10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: about 5 years ago

10.1186/1756-0500-3-10

A collection of bioconductor methods to visualize gene-list annotations
Cited by: 46
Author(s): Gang Feng, Pan Du, Nancy L. Krett, Michael A. Tessel, Steven T. Rosen, Warren A. Kibbe, Simon Lin
Software Mentions: 11
Published: about 16 years ago

10.1371/journal.pone.0256694

Factors contributing to farm-level productivity and household income generation in coastal Bangladesh’s rice-based farming systems
Cited by: 18
Author(s): Shah Al Emran, Timothy J. Krupnik, Sreejith Aravindakshan, Virender Kumar, Cameron M. Pittelkow
Software Mentions: 11
Published: over 4 years ago

10.3390/microorganisms8040550

Long-Term Rewetting of Three Formerly Drained Peatlands Drives Congruent Compositional Changes in Pro- and Eukaryotic Soil Microbiomes through Environmental Filtering
Cited by: 22
Author(s): Micha Weil, Haitao Wang, Mia M. Bengtsson, Daniel Köhn, Anke Günther, Gerald Jurasinski, John Couwenberg, Wakene Negassa, Dominik Zak, Tim Urich
Software Mentions: 11
Published: almost 6 years ago

10.3390/ijerph18041816

Academic Achievement in Spanish Secondary School Students: The Inter-Related Role of Executive Functions, Physical Activity and Gender
Cited by: 7
Author(s): Elena Escolano Pérez, Marta Bestué
Software Mentions: 11
Published: about 5 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: about 6 years ago

10.1186/s12575-021-00152-w

N6-Methyladenosine Related Long Non-Coding RNAs and Immune Cell Infiltration in the Tumor Microenvironment of Gastric Cancer
Cited by: 9
Author(s): Zhong Lin Yu, Zheng Zhu
Software Mentions: 11
Published: over 4 years ago

10.1002/ece3.6044

Variation of chemical compounds in wild Heliconiini reveals ecological factors involved in the evolution of chemical defenses in mimetic butterflies
Cited by: 21
Author(s): Ombeline Sculfort, Érika Cristina Pinheiro de Castro, Krzysztof M. Kozak, Søren Bak, Marianne Élias, Bastien Nay, Violaine Llaurens
Software Mentions: 11
Published: about 6 years ago

10.3389/fmicb.2021.624071

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific
Cited by: 10
Author(s): Miguel Semedo, Eva Lopes, Mafalda S. Baptista, Ainhoa Oller-Ruiz, Javier Gilabert, Maria Paola Tomasino, Catarina Magalhães
Software Mentions: 11
Published: about 5 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: about 12 years ago

10.3389/fphys.2020.00845

Dynamic Courtship Signals and Mate Preferences in Sepia plangon
Cited by: 5
Author(s): Alejandra López Galán, Wen-Sung Chung, N. Justin Marshall
Software Mentions: 11
Published: over 5 years ago

10.15252/msb.20177697

Screening drug effects in patient‐derived cancer cells links organoid responses to genome alterations
Cited by: 153
Author(s): Julia Jabs, Franziska Maria Zickgraf, Jeongbin Park, Sven Wagner, Xiaoqi Jiang, Katharina Jechow, Kortine Kleinheinz, Umut Toprak, Marc A. Schneider, Michael Meister, Saskia Spaich, Marc Sütterlin, Matthias Schlesner, Andreas Trumpp, Martin R. Sprick, Roland Eils, Christian Conrad
Software Mentions: 11
Published: over 8 years ago

10.1371/journal.pone.0188079

Episodic future thinking reduces temporal discounting in healthy adolescents
Cited by: 35
Author(s): Uli Bromberg, Maria Lobatcheva, Jan Peters
Software Mentions: 11
Published: over 8 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: over 8 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: almost 10 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: about 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: about 6 years ago

10.3390/jcm9113643

Diabetic Retinopathy Environment-Wide Association Study (EWAS) in NHANES 2005–2008
Cited by: 10
Author(s): Kevin Blighe, Sarega Gurudas, Ying Lee, Sobha Sivaprasad
Software Mentions: 11
Published: over 5 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: 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: almost 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: over 6 years ago

10.1186/s12879-019-4585-z

Development of a high number, high coverage dog rabies vaccination programme in Sri Lanka
Cited by: 8
Author(s): Carlos Sánchez-Soriano, Andrew D Gibson, Luke Gamble, Jordana L. Burdon Bailey, Samantha Green, Mark Green, Barend M. deC. Bronsvoort, Ian Handel, Richard J. Mellanby, Stella Mazeri
Software Mentions: 11
Published: over 6 years ago

10.3389/fcell.2021.707143

The Prognosis and Immune Checkpoint Blockade Efficacy Prediction of Tumor-Infiltrating Immune Cells in Lung Cancer
Cited by: 11
Author(s): Xiangzheng Liu, Xueqian Shang, Jian Li, Shijie Zhang
Software Mentions: 11
Published: over 4 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: almost 10 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: almost 5 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: over 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: over 4 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: over 7 years ago

10.1371/journal.pntd.0009321

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature
Cited by: 15
Author(s): Camila Farias Amorim, Fernanda O. Novais, Ba Tiep Nguyen, Maurício T. Nascimento, Jamile Lago, Alexsandro S. Lago, Lucas P. Carvalho, Daniel P. Beiting, Phillip Scott
Software Mentions: 11
Published: almost 5 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: about 7 years ago

10.1038/s41598-018-28356-3

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver
Cited by: 34
Author(s): Chris Duncan, Sara A. Grimm, Daniel L. Morgan, Pierre R. Bushel, Brian D. Bennett, John D. Roberts, Frederick L. Tyson, B. Alex Merrick, Paul A. Wade
Software Mentions: 11
Published: over 7 years ago

10.3389/fmolb.2021.559800

KIF18B is a Prognostic Biomarker and Correlates with Immune Infiltrates in Pan-Cancer
Cited by: 9
Author(s): Mengjun Qiu, Qiushuang Wang, Qiuting Li, Lisheng Zhu, Yanan Li, Shengli Yang, Zhifan Xiong
Software Mentions: 11
Published: almost 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: about 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: over 4 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: over 5 years ago

10.3389/fpls.2020.01132

Intra and Inter-specific Variability of Salt Tolerance Mechanisms in Diospyros Genus
Cited by: 3
Author(s): Francisco Gil-Muñoz, Juan G. Pérez-Pérez, Ana Quiñones, María del Mar Naval, M. L. Badenes
Software Mentions: 11
Published: over 5 years ago

10.1111/jcmm.15939

Prognostic value and immune cell infiltration of hypoxic phenotype‐related gene signatures in glioblastoma microenvironment
Cited by: 10
Author(s): Kai Xiao, Jun Tan, Jian Yuan, Gang Peng, Wenyong Long, Jun Su, Yao Xiao, Qian Xiao, Changwu Wu, Chaoying Qin, Lili Hu, Kaili Liu, Shunlian Liu, Hao Zhou, Yichong Ning, Xiaojuan Ding, Qing Liu
Software Mentions: 11
Published: over 5 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: almost 5 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: about 5 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: over 4 years ago

10.1186/s12942-021-00262-4

Estimating the local spatio‐temporal distribution of malaria from routine health information systems in areas of low health care access and reporting
Cited by: 8
Author(s): Elizabeth Hyde, Matthew H. Bonds, Felana Angella Ihantamalala, Ann C. Miller, Laura Cordier, Bénédicte Razafinjato, Herinjaka Andriambolamanana, Marius Randriamanambintsoa, Michèle Barry, Jean Claude Andrianirinarison, Mauricette Andriamananjara, Andrés Garchitorena
Software Mentions: 11
Published: about 5 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: about 5 years ago

10.3389/fgene.2015.00040

Integrating multi-omic features exploiting Chromosome Conformation Capture data
Cited by: 9
Author(s): Ivan Merelli, Fabio Tordini, Maurizio Drocco, Marco Aldinucci, Píetro Lió, Luciano Milanesi
Software Mentions: 11
Published: about 11 years ago

10.1016/j.celrep.2019.05.026

ZIC3 Controls the Transition from Naive to Primed Pluripotency
Cited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: almost 7 years ago

10.3389/fgene.2021.733715

Development and Validation of a Novel Gene Signature for Predicting the Prognosis by Identifying m5C Modification Subtypes of Cervical Cancer
Cited by: 2
Author(s): Jing Yu, Leilei Liang, Jing Liu, Tingting Liu, Jian Li, Lin Xiu, Jia Zeng, Tiantian Wang, Di Wang, Lijun Liang, Dawei Xie, Ding-Xiong Chen, Jusheng An, Lingying Wu
Software Mentions: 11
Published: over 4 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: 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: almost 8 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: almost 7 years ago

10.1099/mgen.0.000503

Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: about 5 years ago

10.1007/s11214-018-0576-4

The Space Physics Environment Data Analysis System (SPEDAS)
Cited by: 295
Author(s): V. Angelopoulos, P. Cruce, Alexander Drozdov, E. W. Grimes, Nick Hatzigeorgiu, David A. King, D. E. Larson, James W. Lewis, J. M. McTiernan, D. A. Roberts, Chuck Russell, Tomoaki Hori, Yoshiya Kasahara, Atsushi Kumamoto, A. Matsuoka, Yukinaga Miyashita, Yoshizumi Miyoshi, I. Shinohara, Masaaki Teramoto, J. Faden, A. J. Halford, Michael McCarthy, R. M. Millan, J. G. Sample, David M. Smith, L. A. Woodger, A. Masson, Ayris Narock, Kazushi Asamura, T. F. Chang, Che‐Ming Chiang, Y. Kazama, K. Keika, Shoya Matsuda, Takehiko Segawa, K. Seki, Shoji Motomizu, Sunny Wing-Yee Tam, Norio Umemura, B. J. Wang, S. Y. Wang, R. J. Redmon, J. V. Rodriguez, H. J. Singer, J. D. Vandegriff, Shuji Abe, M. Nosé, Atsuki Shinbori, Yoshimasa Tanaka, S. Ueno, L. Andersson, P. Dunn, Christopher Fowler, J. S. Halekas, Takuya Hara, Yuki Harada, C. O. Lee, R. J. Lillis, D. L. Mitchell, M. R. Argall, K. R. Bromund, J. L. Burch, I. J. Cohen, Michael Galloy, B. L. Giles, A. N. Jaynes, O. Le Contel, M. Oka, T. D. Phan, Brian M. Walsh, J. H. Westlake, F. D. Wilder, S. D. Bale, R. Livi, M. Pulupa, P. L. Whittlesey, A. W. DeWolfe, B. Harter, Edson Mello Lucas, U. Auster, J. W. Bonnell, C. M. Cully, E. Donovan, R. E. Ergun, H. U. Frey, B. J. Jackel, A. Keiling, H. Korth, J. P. McFadden, Yoshihiro Nishimura, Ferdinand Plaschke, P. Robert, D. L. Turner, J. M. Weygand, R. M. Candey, Russell D. Johnson, T. J. Kovalick, M. H. Liu, R. E. McGuire, A. W. Breneman, K. Kersten, P. Schroeder
Software Mentions: 11
Published: about 7 years ago

10.1371/journal.pone.0242728

Video kills the sentiment—Exploring fans’ reception of the video assistant referee in the English premier league using Twitter data
Cited by: 10
Author(s): Otto Kolbinger, Melanie Knopp
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: over 5 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: over 5 years ago

10.3390/tropicalmed6030115

Agro-Environmental Determinants of Leptospirosis: A Retrospective Spatiotemporal Analysis (2004–2014) in Mahasarakham Province (Thailand)
Cited by: 4
Author(s): Jaruwan Viroj, Claude Julien, Claire Lajaunie, Julien Cappelle, Anamika Kritiyakan, Pornsit Thuainan, Worachead Chewnarupai, Sergé Morand
Software Mentions: 11
Published: over 4 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: about 9 years ago

10.1371/journal.pone.0207126

Prognostic function to estimate the probability of meaningful clinical improvement after surgery - Results of a prospective multicenter observational cohort study on patients with lumbar spinal stenosis
Cited by: 20
Author(s): Ulrike Held, Jakob M Burgstaller, Maria M. Wertli, Giuseppe Pichierri, Sebastian Winklhofer, Florian Brunner, François Porchet, Mazda Farshad, Johann Steurer
Software Mentions: 11
Published: over 7 years ago

10.7717/peerj.4251

Sicegar: R package for sigmoidal and double-sigmoidal curve fitting
Cited by: 28
Author(s): Mehmet Umut Caglar, Ashley I. Teufel, Claus O. Wilke
Software Mentions: 11
Published: about 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: almost 5 years ago

10.1016/j.celrep.2020.107908

Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
Cited by: 174
Author(s): Ying-Wooi Wan, Rami Al‐Ouran, Carl Grant Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine S. Allison, Vivek Swarup, Cory C. Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M. Neuner, Catherine C. Kaczorowski, Vivek Philip, Gareth R. Howell, Heidi Martini‐Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L. Dawson, Ted M. Dawson, Ping‐Chieh Pao, Li‐Huei Tsai, Jean‐Vianney Haure‐Mirande, Michelle E. Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen K. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuß, Ayla Ergün, Philip J. Ebert, David Airey, Sara Mostafavi, Lei Yu, Hans‐Ulrich Klein, Gregory W. Carter, David A. Collier, Todd E. Golde, Aĺlan I. Levey, David A. Bennett, Karol Estrada, T. Matthew Townsend, Bin Zhang, Eric E. Schadt, Philip L. De Jager, Nathan D. Price, Nilüfer Ertekin-Taner, Zhandong Liu, Zhandong Liu, Lara M. Mangravite, Benjamin A. Logsdon
Software Mentions: 11
Published: over 5 years ago

10.1038/s41598-021-92406-6

Plasma lipidomic analysis shows a disease progression signature in mdx mice
Cited by: 3
Author(s): Roula Tsonaka, Alexandre Seyer, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 11
Published: almost 5 years ago

10.1098/rsos.150632

Kinship as a frequency dependent strategy
Cited by: 15
Author(s): Ting Ji, Xiu-Deng Zheng, Qiao-Qiao He, Jiajia Wu, Ruth Mace, Yi Tao
Software Mentions: 11
Published: about 10 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: 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: over 4 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: about 6 years ago

10.1186/s12859-019-2968-1

Visualization methods for differential expression analysis
Cited by: 6
Author(s): Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook
Software Mentions: 11
Published: over 6 years ago

10.1016/j.molcel.2019.03.024

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression
Cited by: 187
Author(s): Nadezda A. Fursova, Neil P. Blackledge, Manabu Nakayama, Shinsuke Ito, Haruhiko Koseki, Anca M. Farcas, Hamish W King, Haruhiko Koseki, Robert J. Klose
Software Mentions: 11
Published: almost 7 years ago

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: over 8 years ago

10.1128/mSystems.00068-21

Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins
Cited by: 14
Author(s): Elaina Thomas, R. Anderson, Viola Li, L Jenni Rogan, Julie A. Huber
Software Mentions: 11
Published: over 4 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: over 4 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: about 17 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: over 4 years ago

10.1038/s41598-021-93411-5

Epidemiological overview of multidimensional chromosomal and genome toxicity of cannabis exposure in congenital anomalies and cancer development
Cited by: 33
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 11
Published: over 4 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: over 5 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: over 4 years ago

10.1002/ece3.6904

Light might suppress both types of sound‐evoked antipredator flight in moths
Cited by: 2
Author(s): Theresa Hügel, Holger R. Goerlitz
Software Mentions: 11
Published: over 5 years ago

10.3389/pore.2021.1609852

Identification of a Gene Prognostic Model of Gastric Cancer Based on Analysis of Tumor Mutation Burden
Cited by: 9
Author(s): Weijun Ma, Weidong Li, Xu Liu, Lu Liu, Xinbing Yu, Liping Yang, Mingxu Da
Software Mentions: 11
Published: over 4 years ago

10.18632/aging.203242

Glycolysis- and immune-related novel prognostic biomarkers of Ewing's sarcoma: glucuronic acid epimerase and triosephosphate isomerase 1
Cited by: 9
Author(s): Jie Jiang, Xinli Zhan, Guoyong Xu, Tuo Liang, Chaojie Yu, Shijie Liao, Liyi Chen, Shengsheng Huang, Xuhua Sun, Ming Yi, Zide Zhang, Yuanlin Yao, Chong Liu
Software Mentions: 11
Published: over 4 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: about 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: almost 5 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: about 17 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: almost 10 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: about 9 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: almost 5 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: about 8 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: almost 6 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: almost 7 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: almost 5 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: about 5 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: about 8 years ago

10.1038/s41598-018-23518-9

The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ
Cited by: 47
Author(s): Na Wei, Tia‐Lynn Ashman
Software Mentions: 11
Published: almost 8 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: about 8 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: about 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: over 7 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: 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: about 6 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: almost 5 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: about 9 years ago

10.1371/journal.pone.0234503

Nest boxes buffer the effects of climate on breeding performance in an African urban raptor
Cited by: 17
Author(s): Petra Sumasgutner, Andrew R. Jenkins, Arjun Amar, Res Altwegg
Software Mentions: 11
Published: over 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: 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: almost 5 years ago