10.3389/fcell.2020.599494

An Eight-CircRNA Assessment Model for Predicting Biochemical Recurrence in Prostate Cancer
Cited by: 61
Author(s): Shuo Wang, Wei Su, Chuanfan Zhong, Taowei Yang, Wenbin Chen, Cheng Guo, Zezhen Liu, Kuan-Hung Wu, Weibo Zhong, Bingkun Li, Xiangming Mao, Jianming Lü
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1004751

metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns
Cited by: 11
Author(s): Charles Joly Beauparlant, Fabien C. Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau, Arnaud Droit
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-021-02348-5

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
Cited by: 65
Author(s): Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Pedro Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pcbi.1002887

Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Cited by: 46
Author(s): S. Huang, David Clarke, Sara J.C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel
Software Mentions: 5
Published: over 13 years ago

10.1186/s12859-021-04240-2

Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
Cited by: 4
Author(s): Hiroaki Kato, Mitsuhiro Shimizu, Takeshi Urano
Software Mentions: 5
Published: about 5 years ago

10.1186/s12890-018-0668-7

Heparin-binding protein in sputum as a marker of pulmonary inflammation, lung function, and bacterial load in children with cystic fibrosis
Cited by: 11
Author(s): Gisela Hovold, Victoria Palmcrantz, Fredrik Kahn, Arne Egesten, Lisa I. Påhlman
Software Mentions: 5
Published: about 8 years ago

10.1186/s12889-016-2893-4

Intimate partner violence norms cluster within households: an observational social network study in rural Honduras
Cited by: 32
Author(s): Holly B. Shakya, Dominic Hughes, Derek Stafford, Nicholas A. Christakis, James H. Fowler, Jay G. Silverman
Software Mentions: 5
Published: over 10 years ago

10.26508/lsa.201900318

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
Cited by: 11
Author(s): Junaid Akhtar, Piyush More, Steffen Albrecht, Fédérico Marini, Walter Kaiser, Apurva Kulkarni, Leszek Wojnowski, Jean-Fred Fontaine, Miguel A. Andrade‐Navarro, Marion Silies, Christian Berger
Software Mentions: 5
Published: almost 7 years ago

10.1002/evl3.129

Methylation and gene expression differences between reproductive and sterile bumblebee workers
Cited by: 48
Author(s): Hollie Marshall, Zoë N. Lonsdale, Eamonn B. Mallon
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-017-3589-6

Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity
Cited by: 14
Author(s): Michael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D. Gallaher, Albert J. Courey
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2105-15-280

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
Cited by: 49
Author(s): Huihuang Yan, Jared M. Evans, Mike Kalmbach, Raymond M. Moore, Sumit Middha, Stanislav Luban, Liguo Wang, Aditya Bhagwate, Ying Liu, Zhifu Sun, Xianfeng Chen, Jean-Pierre A. Kocher
Software Mentions: 5
Published: almost 12 years ago

10.1007/s10096-020-04049-6

The vaginal microbiota in the course of bacterial vaginosis treatment
Cited by: 7
Author(s): Romy D. Zwittink, Ellen H A van den Munckhof, Maurine A. Leverstein–van Hall, Kim E. Boers, Anco Molijn, Cornelis W. Knetsch, Ed J. Kuijper
Software Mentions: 5
Published: almost 6 years ago

10.3390/biology10090907

Dissecting Bread Wheat Heterosis through the Integration of Agronomic and Physiological Traits
Cited by: 6
Author(s): Kevin Gimenez, Pierre Blanc, O. Argillier, Jean-Baptiste Pierre, Jacques Le Gouis, Etienne Paux
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13068-021-01975-1

Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172
Cited by: 14
Author(s): Monika Tõlgo, Silvia Hüttner, Peter Rugbjerg, Nguyễn Thanh Thủy, Vu Nguyen Thanh, Johan Larsbrink, Lisbeth Olsson
Software Mentions: 5
Published: about 5 years ago

10.1016/j.cels.2021.05.005

A time-resolved proteomic and prognostic map of COVID-19
Cited by: 106
Author(s): Vadim Demichev, Pinkus Tober‐Lau, Oliver Lemke, Tatiana Nazarenko, Charlotte Thibeault, Harry J. Whitwell, Annika Röhl, Anja Freiwald, Łukasz Szyrwiel, Daniela Ludwig, Clara Correia‐Melo, Simran Kaur Aulakh, Elisa T Helbig, Paula Stubbemann, Lena J Lippert, Nana‐Maria Grüning, Oleg Blyuss, Spyros Vernardis, Matthew White, Christoph B. Messner, Michael Joannidis, Thomas Sonnweber, Sebastian Klein, Alex Pizzini, Yvonne Wohlfarter, Sabina Sahanic, Richard Hilbe, Benedikt Schaefer, Sonja Wagner, Mirja Mittermaier, Felix Machleidt, Carmen García, Christoph Ruwwe‐Glösenkamp, Tilman Lingscheid, Laure Bosquillon de Jarcy, Miriam Stegemann, Moritz Pfeiffer, Linda Jürgens, Sophy Denker, Daniel Zickler, Philipp Enghard, Aleksej Zelezniak, Archie Campbell, Caroline Hayward, David J. Porteous, Riccardo E. Marioni, Alexander Uhrig, Holger Müller-Redetzky, Heinz Zoller, Judith Löffler‐Ragg
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0236668

When to use one-dimensional, two-dimensional, and Shifted Transversal Design pooling in mycotoxin screening
Cited by: 4
Author(s): Xianbin Cheng, Ruben A. Chavez, Matthew J. Stasiewicz
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13072-015-0045-1

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay
Cited by: 11
Author(s): Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
Software Mentions: 5
Published: over 10 years ago

10.1186/s12859-017-1909-0

DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
Cited by: 52
Author(s): John Gaspar, Ronald P. Hart
Software Mentions: 5
Published: over 8 years ago

10.1080/15592294.2019.1656157

Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes
Cited by: 16
Author(s): Adrian Boström, Andreas Chatzittofis, Diana‐Maria Ciuculete, John N. Flanagan, Regina Krattinger, Marcus Bandstein, Jessica Mwinyi, Gerd A. Kullak‐Ublick, Katarina Görts Öberg, Stefan Arver, Helgi B. Schiöth, Jussi Jokinen
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0223675

Establishing an infrastructure for collaboration in primate cognition research
Cited by: 76
Author(s): Many Primates, Drew Altschul, Michael J. Beran, Manuel Bohn, Josep Call, Sarah E. DeTroy, Shona Duguid, Crystal L. Egelkamp, Claudia Fichtel, Julia Fischer, Molly Flessert, Daniel Hanuš, Daniel B. M. Haun, Lou M. Haux, R. Adriana Hernández‐Aguilar, Eva Herrmann, Lydia M. Hopper, Marine Joly, Fumihiro Kano, Stefanie Keupp, Alicia P. Melis, Alba Motes-Rodrigo, Stephen R. Ross, Alejandro Sánchez-Amaro, Yutaro Sato, Vanessa Schmitt, Manon K. Schweinfurth, Amanda M. Seed, Derry Taylor, Christoph J. Völter, Elizabeth Warren, Sarah F. Brosnan
Software Mentions: 5
Published: over 6 years ago

10.15252/emmm.201911115

Disease modeling of a mutation in α‐actinin 2 guides clinical therapy in hypertrophic cardiomyopathy
Cited by: 77
Author(s): Maksymilian Prondzynski, Marc D. Lemoine, Antonia T.L. Zech, András Horváth, Vittoria Di Mauro, Jussi T. Koivumäki, Nico Kresin, Josefine Busch, T. Krause, Elisabeth Krämer, Saskia Schlossarek, Michael Spohn, Felix W. Friedrich, Julia Münch, Sandra D. Laufer, Charles Redwood, Alexander E Volk, Arne Hansen, Giulia Mearini, Daniele Catalucci, Christian Meyer, Torsten Christ, Monica Patten, Thomas Eschenhagen, Lucie Carrier
Software Mentions: 5
Published: over 6 years ago

10.15252/emmm.201809456

Alternative oxidase‐mediated respiration prevents lethal mitochondrial cardiomyopathy
Cited by: 47
Author(s): Jayasimman Rajendran, Janne Purhonen, Saara Tegelberg, Olli‐Pekka Smolander, Matthias Mörgelin, Jan Rozman, Valérie Gailus‐Durner, Helmut Fuchs, Martin Hrabě de Angelis, Petri Auvinen, Eero Mervaala, Howard T. Jacobs, Marten Szibor, Vineta Fellman, Jukka Kallijärvi
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0232313

Suitability of resampled multispectral datasets for mapping flowering plants in the Kenyan savannah
Cited by: 0
Author(s): David Masereti Makori, Elfatih M. Abdel‐Rahman, Tobias Landmann, Onisimo Mutanga, John Odindi, Evelyn Masereti Nguku, Henri E. Z. Tonnang, Satish Raina
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13148-021-01149-8

Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer
Cited by: 7
Author(s): Javier Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban‐Rodríguez, María Dolores Diestro, Javier Benı́tez, Fátima Sánchez-Cabo, Rafael Álvarez, Javier de Castro
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0214833

Disparate effects of antibiotic-induced microbiome change and enhanced fitness in Daphnia magna
Cited by: 27
Author(s): Asa Motiei, Björn Brindefalk, Martin Ogonowski, Rehab El-Shehawy, Paulina Pastuszek, Karin Ek, Birgitta Liewenborg, Klas I. Udekwu, Elena Gorokhova
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0254556

Simple mapping-based quantification of a mock microbial community using total RNA-seq data
Cited by: 4
Author(s): Shigeharu Moriya
Software Mentions: 5
Published: almost 5 years ago

10.1074/mcp.RA120.002175

Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment
Cited by: 3
Author(s): Kathryn M. Huson, Erwan Atcheson, Nicola A.M. Oliver, Philip M. Best, J.P. Barley, R.E.B. Hanna, Tom N. McNeilly, Yongxiang Fang, Sam Haldenby, Steve Paterson, Mark W. Robinson
Software Mentions: 5
Published: over 5 years ago

10.3390/cancers13123014

Upper Aerodigestive Tract Squamous Cell Carcinomas Show Distinct Overall DNA Methylation Profiles and Different Molecular Mechanisms behind WNT Signaling Disruption
Cited by: 6
Author(s): Sheila Coelho Soares-Lima, Hisham Mehanna, Diego Camuzi, Paulo Thiago de Souza-Santos, Tatiana de Almeida Simão, Pedro Nicolau-Neto, Monique de Souza Almeida Lopes, Cyrille Cuenin, Fazlur Rahman Talukdar, Nikolaos Batis, Izabella Costa, Fernando Luiz Dias, Davide Degli Esposti, Mariana Boroni, Zdenko Herceg, Luís Felipe Ribeiro Pinto
Software Mentions: 5
Published: about 5 years ago

10.3390/cancers13102460

Online, Group-Based Psychological Support for Adolescent and Young Adult Cancer Survivors: Results from the Recapture Life Randomized Trial
Cited by: 16
Author(s): Ursula M Sansom-Daly, Claire E. Wakefield, Sharon Ellis, Brittany C. McGill, Mark Donoghoe, Phyllis Butow, Richard A. Bryant, Susan Μ Sawyer, Pandora Patterson, Antoinette Anazodo, Megan Plaster, Kate Thompson, Lucy Holland, Michael Osborn, Fiona Maguire, Catherine O’Dwyer, Richard De Abreu Lourenço, Richard J. Cohn
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms22041989

Transcriptome Analysis of Subcutaneous Adipose Tissue from Severely Obese Patients Highlights Deregulation Profiles in Coding and Non-Coding Oncogenes
Cited by: 5
Author(s): Federica Rey, Letizia Messa, Cecilia Pandini, Rossella Launi, Bianca Barzaghini, Giancarlo Micheletto, Manuela Teresa Raimondi, Simona Bertoli, Cristina Cereda, Gian Vincenzo Zuccotti, Raffaella Cancello, Stephana Carelli
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-02204-z

Random errors in protein synthesis activate an age-dependent program of muscle atrophy in mice
Cited by: 5
Author(s): James M. Moore, Rashid Akbergenov, Martina Nigri, Patricia Isnard-Petit, Amandine Grimm, Petra Seebeck, Lisa Michelle Restelli, Stephan Frank, Anne Eckert, Kader Thiam, David P Wolfer, Dimitri Shcherbakov, Erik C. Böttger
Software Mentions: 5
Published: about 5 years ago

10.1186/1758-2946-5-12

Computational mass spectrometry for small molecules
Cited by: 124
Author(s): Kerstin Scheubert, Franziska Hufsky, Sebastian Böcker
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pone.0106366

Mapping Seabird Sensitivity to Offshore Wind Farms
Cited by: 64
Author(s): Gareth Bradbury, Mark Trinder, Bob Furness, Alex N. Banks, R. W. G. Caldow, Duncan Hume
Software Mentions: 5
Published: almost 12 years ago

10.1093/database/bax079

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Cited by: 9
Author(s): Leandro Costa do Nascimento, Marcela Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas S. Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
Software Mentions: 5
Published: over 9 years ago

10.3390/microorganisms9051034

A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium
Cited by: 3
Author(s): Carlos Sabater, Lorena Ruíz, Abelardo Margollés
Software Mentions: 5
Published: about 5 years ago

10.18632/oncotarget.23206

Coagulation cascade and complement system in systemic lupus erythematosus
Cited by: 19
Author(s): Yan Liang, Shangbo Xie, Changhao Wu, Yuan Hu, Qin Zhang, Si Li, Yin‐Guang Fan, Rui‐Xue Leng, Hai‐Feng Pan, Huabao Xiong, Dong‐Qing Ye
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.47214

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Cited by: 15
Author(s): Daniel Andergassen, Zachary D. Smith, Jordan P. Lewandowski, Chiara Gerhardinger, Alexander Meissner, John L. Rinn
Software Mentions: 5
Published: over 6 years ago

10.1111/eva.13269

Rapid evolution of knockdown resistance haplotypes in response to pyrethroid selection in <i>Aedes aegypti</i>
Cited by: 13
Author(s): Jennifer Baltzegar, Michael R. Vella, Christian E. Gunning, Gissella M. Vásquez, Helvio Astete, Fred Stell, Michael L. Fisher, Thomas W. Scott, Audrey Lenhart, Alun L. Lloyd, Amy C. Morrison, Fred Gould
Software Mentions: 5
Published: about 5 years ago

10.1093/gigascience/giz083

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences
Cited by: 24
Author(s): Ken Youens‐Clark, Matt Bomhoff, Alise J. Ponsero, Elisha M. Wood‐Charlson, Joshua Lynch, Illyoung Choi, John H. Hartman, Bonnie Hurwitz
Software Mentions: 5
Published: about 7 years ago

10.1007/s11356-020-07660-4

Transcriptional and biochemical biomarker responses in a freshwater mussel (Anodonta anatina) under environmentally relevant Cu exposure
Cited by: 7
Author(s): Gustaf Ekelund Ugge, Annie Jonsson, Björn Olsson, Robert Sjöback, Olof Berglund
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-015-0844-5

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Cited by: 1,843
Author(s): Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian H. Gersuk, Alex K. Shalek, Chloe K. Slichter, Hannah W. Miller, M. Juliana McElrath, Martin Prlic, Peter S. Linsley, Raphaël Gottardo
Software Mentions: 5
Published: over 10 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0089323

Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization
Cited by: 60
Author(s): Xiaoquan Su, Weihua Pan, Baoxing Song, Jian Xu, Kang Ning
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: over 6 years ago

10.1186/s12862-017-1064-2

Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
Cited by: 45
Author(s): Fabrizio Menardo, Coraline R. Praz, Thomas Wicker, Beat Keller
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.64478

Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo
Cited by: 7
Author(s): Darryl A. Wesener, Zachary Beller, Samantha L. Peters, Amir Rajabi, Gianluca Dimartino, Richard J. Giannone, Robert L. Hettich, Jeffrey I. Gordon
Software Mentions: 5
Published: over 5 years ago

10.1002/ctm2.246

Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single‐cell transcriptome analysis
Cited by: 33
Author(s): Haoyu Ruan, Yihang Zhou, Jie Shen, Yue Zhai, Ying Xu, Linyu Pi, Run Huang, Kun Chen, Xiangyu Li, Wendong Ma, Zhiyuan Wu, Xuan Deng, Xiaozhu Wang, Chao Zhang, Ming Guan
Software Mentions: 5
Published: over 5 years ago

10.1186/s12870-019-1685-2

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors
Cited by: 15
Author(s): Konstantin Kozlov, A. K. Singh, Jens Berger, Eric J. B. von Wettberg, Abdullah Kahraman, Abdulkadir Aydoğan, Douglas R. Cook, Sergey V. Nuzhdin, Maria Samsonova
Software Mentions: 5
Published: over 7 years ago

10.1038/s41396-021-00920-2

Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi
Cited by: 72
Author(s): Bryan D. Emmett, Veronique Levesque‐Tremblay, Maria J. Harrison
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-6495-2

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features
Cited by: 8
Author(s): Yang Li, Menggen Dalai, Rongguo Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-10-391

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Cited by: 6
Author(s): Chunguang Liang, Alexander Schmid, María José López‐Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar
Software Mentions: 5
Published: over 16 years ago

10.1038/s41598-021-90744-z

Directional changes in Levallois core technologies between Eastern Africa, Arabia, and the Levant during MIS 5
Cited by: 3
Author(s): James Blinkhorn, Huw S. Groucutt, Eleanor M. L. Scerri, Michael D. Petraglia, Simon Blockley
Software Mentions: 5
Published: about 5 years ago

10.1126/sciadv.abe2592

Aquaculture mediates global transmission of a viral pathogen to wild salmon
Cited by: 24
Author(s): Gideon Mordecai, Kristina M. Miller, Arthur L. Bass, Andrew Bateman, Amy K. Teffer, Jessica M. Caleta, Emiliano Di Cicco, Angela D. Schulze, Karia H. Kaukinen, Shaorong Li, Amy Tabata, Bradley R. Jones, Tobi J. Ming, Jeffrey B. Joy
Software Mentions: 5
Published: about 5 years ago

10.1186/s40478-019-0805-4

Profiling the unique protective properties of intracranial arterial endothelial cells
Cited by: 7
Author(s): Dorien Hermkens, Olga C.G. Stam, Nienke M. de Wit, Ruud D. Fontijn, Aldo Jongejan, Perry D. Moerland, Claire Mackaaij, Ingeborg S. E. Waas, M. J. A. P. Daemen, Helga E. de Vries
Software Mentions: 5
Published: over 6 years ago

10.1016/j.stem.2019.03.017

Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Cited by: 78
Author(s): Tüzer Kalkan, Susanne Bornelöv, Carla Mulas, Evangelia Diamanti, Tim Lohoff, Markus Ralser, Sjors Middelkamp, Patrick Lombard, Jennifer Nichols, Austin Smith
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-018-25748-3

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9
Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: about 8 years ago

10.1186/s13059-021-02460-6

Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability
Cited by: 23
Author(s): Xin Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D. Buckley, Gisela Orozco, Oliver Distler, Andrew P. Morris, Paul Martin, Stephen Eyre, Caroline Ospelt
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-019-40831-z

Preoperative Prediction of Axillary Lymph Node Metastasis in Breast Cancer Using Mammography-Based Radiomics Method
Cited by: 49
Author(s): Jingbo Yang, Tao Wang, Lifeng Yang, Yübo Wang, Hongmei Li, Xiaobo Zhou, Weiling Zhao, Junchan Ren, Xiaoyong Li, Jie Tian, Luqi Huang
Software Mentions: 5
Published: over 7 years ago

10.1111/1755-0998.13257

High quality genome of <i>Erigeron breviscapus</i> provides a reference for herbal plants in Asteraceae
Cited by: 19
Author(s): Simei He, Dong Xiao, Guanghui Zhang, Wei Fan, Shengchang Duan, Hong Shi, Dawei Li, Rui Li, Cuizhi Geng, Guangqiang Long, Yan Zhao, Mo Chen, Mi Yan, Jianli Yang, Yingchun Lu, Yanli Zhou, Wei Chen, Yang Dong, Shengchao Yang
Software Mentions: 5
Published: over 5 years ago

10.1186/s12916-021-01953-2

Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study
Cited by: 50
Author(s): Huan Yang, Lili Chen, Zhiqiang Cheng, Mo Yang, Jianbo Wang, Cheng-Hao Lin, Yuefeng Wang, Leilei Huang, Yangshan Chen, Sui Peng, Zunfu Ke, Weizhong Li
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-021-01716-y

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Cited by: 28
Author(s): Jianbo Yuan, Xiaojun Zhang, Min Wang, Yamin Sun, Xianhui Qin, Shihao Li, Yang Yu, Yi Gao, Fei Liu, Jie Kong, Guangyi Fan, Chengsong Zhang, Lu Feng, Jianhai Xiang, Fuhua Li
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-018-0122-7

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish
Cited by: 44
Author(s): Marianna Pauletto, Tereza Manousaki, Serena Ferraresso, Massimiliano Babbucci, Alexandros Tsakogiannis, Bruno Louro, Nicola Vitulo, Viet Ha Quoc, R. Carraro, Daniela Bertotto, Rafaella Franch, Francesco Maroso, Muhammad Aslam, Anna K. Sonesson, Barbara Simionati, G Malacrida, Alessandro Cestaro, Stefano Caberlotto, Elena Sarropoulou, C. C. Mylonas, Deborah M. Power, Tomaso Patarnello, Adelino V.M. Canário, Costas S. Tsigenopoulos, Luca Bargelloni
Software Mentions: 5
Published: almost 8 years ago

10.1038/s42003-018-0094-7

Evidence of non-tandemly repeated rDNAs and their intragenomic heterogeneity in Rhizophagus irregularis
Cited by: 53
Author(s): Taro Maeda, Yuuki Kobayashi, Hiromu Kameoka, Nao Okuma, Nobuo Takeda, Katsushi Yamaguchi, Takahiro Bino, Shuji Shigenobu, Masayoshi Kawaguchi
Software Mentions: 5
Published: about 8 years ago

10.1038/s42003-021-01859-y

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology
Cited by: 16
Author(s): Sara Calhoun, Tisza Ann Szeremy Bell, Lukas R. Dahlin, Yuliya A. Kunde, Kurt LaButti, Katherine Louie, Andrea Kuftin, Daniel Treen, David Dilworth, Sirma Mihaltcheva, Christopher Daum, Benjamin P. Bowen, Trent Northen, Michael T. Guarnieri, Shawn R. Starkenburg, Igor V. Grigoriev
Software Mentions: 5
Published: over 5 years ago

10.1016/j.celrep.2018.10.072

Heart Regeneration in the Mexican Cavefish
Cited by: 78
Author(s): William T. Stockdale, Madeleine E. Lemieux, Abigail C. Killen, Juanjuan Zhao, Zhilian Hu, Joey Riepsaame, Noémie Hamilton, Tetsuhiro Kudoh, Paul R. Riley, Ronny van Aerle, Yoshiyuki Yamamoto, Mathilda T.M. Mommersteeg
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0226616

Insights into fungal diversity of a shallow-water hydrothermal vent field at Kueishan Island, Taiwan by culture-based and metabarcoding analyses
Cited by: 25
Author(s): Ka−Lai Pang, Sheng−Yu Guo, I-An Chen, Gaëtan Burgaud, Zengwei Luo, Hans-Uwe Dahms, Jiang‐Shiou Hwang, Yi-Li Lin, Jian-Shun Huang, Tsz-Wai Ho, Ling Ming Tsang, Michael Chiang, Hyojung Cha
Software Mentions: 5
Published: over 6 years ago

10.3389/fcell.2014.00040

Quantifying periodicity in omics data
Cited by: 7
Author(s): Cornelia Amariei, Masaru Tomita, Douglas B. Murray
Software Mentions: 5
Published: almost 12 years ago

10.1016/j.celrep.2020.107843

Alzheimer’s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation
Cited by: 194
Author(s): Karpagam Srinivasan, Brad A. Friedman, Ainhoa Etxeberría, Melanie A. Huntley, Marcel P. van der Brug, Oded Foreman, Jonathan S. Paw, Zora Modrušan, Thomas G. Beach, Geidy E. Serrano, David V. Hansen
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0135350

Conservation Status of North American Birds in the Face of Future Climate Change
Cited by: 90
Author(s): Gary Langham, Justin G. Schuetz, Trisha Distler, Candan U. Soykan, Chad B. Wilsey
Software Mentions: 5
Published: almost 11 years ago

10.1016/j.cell.2018.09.043

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance
Cited by: 111
Author(s): Anastasiya Kazachenka, Tessa M. Bertozzi, Marcela K. Sjoberg-Herrera, N Walker, Joseph Gardner, Richard Gunning, Eleni Pahita, Sarah Adams, David J. Adams, Anne C. Ferguson-Smith
Software Mentions: 5
Published: over 7 years ago

10.1002/bimj.201100251

Regression trees for predicting mortality in patients with cardiovascular disease: What improvement is achieved by using ensemble‐based methods?
Cited by: 58
Author(s): Peter C. Austin, Douglas S. Lee, Ewout W. Steyerberg, Jack V. Tu
Software Mentions: 5
Published: about 14 years ago

10.1016/j.cell.2021.03.062

Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: about 5 years ago

10.1186/s12887-020-02411-3

Utility of medical record diagnostic codes to ascertain attention-deficit/hyperactivity disorder and learning disabilities in populations of children
Cited by: 6
Author(s): Yu Shi, Phillip J. Schulte, Andrew C. Hanson, Michael J. Zaccariello, Dayu Hu, Sheri Crow, Randall P. Flick, David O. Warner
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2288-14-99

Detection of independent associations in a large epidemiologic dataset: a comparison of random forests, boosted regression trees, conventional and penalized logistic regression for identifying independent factors associated with H1N1pdm influenza infections
Cited by: 33
Author(s): Yohann Mansiaux, Fabrice Carrat
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12911-020-01271-2

Using machine learning methods to predict in-hospital mortality of sepsis patients in the ICU
Cited by: 64
Author(s): Guilan Kong, Ke Lin, Yonghua Hu
Software Mentions: 5
Published: almost 6 years ago

10.3390/cancers11030280

Observed Survival Interval: A Supplement to TCGA Pan-Cancer Clinical Data Resource
Cited by: 21
Author(s): Jie Xiong, Zhitong Bing, Shengyu Guo
Software Mentions: 5
Published: over 7 years ago

10.3390/cancers12010037

Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 158
Author(s): Magdalena Niemira, François Collin, Anna Szałkowska, Agnieszka Bielska, Karolina Chwiałkowska, Joanna Reszeć, Jacek Nikliński, Mirosław Kwaśniewski, Adam Krętowski
Software Mentions: 5
Published: over 6 years ago

10.1038/srep31153

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases
Cited by: 88
Author(s): Adriana De Palma, Stefan Abrahamczyk, Marcelo A. Aizen, Matthias Albrecht, Yves Basset, Adam J. Bates, Robin J. Blake, Céline Boutin, Rob Bugter, Stuart Connop, Leopoldo Cruz‐López, Saul A. Cunningham, Ben Darvill, Tim Diekötter, Silvia Dorn, Nicola Downing, Martin H. Entling, Nina Farwig, Antonio Felicioli, Steven J. Fonte, Robert Fowler, Markus Franzén, Dave Goulson, Ingo Graß, Mick E. Hanley, Stephen D. Hendrix, Farina Herrmann, Félix Herzog, Andrea Holzschuh, Birgit Jauker, Michael Kessler, M. E. Knight, Andreas Kruess, Patrick Lavelle, Violette Le Féon, Pia E. Lentini, Louise A. Malone, E. J. P. Marshall, Eliana Martínez Pachón, Quinn S. McFrederick, Carolina L. Morales, Sonja Mudri‐Stojnić, Guiomar Nates‐Parra, Sven G. Nilsson, Erik Öckinger, Lynne M. Osgathorpe, Alejandro Parra-H, Carlos A. Peres, Anna Persson, Theodora Petanidou, Katja Poveda, Eileen F. Power, Marino Quaranta, Carolina Quintero, Romina Rader, Miriam H. Richards, T’ai H. Roulston, Laurent Rousseau, John Sadler, Ulrika Samnegård, Nancy A. Schellhorn, Christof Schüepp, Oliver Schweiger, Allan H. Smith-Pardo, Ingolf Steffan‐Dewenter, Jane C. Stout, Rebecca K. Tonietto, Teja Tscharntke, Jason M. Tylianakis, Hans A. F. Verboven, Carlos Vergara, J. Verhulst, Catrin Westphal, Hyung Joo Yoon, Andy Purvis
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pone.0175464

Identification of potential biomarkers in donor cows for in vitro embryo production by granulosa cell transcriptomics
Cited by: 12
Author(s): Gianluca Mazzoni, Suraya Mohamad Salleh, Kristine Freude, Helene Helboe Pedersen, Lotte Stroebech, Henrik Callesen, Poul Hyttel, Haja N. Kadarmideen
Software Mentions: 5
Published: over 9 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-020-73597-w

Pomegranate: 2D segmentation and 3D reconstruction for fission yeast and other radially symmetric cells
Cited by: 9
Author(s): Erod Keaton Baybay, Eric Esposito, Silke Hauf
Software Mentions: 5
Published: almost 6 years ago

10.3390/toxins13050318

Risky Business: The Function of Play in a Venomous Mammal—The Javan Slow Loris (Nycticebus javanicus)
Cited by: 6
Author(s): Meg Barrett, Marco Campera, Thaís Q. Morcatty, Ariana Weldon, Katherine Hedger, Keely Q. Maynard, Muhammad Ali Imron, K. A. I. Nekaris
Software Mentions: 5
Published: about 5 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0201263

The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei
Cited by: 2
Author(s): Anna Kelner, Michele Tinti, Maria Lucia S. Güther, Bernardo J. Foth, Lia Chappell, Matthew Berriman, Victoria H. Cowling, Michael A. J. Ferguson
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0224560

Transcriptional analysis of amino acid, metal ion, vitamin and carbohydrate uptake in butanol-producing Clostridium beijerinckii NRRL B-598
Cited by: 13
Author(s): Maryna Vasylkivska, Katerina Jureckova, Barbora Branská, Karel Sedlář, Jan Kolek, Ivo Provazník, Petra Patáková
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0207250

Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes
Cited by: 12
Author(s): Maxime Caron, Pascal St-Onge, Simon Drouin, Chantal Richer, Thomas Sontag, Stephan Busche, Guillaume Bourque, Tomi Pastinen, Daniel Sinnett
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0215351

The bacterial communities of the small intestine and stool in children with short bowel syndrome
Cited by: 14
Author(s): Steven L. Zeichner, Emmanuel F. Mongodin, Lauren E. Hittle, Szu-Han Huang, Clarivet Torres
Software Mentions: 5
Published: about 7 years ago

10.3390/jcm8101666

The Extended Postoperative Care-Score (EXPO-Score)—An Objective Tool for Early Identification of Indication for Extended Postoperative Care
Cited by: 2
Author(s): Timo Iden, Amke Caliebe, Jochen Renner, Maj-Britt Hertz, Jan Höcker, Päivi Suvanto-Scholz, Markus Steinfath, Norbert Weiler, Matthias Gruenewald
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0256534

Impact of the dog population and household environment for the maintenance of natural foci of Leishmania infantum transmission to human and animal hosts in endemic areas for visceral leishmaniasis in Sao Paulo state, Brazil
Cited by: 8
Author(s): Patrícia Sayuri Silvestre Matsumoto, Roberto Mitsuyoshi Hiramoto, Virgínia Bodelão Richini-Pereira, Valéria Medina Camprigher, Helena Hilomi Taniguchi, José Eduardo de Raeffray Barbosa, Luiz Ricardo Paes de Barros Cortez, Elivelton da Silva Fonseca, Raúl Borges Guimarães, José Eduardo Tolezano
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0210164

Marine mammals and sea turtles listed under the U.S. Endangered Species Act are recovering
Cited by: 37
Author(s): Abel Valdivia, Shaye Wolf, Kierán Suckling
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0146194

The Frequency of Rapid Pupil Dilations as a Measure of Linguistic Processing Difficulty
Cited by: 53
Author(s): Vera Demberg, Asad Sayeed
Software Mentions: 5
Published: over 10 years ago

10.3390/insects11110783

Colony-Level Effects of Amygdalin on Honeybees and Their Microbes
Cited by: 5
Author(s): James P. Tauber, Cansu Özge Tozkar, Ryan S. Schwarz, Dawn Lopez, Rebecca E. Irwin, Lynn S. Adler, Jay D. Evans
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0220165

PS-SiZer map to investigate significant features of body-weight profile changes in HIV infected patients in the IeDEA Collaboration
Cited by: 0
Author(s): Jaroslaw Harezlak, Samiha Sarwat, Kara Wools‐Kaloustian, Michael Schomaker, Eric Balestre, Matthew Law, Sasisopin Kiertiburanakul, Matthew P. Fox, Diana Huis in ʼt Veld, Beverly Musick, Constantin T. Yiannoutsos
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.6776

An affordable and automated imaging approach to acquire highly resolved individual data—an example of copepod growth in response to multiple stressors
Cited by: 6
Author(s): Jan Heuschele, Torben Lode, Tom Andersen, Katrine Borgå, Josefin Titelman
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0217121

Removal of an established invader can change gross primary production of native macroalgae and alter carbon flow in intertidal rock pools
Cited by: 1
Author(s): Francesca Rossi, Rosa M. Viejo, Linney Duarte, Fátima Vaz-Pinto, Ignácio Gestoso, Celia Olabarria
Software Mentions: 5
Published: over 6 years ago

10.1016/j.dib.2019.103909

RNA-sequencing data highlighting the time-of-day-dependent transcriptome of the central circadian pacemaker in Sox2-deficient mice
Cited by: 4
Author(s): Arthur H. Cheng, Pascale Bouchard-Cannon, Rob W. Ness, Hai-Ying Mary Cheng
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pgen.1007631

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic
Cited by: 16
Author(s): Peter A. Combs, Hunter B. Fraser
Software Mentions: 5
Published: over 7 years ago