie U. Wingen, Brigitte Schlegelberger, Doris Steinemann
Software Mentions: 11
Published: over 17 years ago

10.1371/journal.pgen.1008748

Polygenic adaptation of rosette growth in Arabidopsis thaliana
Cited by: 19
Author(s): Benedict Wieters, Kim A. Steige, Fei He, Evan Koch, Sebastián E. Ramos-Onsins, Hongya Gu, Ya‐Long Guo, Shamil Sunyaev, Juliette de Meaux
Software Mentions: 11
Published: over 5 years ago

10.3389/fnut.2021.676026

Food Sources Contributing to Intake of Choline and Individual Choline Forms in a Norwegian Cohort of Patients With Stable Angina Pectoris
Cited by: 8
Author(s): Anthea Van Parys, Therese Karlsson, Kathrine J. Vinknes, Trond E. Olsen, Jannike Øyen, Jutta Dierkes, Ottar Nygård, Vegard Lysne
Software Mentions: 11
Published: over 5 years ago

10.1038/srep42192

Application of Machine-Learning Models to Predict Tacrolimus Stable Dose in Renal Transplant Recipients
Cited by: 86
Author(s): Jie Tang, Rong Liu, Yueli Zhang, Mou-Ze Liu, HU Yong-fang, Minghai Shao, Lan Zhu, Hua‐Wen Xin, Feng Gao, Wenjun Shang, Xiang‐Gao Meng, Lirong Zhang, Yingzi Ming, Wei Zhang
Software Mentions: 11
Published: over 9 years ago

10.1371/journal.pone.0133625

Sub-Classification of Lateral Cervical Lymph Node Metastasis in Papillary Thyroid Carcinoma by Pathologic Criteria
Cited by: 11
Author(s): Min Ji Jeon, Won Gu Kim, Eun Kyung Jang, Yun Mi Choi, Dong Eun Song, Tae‐Yon Sung, Jong Ho Yoon, Ki-Wook Chung, Suck Joon Hong, Jin‐Sook Ryu, Ji Min Han, Tae Yong Kim, Young Kee Shong
Software Mentions: 11
Published: about 11 years ago

10.3390/ijms19030742

Effect of Presence and Concentration of Plasticizers, Vegetable Oils, and Surfactants on the Properties of Sodium-Alginate-Based Edible Coatings
Cited by: 48
Author(s): Tugce Sentürk Parreidt, Michael Schott, Markus Schmid, Kajetan Müller
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: over 9 years ago

10.1016/j.scitotenv.2018.08.122

Prediction of bioconcentration factors in fish and invertebrates using machine learning
Cited by: 56
Author(s): Thomas H. Miller, Matteo D. Gallidabino, James I. MacRae, Stewart F. Owen, Nicolas R. Bury, Leon Barron
Software Mentions: 11
Published: over 7 years ago

10.3389/fmicb.2020.619226

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island
Cited by: 4
Author(s): Ahmed Taïbi, Ronan Rivallan, Véronique Broussolle, Dominique Pallet, Sylvie Lortal, Jean-Christophe Meile, Florentin Constancias
Software Mentions: 11
Published: over 5 years ago

10.1002/cam4.2983

Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm
Cited by: 30
Author(s): Jun Luo, Yi Xie, Yuxiao Zheng, Chenji Wang, Feng Qi, Jiateng Hu, Yixiang Xu
Software Mentions: 11
Published: over 6 years ago

10.1016/j.isci.2021.102882

Integrated analysis of glycan and RNA in single cells
Cited by: 22
Author(s): Fumi Minoshima, Haruka Ozaki, Haruki Odaka, Hiroaki Tateno
Software Mentions: 11
Published: about 5 years ago

10.3390/ijms20225621

APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival
Cited by: 45
Author(s): Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe, Santosh K. Patnaik
Software Mentions: 11
Published: almost 7 years ago

10.1111/1755-0998.13220

High‐contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm <i>Lamellibrachia barhami</i>
Cited by: 6
Author(s): Corinna Breusing, Darrin T. Schultz, Sebastian Sudek, Alexandra Z. Worden, Charles W. Young
Software Mentions: 11
Published: about 6 years ago

10.1016/j.devcel.2018.11.009

From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo
Cited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: almost 8 years ago

10.1371/journal.pone.0249986

Openness Toward Organizational Change Scale (OTOCS): Validity evidence from Brazil and Portugal
Cited by: 4
Author(s): Jorge Sinval, Vernon D. Miller, João Marôco
Software Mentions: 11
Published: over 5 years ago

10.1186/s13059-021-02329-8

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
Cited by: 13
Author(s): Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos
Software Mentions: 11
Published: over 5 years ago

10.1016/j.ebiom.2018.04.010

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial
Cited by: 28
Author(s): Antonio J. Berlanga‐Taylor, Katharine Plant, Andrew Dahl, Evelyn Lau, Michael Hill, David Sims, Andreas Heger, Jonathan Emberson, Jane Armitage, Robert Clarke, Julian C. Knight
Software Mentions: 11
Published: over 8 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: over 6 years ago

10.7717/peerj.1140

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls
Cited by: 190
Author(s): Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez‐Losada, Sarven Sabuncyan, Emily G. Severance, Faith Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall
Software Mentions: 11
Published: about 11 years ago

10.1080/0886022X.2021.1960563

Derivation and validation of a model to predict acute kidney injury following cardiac surgery in patients with normal renal function
Cited by: 8
Author(s): Penghua Hu, Zhiming Mo, Yuanhan Chen, Yanhua Wu, Li Song, Li Zhang, Zhilian Li, Lei Fu, Huaban Liang, Yiming Tao, Shuangxin Liu, Zhiming Ye, Xinling Liang
Software Mentions: 11
Published: over 5 years ago

10.1186/s12859-018-2264-5

Random forest versus logistic regression: a large-scale benchmark experiment
Cited by: 396
Author(s): Raphäel Couronné, Philipp Probst, Anne‐Laure Boulesteix
Software Mentions: 11
Published: about 8 years ago

10.1093/g3journal/jkab104

Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species
Cited by: 2
Author(s): Astra S. Bryant, Stephanie F. DeMarco, Elissa A. Hallem
Software Mentions: 11
Published: over 5 years ago

10.1167/jov.21.1.1

Flexible contextual modulation of naturalistic texture perception in peripheral vision
Cited by: 9
Author(s): Daniel Herrera-Esposito, Ruben Coen-Cagli, Leonel Gómez-Sena
Software Mentions: 11
Published: over 5 years ago

10.1128/mSphere.00481-19

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
Cited by: 15
Author(s): Ryan B. Ghannam, Laura G. Schaerer, Timothy Butler, Stephen M. Techtmann
Software Mentions: 11
Published: over 6 years ago

10.1038/s42003-021-02463-w

Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment
Cited by: 18
Author(s): Kauê de Sousa, Jacob van Etten, Jesse Poland, Carlo Fadda, Jean‐Luc Jannink, Yosef Gebrehawaryat Kidane, Basazen Fantahun, Deȷene K. Mengistu, Mario Enrico Pè, Svein Øivind Solberg, Matteo Dell’Acqua
Software Mentions: 11
Published: about 5 years ago

10.1186/cc13993

Relationship between acid–base status and inflammation in the critically ill
Cited by: 38
Author(s): Fernando Godinho Zampieri, John A. Kellum, Marcelo Park, Otávio T. Ranzani, Hermes Vieira Barbeiro, Heraldo Possolo de Souza, Luiz Monteiro da Cruz Neto, Fabiano Pinheiro da Silva
Software Mentions: 11
Published: over 12 years ago

10.1038/s41598-020-59494-2

Unstable crop yields reveal opportunities for site-specific adaptations to climate variability
Cited by: 30
Author(s): Rafael A. Martinez-Feria, Bruno Basso
Software Mentions: 11
Published: over 6 years ago

10.1016/j.cell.2018.08.067

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease
Cited by: 396
Author(s): James Kinchen, Hannah H. Chen, Kaushal Parikh, Agne Antanaviciute, Marta Jagielowicz, David Fawkner-Corbett, Neil Ashley, Laura Cubitt, Esther Mellado-Gomez, Moustafa Attar, Eshita Sharma, Quin F. Wills, Rory Bowden, Felix Clemens Richter, David Ahern, Kamal D. Puri, Jill Hénault, François G. Gervais, Hashem Koohy, Alison Simmons
Software Mentions: 11
Published: almost 8 years ago

10.1038/s41598-020-68780-y

Protecting endangered species in the USA requires both public and private land conservation
Cited by: 15
Author(s): Niall G. Clancy, John P. Draper, J. Marshall Wolf, Umarfarooq A. Abdulwahab, Maya Pendleton, Soren Brothers, Janice Brahney, Jennifer Weathered, Edd Hammill, Trisha B. Atwood
Software Mentions: 11
Published: about 6 years ago

10.1371/journal.pcbi.1007665

CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data
Cited by: 8
Author(s): Thilde Terkelsen, Anders Krogh, Elena Papaleo
Software Mentions: 11
Published: over 6 years ago

10.1042/BSR20210527

Construction of a prognostic model for non-small-cell lung cancer based on ferroptosis-related genes
Cited by: 10
Author(s): Ke Han, Jukun Wang, Kun Qian, Teng Zhao, Xingsheng Liu, Yi Zhang
Software Mentions: 11
Published: over 5 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 7 years ago

10.1371/journal.pone.0225734

PyLandStats: An open-source Pythonic library to compute landscape metrics
Cited by: 19
Author(s): Martí Bosch
Software Mentions: 11
Published: almost 7 years ago

10.1242/jeb.210302

Time-critical influences of gestational diet in a seahorse model of male pregnancy
Cited by: 7
Author(s): Francisco Otero‐Ferrer, Freddy Lättekivi, James Ord, Ene Reimann, Sulev Kõks, Marisol Izquierdo, William V. Holt, Alireza Fazeli
Software Mentions: 11
Published: over 7 years ago

10.1371/journal.pgen.1009240

Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior
Cited by: 5
Author(s): Colleen M Palmateer, Shawn C. Moseley, Surjyendu Ray, Savannah G Brovero, Michelle N. Arbeitman
Software Mentions: 11
Published: over 5 years ago

10.12688/wellcomeopenres.16430.2

Polysomal mRNA Association and Gene Expression in Trypanosoma brucei
Cited by: 0
Author(s): Michele Tinti, Anna Kelner-Mirôn, Lizzie J. Marriott, Michael A. J. Ferguson
Software Mentions: 11
Published: about 5 years ago

10.1186/s12859-017-1579-y

metaX: a flexible and comprehensive software for processing metabolomics data
Cited by: 402
Author(s): Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
Software Mentions: 11
Published: over 9 years ago

10.3389/fimmu.2019.00827

Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space
Cited by: 60
Author(s): Masato Ogishi, Hiroshi Yotsuyanagi
Software Mentions: 11
Published: over 7 years ago

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: almost 6 years ago

10.3389/fcell.2021.621618

Functional Assessment of Four Novel Immune-Related Biomarkers in the Pathogenesis of Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Daojun Lv, Xiangkun Wu, Ming Wang, Wenzhe Chen, Shuxin Yang, Yongda Liu, Guohua Zeng, Danan Gu
Software Mentions: 11
Published: over 5 years ago

10.1186/s42523-020-00045-5

Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)
Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: about 6 years ago

10.1371/journal.pone.0156825

Inundation and Fire Shape the Structure of Riparian Forests in the Pantanal, Brazil
Cited by: 32
Author(s): Wellinton de Sá Arruda, Jens Oldeland, Antônio Conceição Paranhos Filho, Arnildo Pott, Nicolay Leme da Cunha, Iria Hiromi Ishii, Geraldo Alves Damasceno
Software Mentions: 11
Published: over 10 years ago

10.1177/1176934320956575

Vesicle Transport in Plants: A Revised Phylogeny of SNARE Proteins
Cited by: 10
Author(s): Xiaoyan Gu, Adrian C. Brennan, Wenbin Wei, Guang-Qin Guo, Keith Lindsey
Software Mentions: 11
Published: over 6 years ago

10.7717/peerj.10411

Data quantity is more important than its spatial bias for predictive species distribution modelling
Cited by: 10
Author(s): Willson Gaul, Dinara Sadykova, Hannah J. White, Lupe León‐Sánchez, Paul Caplat, Mark Emmerson, Jon Yearsley
Software Mentions: 11
Published: almost 6 years ago

10.1016/j.mex.2018.07.003

A practical method to control spatiotemporal confounding in environmental impact studies
Cited by: 4
Author(s): Rezvan Hatami
Software Mentions: 11
Published: over 8 years ago

10.1128/mBio.02699-19

The Toxoplasma gondii Cyst Wall Interactome
Cited by: 24
Author(s): Vincent Tu, Tadakimi Tomita, Tatsuki Sugi, Joshua Mayoral, Bing Han, Rama R. Yakubu, Tere Williams, Aline Luciano Horta, Yanfen Ma, Louis M. Weiss
Software Mentions: 11
Published: over 6 years ago

10.1111/tpj.14784

Segmental duplications are hot spots of copy number variants affecting barley gene content
Cited by: 4
Author(s): Gianluca Bretani, Laura Rossini, Chiara Ferrandi, Joanne Russell, Robbie Waugh, Benjamin Kilian, Paolo Bagnaresi, Luigi Cattivelli, Agostino Fricano
Software Mentions: 11
Published: over 6 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: almost 6 years ago

10.7717/peerj.4395

COREMIC: a web-tool to search for a niche associated CORE MICrobiome
Cited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: over 8 years ago

10.1186/s12862-021-01786-w

Phenology-mediated effects of phenotype on the probability of social polygyny and its fitness consequences in a migratory passerine
Cited by: 6
Author(s): David Cañal, Lotte Schlicht, Simone Santoro, Carlos Camacho, Jesús Martínez‐Padilla, Jaime Potti
Software Mentions: 11
Published: over 5 years ago

10.1074/mcp.TIR120.002155

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis
Cited by: 129
Author(s): Johannes Griss, Guilherme Viteri, Konstantinos Sidiropoulos, Vy Kim Nguyen, Antonio Fabregat, Henning Hermjakob
Software Mentions: 11
Published: almost 6 years ago

10.18632/oncotarget.22928

Comparing the genomes of cutaneous melanoma tumors to commercially available cell lines
Cited by: 10
Author(s): Stephen A. Luebker, Weiwei Zhang, Scott A. Koepsell
Software Mentions: 11
Published: almost 9 years ago

10.3390/foods10010143

Intramuscular Fat Prediction Using Color and Image Analysis of Bísaro Pork Breed
Cited by: 7
Author(s): Alfredo Teixeira, Severiano Silva, Marianne Hasse, José Almeida, Luís G. Dias
Software Mentions: 11
Published: over 5 years ago

10.7554/eLife.65372

Image3C, a multimodal image-based and label-independent integrative method for single-cell analysis
Cited by: 6
Author(s): Alice Accorsi, Andrew Box, Robert Peuß, Christopher J. Wood, Alejandro Sánchez Alvarado, Nicolas Rohner
Software Mentions: 11
Published: about 5 years ago

10.1007/s00394-020-02351-9

Gluten intake and metabolic health: conflicting findings from the UK Biobank
Cited by: 13
Author(s): Inken Behrendt, Mathias Faßhauer, Gerrit Eichner
Software Mentions: 11
Published: about 6 years ago

10.1016/j.molcel.2019.12.001

PRC1 Catalytic Activity Is Central to Polycomb System Function
Cited by: 163
Author(s): Neil P. Blackledge, Nadezda A. Fursova, Jessica R. Kelley, Miles K. Huseyin, Angelika Feldmann, Robert J. Klose
Software Mentions: 11
Published: over 6 years ago

10.1038/s41392-021-00753-7

Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patients
Cited by: 18
Author(s): Xiang-Na Zhao, Yue You, Xiaoming Cui, Han Gao, Guolin Wang, Shengbo Zhang, Lilin Ye, Lei Duan, Ka-Li Zhu, Yuling Wang, Li Li, Jianhua Lu, Haibin Wang, Jingfang Fan, Huanwei Zheng, Erfu Dai, Luyi Tian, Mai‐Juan Ma
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pone.0235283

Targeting the oral plaque microbiome with immobilized anti-biofilm peptides at tooth-restoration interfaces
Cited by: 18
Author(s): Dina G. Moussa, Conrado Aparicio
Software Mentions: 11
Published: about 6 years ago

10.1371/journal.pone.0089470

Analytic Programming with fMRI Data: A Quick-Start Guide for Statisticians Using R
Cited by: 9
Author(s): Ani Eloyan, Shanshan Li, John Muschelli, James J. Pekar, Stewart H. Mostofsky, Brian Caffo
Software Mentions: 11
Published: over 12 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: over 6 years ago

10.1534/g3.120.401612

A Reference Genome Sequence for Giant Sequoia
Cited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: almost 6 years ago

10.1371/journal.pone.0245127

Adaptation and validation of a German version of the Strengths Use and Deficit Correction (SUDCO) questionnaire
Cited by: 2
Author(s): Timo Lorenz, Kathrin Heinitz, Clemens Beer, Marianne van Woerkom
Software Mentions: 11
Published: over 5 years ago

10.3389/fimmu.2021.664845

CD2 Is a Novel Immune-Related Prognostic Biomarker of Invasive Breast Carcinoma That Modulates the Tumor Microenvironment
Cited by: 24
Author(s): Yanzhu Chen, Zhishang Meng, Lin Zhang, Feng Liu
Software Mentions: 11
Published: over 5 years ago

10.2196/10754

Predicting Adherence to Internet-Delivered Psychotherapy for Symptoms of Depression and Anxiety After Myocardial Infarction: Machine Learning Insights From the U-CARE Heart Randomized Controlled Trial
Cited by: 44
Author(s): John Wallert, Emelie Gustafson, Claes Held, Guy Madison, Fredrika Norlund, Louise von Essén, Erik Olsson
Software Mentions: 11
Published: almost 8 years ago

10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Cited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 10 years ago

10.1371/journal.pcbi.1008316

Ten simple rules for writing Dockerfiles for reproducible data science
Cited by: 36
Author(s): Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J. Eglen, T. Head, Tony Hirst, Benjamin D. Evans
Software Mentions: 11
Published: almost 6 years ago

10.1111/jcmm.16552

Identification of autophagy‐related genes signature predicts chemotherapeutic and immunotherapeutic efficiency in bladder cancer (BLCA)
Cited by: 8
Author(s): Rui Cao, Bo Ma, Gang Wang, Yaoyi Xiong, Ye Tian, Lushun Yuan
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-96712-x

Pan-transcriptome identifying master genes and regulation network in response to drought and salt stresses in Alfalfa (Medicago sativa L.)
Cited by: 12
Author(s): César A. Medina, Deborah A. Samac, Long‐Xi Yu
Software Mentions: 11
Published: about 5 years ago

10.3389/fgene.2021.625145

Identification of Tumor Microenvironment-Related Prognostic Biomarkers for Ovarian Serous Cancer 3-Year Mortality Using Targeted Maximum Likelihood Estimation: A TCGA Data Mining Study
Cited by: 2
Author(s): Lu Wang, Xiaoru Sun, Chuandi Jin, Yue Fan, Fuzhong Xue
Software Mentions: 11
Published: over 5 years ago

10.12688/f1000research.26771.2

HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas
Cited by: 1
Author(s): Tim O. Nieuwenhuis, Marc K. Halushka
Software Mentions: 11
Published: over 5 years ago

10.3390/ijms22147269

Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula
Cited by: 3
Author(s): Jean-Stéphane Venisse, Eele Õunapuu-Pikas, Maxime Dupont, Aurélie Gousset-Dupont, Mouadh Saadaoui, Mohamed Faize, Song Chen, Su Chen, Gilles Pétel, Boris Fumanal, Patricia Roeckel‐Drevet, Arne Sellin, Philippe Label
Software Mentions: 11
Published: about 5 years ago

10.1017/S003329171800315X

A machine learning ensemble to predict treatment outcomes following an Internet intervention for depression
Cited by: 37
Author(s): Rahel Pearson, Derek Pisner, Björn Meyer, Jason Shumake, Christopher G. Beevers
Software Mentions: 11
Published: almost 8 years ago

10.3390/nu12020302

The Role of Glycemic Index and Glycemic Load in the Development of Real-Time Postprandial Glycemic Response Prediction Models for Patients with Gestational Diabetes
Cited by: 14
Author(s): Evgenii Pustozerov, Aleksandra Tkachuk, Elena Vasukova, А. В. Дронова, Ekaterina S. Shilova, Anna D. Anopova, Faina Piven, Tatiana Pervunina, Elena Vasilieva, Elena Grineva, Polina Popova
Software Mentions: 11
Published: over 6 years ago

10.1186/s13059-020-1926-6

Eleven grand challenges in single-cell data science
Cited by: 646
Author(s): David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan‐Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M. Kiełbasa, Jan Korbel, Alexey M Kozlov, Tzu Hao Kuo, Boudewijn P. F. Lelieveldt, Ion Măndoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz Rączkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alexander Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
Software Mentions: 11
Published: over 6 years ago

10.3389/fgene.2021.609174

METTL14 Acts as a Potential Regulator of Tumor Immune and Progression in Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Tianbo Xu, Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-94324-z

Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer’s disease
Cited by: 17
Author(s): Ruth Jones, Robert Andrews, Peter Holmans, Matthew Hill, Philip R. Taylor
Software Mentions: 11
Published: about 5 years ago

10.3389/fonc.2021.614052

MRI Radiomics Signature as a Potential Biomarker for Predicting KRAS Status in Locally Advanced Rectal Cancer Patients
Cited by: 9
Author(s): Zhiyuan Zhang, Lijun Shen, Yan Wang, Jiazhou Wang, Hui Zhang, Xuesen Fan, Juefeng Wan
Software Mentions: 11
Published: over 5 years ago

10.1155/2021/6616908

Interpreting the Molecular Mechanisms of Yinchenhao Decoction on Hepatocellular Carcinoma through Absorbed Components Based on Network Pharmacology
Cited by: 5
Author(s): Jijia Sun, Tao Han, Tao Yang, Yunhui Chen, Jihan Huang
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0238026

Funding sources and breast cancer research frame
Cited by: 3
Author(s): Wonkwang Jo
Software Mentions: 11
Published: about 6 years ago

10.1038/srep26929

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing
Cited by: 43
Author(s): Fábio Pértille, Carlos Guerrero-Bosagna, Vinícius da Silva, Clarissa Boschiero, José de Ribamar da Silva Nunes, Mônica Corrêa Ledur, Per Jensen, Luiz Lehmann Coutinho
Software Mentions: 11
Published: over 10 years ago

10.1107/S1600577518016570

Automated data collection and real-time data analysis suite for serial synchrotron crystallography
Cited by: 34
Author(s): Shibom Basu, Jakub Wojciech Kaminski, Ezequiel Panepucci, Chia‐Ying Huang, Rangana Warshamanage, Meitian Wang, Justyna Aleksandra Wojdyla
Software Mentions: 11
Published: over 7 years ago

10.3389/fimmu.2016.00339

IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
Cited by: 38
Author(s): Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie‐Paule Lefranc
Software Mentions: 11
Published: about 10 years ago

10.1371/journal.pcbi.1003929

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Cited by: 18
Author(s): Hai Fang
Software Mentions: 11
Published: almost 12 years ago

10.1002/1878-0261.12117

Recurrence-associated gene signature optimizes recurrence-free survival prediction of colorectal cancer
Cited by: 37
Author(s): Xianglong Tian, Xiaoqiang Zhu, Tingting Yan, Chuangqi Yu, Chaoqin Shen, Ye Hu, Jie Hong, Haoyan Chen, Jing‐Yuan Fang
Software Mentions: 11
Published: about 9 years ago

10.1371/journal.pone.0220961

Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data
Cited by: 4
Author(s): Amanda H. Pendegraft, Boyi Guo, Nengjun Yi
Software Mentions: 11
Published: about 7 years ago

10.1128/mSystems.00404-19

Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria <i>In Vitro</i>
Cited by: 13
Author(s): Kaitlyn Oliphant, Kyla Cochrane, Kathleen Schroeter, Michelle Daigneault, Sandi Yen, Elena F. Verdú, Emma Allen‐Vercoe
Software Mentions: 11
Published: over 6 years ago

10.3389/fcvm.2021.624714

Identification of Potential Biomarkers and Immune Infiltration Characteristics in Idiopathic Pulmonary Arterial Hypertension Using Bioinformatics Analysis
Cited by: 21
Author(s): Haowei Zeng, Xiaoqin Liu, Yushun Zhang
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: almost 9 years ago