10.1371/journal.pone.0236882

Mutations in m6A consensus motifs are suppressed in the m6A modified genes in human cancer cells
Cited by: 3
Author(s): Mingzi An, Wang Hui-yun, Yingqian Zhu
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0179567

A sorghum (Sorghum bicolor) mutant with altered carbon isotope ratio
Cited by: 4
Author(s): Govinda Rizal, Shanta Karki, Vivek Thakur, Samart Wanchana, Hugo Alonso-Cantabrana, Jacque Dionora, J. E. Sheehy, Robert T. Furbank, Susanne von Caemmerer, W. Paul Quick
Software Mentions: 1
Published: about 9 years ago

10.1016/j.isci.2020.101698

The Rigor and Transparency Index Quality Metric for Assessing Biological and Medical Science Methods
Cited by: 36
Author(s): Joe Menke, Martijn Roelandse, İbrahim Burak Özyurt, Maryann E. Martone, Anita Bandrowski
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0195142

Surprisal analysis of genome-wide transcript profiling identifies differentially expressed genes and pathways associated with four growth conditions in the microalga Chlamydomonas
Cited by: 6
Author(s): Kenny A. Bogaert, Sheeba Santhini Manoharan-Basil, Emilie Perez, R. D. Levine, Françoise Remacle, Claire Remacle
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0152405

Subtype-Selective Small Molecule Inhibitors Reveal a Fundamental Role for Nav1.7 in Nociceptor Electrogenesis, Axonal Conduction and Presynaptic Release
Cited by: 144
Author(s): Aristos J. Alexandrou, Adam R. Brown, Mark L. Chapman, Mark Estacion, Jamie Turner, Malgorzata A. Mis, Anna Wilbrey, Elizabeth C. Payne, Alex Gutteridge, Peter Cox, Rachel Doyle, David Printzenhoff, Zhixin Lin, Brian E. Marron, Christopher W. West, Nigel A. Swain, Richard Storer, Paul A. Stupple, Neil A. Castle, James A. Hounshell, Mirko Rivara, Andrew D. Randall, Sulayman D. Dib‐Hajj, Douglas S. Krafte, Stephen G. Waxman, Manoj K. Patel, Richard P. Butt, Edward B. Stevens
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0100153

The Relationship between Therapeutic Alliance and Service User Satisfaction in Mental Health Inpatient Wards and Crisis House Alternatives: A Cross-Sectional Study
Cited by: 62
Author(s): Angela Sweeney, Sarah Fahmy, Fiona Nolan, Nicola Morant, Zoë Fox, Brynmor Lloyd‐Evans, David Osborn, Emma Burgess, Helen Gilburt, Rose McCabe, Mike Slade, Sonia Johnson
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0174436

Computational identifying and characterizing circular RNAs and their associated genes in hepatocellular carcinoma
Cited by: 16
Author(s): Yan Li, Yongcheng Dong, Ziyan Huang, Qifan Kuang, Yiming Wu, Yizhou Li, Menglong Li
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0141214

Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood
Cited by: 503
Author(s): Sebastian Memczak, Panagiotis Papavasileiou, Oliver Peters, Nikolaus Rajewsky
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0078586

Rapid Kill—Novel Endodontic Sealer and Enterococcus faecalis
Cited by: 27
Author(s): Nurit Beyth, Dana Kesler Shvero, Nathan Zaltsman, Yael Houri‐Haddad, Itzhak Abramovitz, Michael Perez Davidi, Ervin I. Weiss
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-021-90510-1

Human induced pluripotent stem cell derived hepatocytes provide insights on parenteral nutrition associated cholestasis in the immature liver
Cited by: 4
Author(s): T. Hang Nghiem-Rao, Courtney Pfeifer, Michelle Asuncion, Joshua Nord, Daniel J. Schill, Kirthi Pulakanti, Shailendra B. Patel, Lisa Ann Cirillo, Sridhar Rao
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0221109

Antibiotic treatment of Chlamydia-induced cystitis in the koala is linked to expression of key inflammatory genes in reactive oxygen pathways
Cited by: 5
Author(s): Samuel Phillips, Bonnie Chaban, Ammar Aziz, Wendy Bergen, Rosemary Booth, Michael Pyne, Peter Timms
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0177340

Metagenomic sequencing complements routine diagnostics in identifying viral pathogens in lung transplant recipients with unknown etiology of respiratory infection
Cited by: 52
Author(s): Dagmara W. Lewandowska, Peter W. Schreiber, Macé M. Schuurmans, Bettina Ruehe, Osvaldo Zagordi, Cornelia Bayard, Michael Greiner, Fabienne D. Geissberger, Riccarda Capaul, Andrea Zbinden, Jürg Böni, Christian Benden, Nicolas J. Mueller, Alexandra Trkola, Michael Huber
Software Mentions: 1
Published: about 9 years ago

10.1186/s12885-021-08616-8

Differential effects of HIF2α antagonist and HIF2α silencing in renal cancer and sensitivity to repurposed drugs
Cited by: 5
Author(s): Esther Arnaiz, Ana Miar, Esther Bridges, Naveen Prasad, Stephanie B. Hatch, Daniel Ebner, Charles H. Lawrie, Adrian L. Harris
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-021-92529-w

The ATF6β-calreticulin axis promotes neuronal survival under endoplasmic reticulum stress and excitotoxicity
Cited by: 8
Author(s): Dinh Thi Nguyen, Thuong Manh Le, Tsuyoshi Hattori, Mika Takarada-Iemata, Hiroshi Ishii, Jureepon Roboon, Takashi Tamatani, Takayuki Kannon, Kazuyoshi Hosomichi, Atsushi Tajima, Shusuke Taniuchi, Masato Miyake, Seiichi Oyadomari, Takashi Tanaka, Nobuo Kato, Shunsuke Saito, Kazutoshi Mori, Osamu Hori
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0129183

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
Cited by: 104
Author(s): Shamsuzzoha Bayzid, Siavash Mirarab, Bastien Boussau, Tandy Warnow
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0134958

A Biochemical Approach to Understand the Pathogenesis of Advanced Pulmonary Arterial Hypertension: Metabolomic Profiles of Arginine, Sphingosine-1-Phosphate, and Heme of Human Lung
Cited by: 38
Author(s): Yidan Zhao, Lei Chu, Kathleen Watson Lin, Elise Granton, Li Yin, Jiming Peng, Michael Hsin, Licun Wu, Amy Yu, Thomas K. Waddell, Shaf Keshavjee, John Granton, Marc de Perrot
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12885-019-5572-x

Nonsynonymous, synonymous and nonsense mutations in human cancer-related genes undergo stronger purifying selections than expectation
Cited by: 59
Author(s): Duan Chu, Lai Wei
Software Mentions: 1
Published: about 7 years ago

10.1186/s12915-020-00840-1

Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes
Cited by: 15
Author(s): Arnaud Lavergne, Estefanía Tarifeño-Saldivia, Justine Pirson, Anne-Sophie Reuter, Lydie Flasse, Isabelle Manfroid, Marianne L. Voz, Bernard Peers
Software Mentions: 1
Published: almost 6 years ago

10.18632/aging.102024

Mitofusin 2 plays a role in oocyte and follicle development, and is required to maintain ovarian follicular reserve during reproductive aging
Cited by: 49
Author(s): Man Zhang, Muhammed Burak Bener, Zongliang Jiang, Tianren Wang, Ecem Esencan, Richard T. Scott, Tamás L. Horváth, Emre Seli
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-021-91358-1

Neoantigens elicit T cell responses in breast cancer
Cited by: 13
Author(s): Takafumi Morisaki, Makoto Kubo, Masayo Umebayashi, Poh Yin Yew, Satoshi Yoshimura, Jae-Hyun Park, Kazuma Kiyotani, Masaya Kai, Mai Yamada, Yoshinao Oda, T. Morisaki, Masafumi Nakamura
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-93180-1

Florigen governs shoot regeneration
Cited by: 4
Author(s): Yaarit Kutsher, Michal Fisler, Adi Faigenboim, Moshe Reuveni
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0254709

Comparative transcriptome analysis of unripe and ripe banana (cv. Nendran) unraveling genes involved in ripening and other related processes
Cited by: 5
Author(s): Karambir Kaur, Praveen Awasthi, Siddharth Tiwari
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0229030

Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes
Cited by: 26
Author(s): Nuria Morfin, Paul H. Goodwin, Ernesto Guzmán-Novoa
Software Mentions: 1
Published: over 6 years ago

10.1186/s12915-021-00989-3

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant
Cited by: 18
Author(s): Elise Gay, Jessica L. Soyer, Nicolas Lapalu, Juliette Linglin, Isabelle Fudal, Corinne Da Silva, Patrick Wincker, Jean‐Marc Aury, Corinne Cruaud, Anne Levrel, Jocelyne Lemoine, Régine Delourme, Thierry Rouxel, Marie‐Hélène Balesdent
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0197105

Rapamycin-independent IGF2 expression in Tsc2-null mouse embryo fibroblasts and human lymphangioleiomyomatosis cells
Cited by: 7
Author(s): Blanca E. Himes, Kseniya Obraztsova, Lurong Lian, Maya Shumyatcher, Ryan W. Rue, Elena N. Atochina‐Vasserman, Stella K. Hur, Marisa S. Bartolomei, Jilly F. Evans, Vera P. Krymskaya
Software Mentions: 1
Published: about 8 years ago

10.1186/s12915-020-00879-0

Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences
Cited by: 5
Author(s): Wenxia Yu, Jianan Li, Shisheng Huang, Xiangyang Li, Ping Li, Guanglei Li, Aibin Liang, Chao Tian, Xingxu Huang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0130228

A Modelling Framework to Assess the Effect of Pressures on River Abiotic Habitat Conditions and Biota
Cited by: 19
Author(s): Jochem Kail, Björn Guse, Johannes Radinger, Maria Schröder, Jens Kiesel, Maarten G. Kleinhans, F. Schuurman, Nicola Fohrer, Daniel Hering, Christian Wolter
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0127871

A Novel Chitin Binding Crayfish Molar Tooth Protein with Elasticity Properties
Cited by: 9
Author(s): Jenny Tynyakov, Shmuel Bentov, Shai Abehsera, Isam Khalaila, Rivka Manor, Lihie Katzir Abilevich, Shalva Weil, Eliahu D. Aflalo, Amir Sagi
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0224062

Correction: A comparative study of RNA-Seq and microarray data analysis on the two examples of rectal-cancer patients and Burkitt Lymphoma cells
Cited by: 0
Author(s): Alexander Wolff, Michaela Bayerlová, Jochen Gaedcke, Dieter Kube, Tim Beißbarth
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0218381

Transcriptome analysis identified aberrant gene expression in pollen developmental pathways leading to CGMS in cotton (Gossypium hirsutum L.)
Cited by: 20
Author(s): Rasmieh Hamid, Hassan Marashi, R. S. Tomar, Saeid Malekzadeh-Shafaroudi, Pritesh Sabara
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0250149

Estimating COVID-19 cases in Makkah region of Saudi Arabia: Space-time ARIMA modeling
Cited by: 25
Author(s): Fuad A. Awwad, Moataz A. Mohamoud, Mohamed R. Abonazel
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-019-2597-8

pblat: a multithread blat algorithm speeding up aligning sequences to genomes
Cited by: 55
Author(s): Meng Wang, Lei Kong
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0169614

Expression of Calgranulin Genes S100A8, S100A9 and S100A12 Is Modulated by n-3 PUFA during Inflammation in Adipose Tissue and Mononuclear Cells
Cited by: 22
Author(s): Rachana Shah, Chenyi Xue, Hanrui Zhang, Sony Tuteja, Mingyao Li, Muredach P. Reilly, Jane F. Ferguson
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.102326

Cognitive impairment and transcriptomic profile in hippocampus of young mice after multiple neonatal exposures to sevoflurane
Cited by: 25
Author(s): Shaoyong Song, Xiaowen Meng, Zhengyuan Xia, Hong Liu, Juan Zhang, Qingcai Chen, Hua-yue Liu, Fuhai Ji, Ke Peng
Software Mentions: 1
Published: almost 7 years ago

10.1016/j.isci.2021.103013

Brain hierarchy score: Which deep neural networks are hierarchically brain-like?
Cited by: 29
Author(s): Soma Nonaka, Kei Majima, Shuntaro C. Aoki, Yukiyasu Kamitani
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.isci.2021.103080

Prediction and identification of synergistic compound combinations against pancreatic cancer cells
Cited by: 2
Author(s): Yasaman KalantarMotamedi, Ran Joo Choi, Siang-Boon Koh, Jo L. Bramhall, Tai-Ping Fan, Andreas Bender
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0148230

The Genetic Architecture of Murine Glutathione Transferases
Cited by: 14
Author(s): Lu Lu, Ashutosh Kumar Pandey, M. Trevor Houseal, Megan K. Mulligan
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0147823

Chamber Specific Gene Expression Landscape of the Zebrafish Heart
Cited by: 23
Author(s): Amarjeet Singh, Ambily Sivadas, Ankit Sabharwal, Shamsudheen Karuthedath Vellarikal, Rijith Jayarajan, Ankit Verma, Shruti Kapoor, Adita Joshi, Vinod Scaria, Sridhar Sivasubbu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0185079

In vitro and in vivo effects of 2,4 diaminoquinazoline inhibitors of the decapping scavenger enzyme DcpS: Context-specific modulation of SMN transcript levels
Cited by: 16
Author(s): Jonathan J. Cherry, Christine J. DiDonato, Elliot J. Androphy, Alessandro Calò, Kyle Potter, Sara K. Custer, Sarah Du, Timothy L. Foley, Ariamala Gopalsamy, Emily J. Reedich, Susana Gordo, William Gordon, Natalie Hosea, Lyn H. Jones, Daniel Krizay, Gregory J. LaRosa, Hongxia Li, Sachin Mathur, Carol A. Menard, Paraj Patel, Rebeca Ramos-Zayas, Anne Rietz, Haojing Rong, Baohong Zhang, Michael A. Tones
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0201554

iMapSplice: Alleviating reference bias through personalized RNA-seq alignment
Cited by: 7
Author(s): Xinan Liu, James N. MacLeod, Jinze Liu
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0021915

Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene
Cited by: 31
Author(s): Gabriel Marais, Alan Forrest, Esther Kamau, Jos Käfer, Vincent Daubin, Deborah Charlesworth
Software Mentions: 1
Published: almost 15 years ago

10.1038/s41598-021-95630-2

Transcriptomic, proteomic, and metabolomic analyses identify candidate pathways linking maternal cadmium exposure to altered neurodevelopment and behavior
Cited by: 11
Author(s): Kathleen M Hudson, Emily Shiver, Jianshi Yu, Sanya Mehta, Dereje D. Jima, Maureen A. Kane, Heather B. Patisaul, Michael Cowley
Software Mentions: 1
Published: almost 5 years ago

10.18632/aging.101836

Alternative polyadenylation dependent function of splicing factor SRSF3 contributes to cellular senescence
Cited by: 32
Author(s): Ting Shen, Huan Li, Yifang Song, Li Li, Jinzhong Lin, Gang Wei, Ting Ni
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0215154

Mutational landscape of canine B-cell lymphoma profiled at single nucleotide resolution by RNA-seq
Cited by: 14
Author(s): Diana Giannuzzi, Laura Marconato, Luciano Cascione, S. Comazzi, Ramy Elgendy, Sara Pegolo, Alessio Cecchinato, Francesco Bertoni, Luca Aresu, Serena Ferraresso
Software Mentions: 1
Published: about 7 years ago

10.1186/s12859-018-2203-5

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi
Cited by: 154
Author(s): Jens Keilwagen, Frank Hartung, Michael Paulini, Sven Twardziok, Jan Grau
Software Mentions: 1
Published: about 8 years ago

10.18632/oncotarget.7242

Pinin interacts with C-terminal binding proteins for RNA alternative splicing and epithelial cell identity of human ovarian cancer cells
Cited by: 28
Author(s): Yanli Zhang, Jamie Sui-Lam Kwok, Pui–Wah Choi, Minghua Liu, Junzheng Yang, Margit Singh, Shu‐Kay Ng, William R. Welch, Michael G. Muto, Stephen Kwok Wing Tsui, Stephen P. Sugrue, Ross S. Berkowitz, Shu-Wing Ng
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0135422

Generalization of Auditory Sensory and Cognitive Learning in Typically Developing Children
Cited by: 11
Author(s): Cristina Ferraz Borges Murphy, David R. Moore, Eliane Schochat
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0251107

Statistical inconsistency of the unrooted minimize deep coalescence criterion
Cited by: 1
Author(s): Ayed A. R. Alanzi, J.H. Degnan
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-97087-9

Dectin-2 mediates phagocytosis of Lactobacillus paracasei KW3110 and IL-10 production by macrophages
Cited by: 7
Author(s): Mia Yoshikawa, Shoichi Yamada, Miho Sugamata, Osamu Kanauchi, Yuji Morita
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-021-96854-y

Multi-tissue transcriptome analysis of two Begonia species reveals dynamic patterns of evolution in the chalcone synthase gene family
Cited by: 3
Author(s): Katie Emelianova, Andrea Martínez Martínez, Lucia Campos-Domínguez, Catherine Kidner
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0222512

HaTSPiL: A modular pipeline for high-throughput sequencing data analysis
Cited by: 4
Author(s): Edoardo Morandi, Matteo Cereda, Danny Incarnato, Caterina Parlato, Giulia Basile, Francesca Anselmi, Andrea Lauria, Lisa Marie Simon, Isabelle Laurence Polignano, Francesca Arruga, Silvia Deaglio, Elisa Tirtei, Franca Fagioli, Salvatore Oliviero
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0184365

Characterization of the microDNA through the response to chemotherapeutics in lymphoblastoid cell lines
Cited by: 30
Author(s): Pamela Mehanna, Vincent Gagné, Mathieu Lajoie, Jean-François Spinella, Pascal St-Onge, Daniel Sinnett, Ivan Brukner, Maja Krajinović
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0213177

Drosophila melanogaster tPlus3a and tPlus3b ensure full male fertility by regulating transcription of Y-chromosomal, seminal fluid, and heat shock genes
Cited by: 2
Author(s): Tim Hundertmark, Sabrina Kreutz, Nastasja Merle, Andrea Nist, Boris Lamp, Thorsten Stiewe, Alexander Brehm, Renate Renkawitz‐Pohl, Christina Rathke
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0122420

High Resolution Mapping of Enhancer-Promoter Interactions
Cited by: 3
Author(s): Christopher Reeder, Michael Closser, Huay Mei Poh, Kuljeet Singh Sandhu, Hynek Wichterle, David K. Gifford
Software Mentions: 1
Published: about 11 years ago

10.18632/aging.202296

Mutation in histone deacetylase HDA-3 leads to shortened locomotor healthspan in Caenorhabditis elegans
Cited by: 4
Author(s): Kazuto Kawamura, Ichiro Maruyama
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0219267

Schlafen 3 knockout mice display gender-specific differences in weight gain, food efficiency, and expression of markers of intestinal epithelial differentiation, metabolism, and immune cell function
Cited by: 15
Author(s): Emilie E. Vomhof-DeKrey, Jun Lee, Jack Lansing, Calvin Brown, Diane C. Darland, Marc D. Basson
Software Mentions: 1
Published: about 7 years ago

10.18632/oncotarget.9033

Functional networks of aging markers in the glomeruli of IgA nephropathy: a new therapeutic opportunity
Cited by: 19
Author(s): Hong Jiang, Ludan Liang, Jing Qin, Yingying Lu, Bingjue Li, Yucheng Wang, Ching‐Long Lin, Qin Zhou, Shi Feng, Shun H. Yip, Feng Xu, En Yin Lai, Junwen Wang, Jianghua Chen
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0212193

Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing
Cited by: 20
Author(s): Jérôme Bouquet, Tony Li, Jennifer L. Gardy, Xiaoying Kang, Staci R. Stevens, Jared Stevens, Mark VanNess, Christopher R. Snell, James E. Potts, Ruth R. Miller, Muhammad Morshed, Mark McCabe, Shoshana Parker, Miguel Uyaguari, Patrick Tang, Theodore S. Steiner, Wee‐Shian Chan, Astrid-Marie De Souza, André Mattman, David M. Patrick, Charles Y. Chiu
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0030020

Prognostic Significance and Gene Expression Profiles of p53 Mutations in Microsatellite-Stable Stage III Colorectal Adenocarcinomas
Cited by: 28
Author(s): Venkat R. Katkoori, Chandrakumar Shanmugam, Xiaoqian Jia, Swaroop P. Vitta, Meenakshi Sthanam, Tom Callens, Ludwine Messiaen, Dongquan Chen, Bin Zhang, Harvey L. Bumpers, Temesgen Samuel, Upender Manne
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-019-3088-7

Exploratory analysis of transposable elements expression in the C. elegans early embryo
Cited by: 16
Author(s): Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich, Remo Sanges
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-3234-2

deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes
Cited by: 2
Author(s): Hatice Akarsu, Lisandra Aguilar-Bultet, Laurent Falquet
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-8-125

Detecting microsatellites within genomes: significant variation among algorithms
Cited by: 79
Author(s): Sébastien Leclercq, Éric Rivals, Philippe Jarne
Software Mentions: 1
Published: about 19 years ago

10.1186/s12859-015-0741-7

Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor
Cited by: 3
Author(s): Altan Kara, Martin Vickers, Martin Swain, David E. Whitworth, Narcís Fernández-Fuentes
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pntd.0007053

A longitudinal systems immunologic investigation of acute Zika virus infection in an individual infected while traveling to Caracas, Venezuela
Cited by: 5
Author(s): Aaron F. Carlin, Jianping Wen, Edward A. Vizcarra, Melanie McCauley, Antoine Chaillon, Kevan Akrami, Cheryl Kim, Annie Elong Ngono, Maria Luz Lara-Marquez, Davey M. Smith, Christopher K. Glass, Robert T. Schooley, Chris Benner, Sujan Shresta
Software Mentions: 1
Published: over 7 years ago

10.1155/2017/5202913

Genetic Variability of Exotic Sugarcane Genotypes
Cited by: 6
Author(s): M. N. Alam, Ujjal Kumar Nath, K. M. Rezaul Karim, Mostak Ahmed, R. Y. Mitul
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-7-165

Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae
Cited by: 28
Author(s): Hyunsoo Kim, William Hu, Yuval Kluger
Software Mentions: 1
Published: over 20 years ago

10.3390/s140813759

Confronting Passive and Active Sensors with Non-Gaussian Statistics
Cited by: 34
Author(s): Pablo Rodríguez‐Gonzálvez, Jesús García-Gago, Javier Gómez-Lahoz, Diego González‐Aguilera
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-8-382

XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
Cited by: 139
Author(s): Aaron M. Newman, J. B. Cooper
Software Mentions: 1
Published: over 18 years ago

10.3390/s16122168

A Modified Magnetic Gradient Contraction Based Method for Ferromagnetic Target Localization
Cited by: 25
Author(s): Chen Wang, Xiaojuan Zhang, Xiaodong Qu, Xiaoqing Pan, Guangyou Fang, Luzhao Chen
Software Mentions: 1
Published: over 9 years ago

10.3390/s19183861

Superpixel-Based Temporally Aligned Representation for Video-Based Person Re-Identification
Cited by: 4
Author(s): Changxin Gao, Jin Wang, Leyuan Liu, Jin-Gang Yu, Nong Sang
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pntd.0007637

Pre-operative trichiatic eyelash pattern predicts post-operative trachomatous trichiasis
Cited by: 9
Author(s): Emily W. Gower, Beatriz Muñoz, Saul Rajak, Esmael Habtamu, Sheila K. West, Shannath L. Merbs, Jennifer C. Harding, Wondu Alemayehu, E. Kelly Callahan, Paul M. Emerson, Teshome Gebre, Matthew J. Burton
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12859-015-0654-5

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
Cited by: 122
Author(s): Hani Z. Girgis
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pntd.0002318

Ilheus Virus Isolation in the Pantanal, West-Central Brazil
Cited by: 46
Author(s): Alex Pauvolid‐Corrêa, Joan L. Kenney, Dinair Couto-Lima, Zilca Campos, Hermann G. Schatzmayr, Rita Maria Ribeiro Nogueira, Aaron C. Brault, Nicholas Komar
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0005015

Transcriptomic Study on Ovine Immune Responses to Fasciola hepatica Infection
Cited by: 39
Author(s): Yan Fu, Andréas Lazaros Chryssafidis, John A. Browne, Jack O’Sullivan, Paul A. McGettigan, Grace Mulcahy
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pmed.1002162

Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study
Cited by: 131
Author(s): Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A. Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J. Bouk, Joseph F. Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T. Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal N. Marconett, Ite A. Laird-Offringa, Ian G. Mills, Neil E. Caporaso, Mitchell H. Gail, Angela Cecilia Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J. Chanock, Maria Teresa Landi
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006281

c-Fos Repression by Piwi Regulates Drosophila Ovarian Germline Formation and Tissue Morphogenesis
Cited by: 28
Author(s): Jonathon Klein, Chunxu Qu, Xiaoyang Yang, Yiping Fan, Chunlao Tang, Jamy C. Peng
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12859-018-2436-3

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Cited by: 25
Author(s): Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-020-03593-4

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
Cited by: 5
Author(s): Stefan Niebler, André C. Müller, Thomas Hankeln, Bertil Schmidt
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pgen.1007721

Locus suicide recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues
Cited by: 15
Author(s): Iman Dalloul, François Boyer, Zeinab Dalloul, Amandine Pignarre, Gersende Caron, Thierry Fest, Fabrice Chatonnet, Céline Delaloy, Anne Durandy, Robin Jeannet, Emilie Lereclus, Hend Boutouil, Jean-Claude Aldigier, Sophie Péron, Sandrine Le Noir, Jeanne Cook-Moreau, Michel Cogné
Software Mentions: 1
Published: about 7 years ago

10.1186/2193-1801-3-53

The supporting effects of high luminous conditions on grade 3 oral reading fluency scores
Cited by: 10
Author(s): Michael S. Mott, Daniel H. Robinson, Thea Williams-Black, Susan McClelland
Software Mentions: 1
Published: over 12 years ago

10.1186/s40064-016-2657-8

Formal analysis of imprecise system requirements with Event-B
Cited by: 3
Author(s): Hong Anh Le, Shinichi Nakajima, Ninh Thuan Truong
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1007409

TGFβ signaling limits lineage plasticity in prostate cancer
Cited by: 8
Author(s): Yi Hao, Srikala Raghavan, Karolina Pietrzak, Tiffany A. Melhuish, Yu Han, Stephen D. Turner, Henry F. Frierson, David Wotton
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-020-03869-9

TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification
Cited by: 12
Author(s): Yuchen Tang, Yu Wang, Hua Wang, Miao Li, Linmin Peng, Guochao Wei, Yixing Zhang, Li Jin, Zhibo Gao
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1008460

A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing
Cited by: 17
Author(s): Tao Chen, Bin Zhang, Thomas Ziegenhals, Archana Bairavasundaram Prusty, Sebastian Fröhler, Clemens Grimm, Yuhui Hu, Bernhard Schaefke, Liang Fang, Min Zhang, Nadine Kraemer, Angela M. Kaindl, Utz Fischer, Wei Chen
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-019-2786-5

Ryūtō: network-flow based transcriptome reconstruction
Cited by: 20
Author(s): Thomas Gatter, Peter F. Stadler
Software Mentions: 1
Published: about 7 years ago

10.1016/j.stemcr.2019.09.011

Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories
Cited by: 41
Author(s): Agnieszka D’Antonio‐Chronowska, Maureen D. Donovan, William W. Greenwald, Jennifer P. Nguyen, Kyohei Fujita, Sherin I. Hashem, Hiroko Matsui, Francesca Soncin, Mana M. Parast, Michelle C. Ward, Florence Coulet, Erin N. Smith, Eric Adler, Matteo D’Antonio, Kelly A. Frazer
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1007206

Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC
Cited by: 7
Author(s): Xin Bai, Ji An An Jia, Meng Fang, Shipeng Chen, Xiaotao Liang, Shanfeng Zhu, Shuqin Zhang, Jianfeng Feng, Fengzhu Sun, Chunfang Gao
Software Mentions: 1
Published: over 8 years ago

10.1016/j.stemcr.2020.01.008

Autophagy Reprograms Alveolar Progenitor Cell Metabolism in Response to Lung Injury
Cited by: 28
Author(s): Xue Li, Junping Wu, Xin Sun, Qi Wu, Yue Li, Kuan Li, Qiuyang Zhang, Yu Liu, E. Dale Abel, Huaiyong Chen
Software Mentions: 1
Published: over 6 years ago

10.1002/advs.202004303

Copper Promotes Tumorigenesis by Activating the PDK1‐AKT Oncogenic Pathway in a Copper Transporter 1 Dependent Manner
Cited by: 54
Author(s): Jianping Guo, Ji Cheng, Nana Zheng, Xiaomei Zhang, Xiaoming Dai, Linli Zhang, C. Hu, Xueji Wu, Qiwei Jiang, Depei Wu, Hitoshi Okada, Pier Paolo Pandolfi
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pgen.1007496

Specification of Drosophila neuropeptidergic neurons by the splicing component brr2
Cited by: 3
Author(s): Ignacio Monedero Cobeta, Caroline Bivik Stadler, Li Jin, Peng Yu, Stefan Thor, Jonathan Benito‐Sipos
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1007587

Transcription factor ASCL2 is required for development of the glycogen trophoblast cell lineage
Cited by: 19
Author(s): Aaron B. Bogutz, Rosemary Oh-McGinnis, Karen J. Jacob, Rita Ho-Lau, Ting Gu, Marina Gertsenstein, András Nagy, Louis Lefebvre
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.stemcr.2021.06.013

Hypersensitivity response has negligible impact on Hematopoietic Stem Cells
Cited by: 1
Author(s): Nir Bujanover, Roshina Thapa, Oron Goldstein, Leonid Olender, Omri Sharabi, Michael D. Milsom, Roi Gazit
Software Mentions: 1
Published: almost 5 years ago

10.5713/ajas.19.0097

Analysis of allele-specific expression using RNA-seq of the Korean native pig and Landrace reciprocal cross
Cited by: 3
Author(s): Byeongyong Ahn, Mi Hyun Choi, Joori Yum, In-Cheol Cho, Jin‐Hoi Kim, Chankyu Park
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009320

Lhx6 regulates canonical Wnt signaling to control the fate of mesenchymal progenitor cells during mouse molar root patterning
Cited by: 8
Author(s): Jinzhi He, Junjun Jing, Jifan Feng, Xia Han, Yuan Yuan, Tingwei Guo, Fei Pei, Yuanyuan Ma, Courtney Cho, Thach-Vu Ho, Yang Chai
Software Mentions: 1
Published: over 5 years ago

10.1186/s13287-019-1319-5

The role of insulin as a key regulator of seeding, proliferation, and mRNA transcription of human pluripotent stem cells
Cited by: 6
Author(s): Mohammad Shahbazi, Paige Cundiff, Wenyu Zhou, Philip Lee, Amar Patel, Sunita L. D’Souza, Fahim Abbasi, Thomas Quertermous, Joshua W. Knowles
Software Mentions: 1
Published: almost 7 years ago

10.18632/oncotarget.17765

Intra-tumour molecular heterogeneity of clear cell renal cell carcinoma reveals the diversity of the response to targeted therapies using patient-derived xenograft models
Cited by: 17
Author(s): Bo Hong, Yong Yang, Sheng Guo, Shayiremu Duoerkun, Xiaohu Deng, Fan Chen, Shijun Yu, Wubin Qian, Qi-Xiang Li, Qing Li, Kan Gong, Ning Zhang
Software Mentions: 1
Published: about 9 years ago

10.1186/s12967-021-02837-y

The role of transcriptomic biomarkers of endometrial receptivity in personalized embryo transfer for patients with repeated implantation failure
Cited by: 23
Author(s): Anbang He, Yangyun Zou, Cheng Wan, Jing Zhao, Qiong Zhang, Zhongyuan Yao, Tian Fen, Hong Wu, Xi Huang, Jing Fu, Chunxu Hu, Yue Sun, Lanbo Xiao, Tianli Yang, Zhaojuan Hou, Xin Dong, Sijia Lü, Yanping Li
Software Mentions: 1
Published: about 5 years ago

10.1186/s12967-021-03041-8

Platelet transcriptome profiles provide potential therapeutic targets for elderly acute myelocytic leukemia patients
Cited by: 2
Author(s): Bao Ji-zhang, Xinhua Zhao, Jiahui Lü, Zhaoyang Hu, Minghui Hu, Xiaoxia Hu, Libing Wang, Qi Hu, Wei Sun, Jie Wang, Hailin Chen, Hao Lü, Changgui Li, Jianing Xu, Yongming Zhou, Weiliang Zhu
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pgen.1003714

A Shift to Organismal Stress Resistance in Programmed Cell Death Mutants
Cited by: 36
Author(s): Meredith E. Judy, Ayumi Nakamura, Anne Huang, Harli Grant, Helen McCurdy, Kurt F. Weiberth, Fuying Gao, Giovanni Coppola, Cynthia Kenyon, Aimee W. Kao
Software Mentions: 1
Published: almost 13 years ago

10.1186/s13287-021-02485-5

Divergence in chondrogenic potential between in vitro and in vivo of adipose- and synovial-stem cells from mouse and human
Cited by: 2
Author(s): Ryota Chijimatsu, Shinji Miwa, Gensuke Okamura, Junya Miyahara, Naohiro Tachibana, Hisatoshi Ishikura, Junya Higuchi, Yuji Maenohara, Shinsaku Tsuji, Shin Sameshima, Kentarô Takagi, Keiu Nakazato, Kohei Kawaguchi, Ryota Yamagami, Hiroshi Inui, Shuji Taketomi, Sakae Tanaka, Taku Saito
Software Mentions: 1
Published: almost 5 years ago