cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.7150/jca.51321

AURKA and FAM83A are prognostic biomarkers and correlated with Tumor-infiltrating Lymphocytes in smoking related Lung Adenocarcinoma
Cited by: 7
Author(s): Mengyu Zhang, Huo Chen, Yingxiao Jiang, Jianyu Liu, Yi-Can Yang, Yunhong Yin, Yi-Qing Qu
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.51173

Identification of a Prognostic Signature Model with Tumor Microenvironment for predicting Disease-free Survival after Radical Prostatectomy
Cited by: 6
Author(s): Hao Zhao, Xuening Zhang, Zhan Shi, Bingxin Guo, Wenli Zhang, Kun He, Xueqi Hu, Songhe Shi
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.8541

Rhizosphere bacterial and fungal communities during the growth of Angelica sinensis seedlings cultivated in an Alpine uncultivated meadow soil
Cited by: 12
Author(s): An Zhigang, Fengjing Guo, Yuan Chen, Gang Bai, Zhengjun Chen
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-90226-2

Refinement of 16S rRNA gene analysis for low biomass biospecimens
Cited by: 8
Author(s): Remy Villette, Gaëlle Autaa, Sophie Hind, Johanna B. Holm, Alicia Moreno-Sabater, Martin Larsen
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.7844

Effects of research disturbance on nest survival in a mixed colony of waterbirds
Cited by: 4
Author(s): Matthieu Guillemain, Hugo Carré, Lisa Gili
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-02193-2

Multitrophic Effects of Belowground Parasitoid Learning
Cited by: 17
Author(s): Denis S. Willett, Hans T. Alborn, Lukasz L. Stelinski
Software Mentions: 4
Published: about 9 years ago

10.7717/peerj.5022

Relationship betweenAcropora milleporajuvenile fluorescence and composition of newly establishedSymbiodiniumassemblage
Cited by: 4
Author(s): Kate M. Quigley, Marie E. Strader, Mikhail V. Matz
Software Mentions: 4
Published: about 8 years ago

10.2196/jmir.6342

Methods for Evaluating Respondent Attrition in Web-Based Surveys
Cited by: 61
Author(s): Camille J. Hochheimer, Roy Sabo, Alex H. Krist, Teresa Day, John Cyrus, Steven H. Woolf
Software Mentions: 4
Published: over 9 years ago

10.1186/1472-6947-11-31

PKreport: report generation for checking population pharmacokinetic model assumptions
Cited by: 6
Author(s): Xiaoyong Sun, Jun Li
Software Mentions: 4
Published: about 15 years ago

10.3389/fgene.2019.01036

Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase
Cited by: 5
Author(s): Sandra Grossi Gava, Naiara Clemente Tavares, Franco H. Falcone, Guilherme Oliveira, Marina Moraes Mourão
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-021-90088-8

Targeted neuromodulation of pelvic floor nerves in aging and multiparous rabbits improves continence
Cited by: 3
Author(s): Ana G. Hernández-Reynoso, Dora Luz Corona‐Quintanilla, Kenia López-García, Ana A. Horbovetz, Francisco Castelán, Philippe E. Zimmern, Margarita Martı́nez–Gómez, Mario I. Romero-Ortega
Software Mentions: 4
Published: about 5 years ago

10.1038/s41437-020-0348-2

The influence of a priori grouping on inference of genetic clusters: simulation study and literature review of the DAPC method
Cited by: 65
Author(s): Joshua M. Miller, Catherine I. Cullingham, Rhiannon Peery
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-15-91

Differential meta-analysis of RNA-seq data from multiple studies
Cited by: 88
Author(s): Andrea Rau, Guillemette Marot, Florence Jaffrézic
Software Mentions: 4
Published: about 12 years ago

10.1016/j.heliyon.2021.e07748

Massive surge of mRNA expression of clonal B-cell receptor in patients with COVID-19
Cited by: 4
Author(s): Yohei Funakoshi, Goh Ohji, Kimikazu Yakushijin, Kei Ebisawa, Yu Arakawa, Jun Saegusa, Hidenari Matsumoto, Tatsuya Imanishi, Eriko Fukuda, Takaji Matsutani, Yasuko Mori, Kentaro Iwata, Hironobu Minami
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12920-020-00757-2

Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma
Cited by: 40
Author(s): Arash Poursheikhani, Mohammad Reza Abbaszadegan, Negin Nokhandani, Mohammad Amin Kerachian
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2164-14-675

Efficient and accurate whole genome assembly and methylome profiling of E. coli
Cited by: 40
Author(s): Jason Powers, Victor Weigman, Jenny Shu, John Pufky, Donald Cox, Patrick Hurban
Software Mentions: 4
Published: over 13 years ago

10.3389/fgene.2020.00796

Genome-Wide Profiling of Alternative Splicing Signature Reveals Prognostic Predictor for Esophageal Carcinoma
Cited by: 5
Author(s): Jian-Rong Sun, Chen-Fan Kong, Yanni Lou, Ran Yu, Xiang-Ke Qu, Liqun Jia
Software Mentions: 4
Published: almost 6 years ago

10.3390/plants9081019

High pH Stress Affects Root Morphology and Nutritional Status of Hydroponically Grown Rhododendron (Rhododendron spp.)
Cited by: 5
Author(s): Ashley J. Turner, Camila I. Arzola, Gerardo H. Nunez
Software Mentions: 4
Published: almost 6 years ago

10.3389/fmicb.2020.01721

Alpine Snow Algae Microbiome Diversity in the Coast Range of British Columbia
Cited by: 19
Author(s): Kurt M. Yakimovich, Casey B. Engstrom, Lynne M. Quarmby
Software Mentions: 4
Published: almost 6 years ago

10.1080/20002297.2021.1946316

Microbial characteristics across different tongue coating types in a healthy population
Cited by: 5
Author(s): Hairong Chen, Qingwei Li, Min Li, Sheng Liu, Chensi Yao, Zixiong Wang, Zhixin Zhao, Ping Liu, Fan Yang, Xinjian Li, Jun Wang, Yi-Xin Zeng, Xiaolin Tong
Software Mentions: 4
Published: over 5 years ago

10.1186/s12920-021-00954-7

Identification of genes and pathways involved in malignant pleural mesothelioma using bioinformatics methods
Cited by: 3
Author(s): Xingsheng Liu, Kun Qian, Gaojun Lu, Peng Chen, Yi Zhang
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-89607-4

Viral load, not food availability or temperature, predicts colony longevity in an invasive eusocial wasp with plastic life history
Cited by: 7
Author(s): Kevin J. Loope, Erin E. Wilson Rankin
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.2003862

Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice
Cited by: 290
Author(s): Joseph Edwards, Christian Santos‐Medellín, Zachary Liechty, Bao‐Anh Thi Nguyen, Eugene Lurie, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pbio.3000374

Tagger—A Swiss army knife for multiomics to dissect cell type–specific mechanisms of gene expression in mice
Cited by: 11
Author(s): Lech Kaczmarczyk, V. Bansal, Ashish Rajput, Raza-Ur Rahman, Wiesław Krzyżak, Joachim Degen, Stefanie Poll, Martin Fuhrmann, Stefan Bonn, Walker S. Jackson
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pbio.3001107

Assessment of transparency indicators across the biomedical literature: How open is open?
Cited by: 62
Author(s): Stylianos Serghiou, Despina G. Contopoulos‐Ioannidis, Kevin W. Boyack, Nico Riedel, John R. Wallach, John P. A. Ioannidis
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2021.654657

Discovery and Verification of an Immune-Related Gene Pairs Signature for Predicting Prognosis in Head and Neck Squamous Cell Carcinoma
Cited by: 0
Author(s): Jiarong He, Xinqi Fang, Mingming Han
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.3000849

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age
Cited by: 203
Author(s): Nicole A P Lieberman, Vikas Peddu, Hong Xie, Lasata Shrestha, Meei Li Huang, Megan Mears, Maria N.B. Cajimat, Dennis A. Bente, Pei Yong Shi, Francesca T. Bovier, Pavitra Roychoudhury, Keith R. Jerome, Anne Moscona, Matteo Porotto, Alexander L. Greninger
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pbio.3000214

Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana
Cited by: 31
Author(s): François Vasseur, Louise Fouqueau, Dominique de Vienne, Thibault Nidelet, Cyrille Violle, Detlef Weigel
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-021-04235-z

Putative markers for the detection of early-stage bladder cancer selected by urine metabolomics
Cited by: 11
Author(s): Jia You Lin, Bao Rong Juo, Yu Hsuan Yeh, Shu Hsuan Fu, Yi Ting Chen, Chien Lun Chen, Kun Wu
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2018.01607

Comparison of Microbiota in Patients Treated by Surgery or Chemotherapy by 16S rRNA Sequencing Reveals Potential Biomarkers for Colorectal Cancer Therapy
Cited by: 69
Author(s): Xingming Deng, Zhuofei Li, Li Guan, Bei Li, Xinhan Jin, Guoqing Lyu
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2018.01161

Detection of the Entomopathogenic Fungus Beauveria bassiana in the Rhizosphere of Wound-Stressed Zea mays Plants
Cited by: 33
Author(s): Aimee C. McKinnon, Travis R. Glare, Hayley J. Ridgway, Artemio Mendoza‐Mendoza, Andrew Holyoake, William Godsoe, Jennifer L. Bufford
Software Mentions: 4
Published: about 8 years ago

10.1007/s00432-019-03078-9

Transcriptome analysis reveals overlap in fusion genes in a phase I clinical cohort of TNBC and HGSOC patients treated with buparlisib and olaparib
Cited by: 4
Author(s): Julia Eismann, Yujing J. Heng, Johannes M. Waldschmidt, Ioannis S. Vlachos, Kathryn P. Gray, Ursula A. Matulonis, Panagiotis A. Konstantinopoulos, Charles J. Murphy, Sheida Nabavi, Gerburg M. Wulf
Software Mentions: 4
Published: over 6 years ago

10.1007/s00432-021-03557-y

Are there sex differences among colorectal cancer patients in treatment and survival? A Swiss cohort study
Cited by: 1
Author(s): Manuela Limam, Katarina L. Matthes, Giulia Pestoni, Eleftheria Michalopoulou, Leonhard Held, Silvia Dehler, Dimitri Korol, Sabine Rohrmann
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.203184

The circadian clock is associated with prognosis and immune infiltration in stomach adenocarcinoma
Cited by: 13
Author(s): Zhihao Huang, Aoxiao He, Jiakun Wang, Hongmei Lü, Rongguiyi Zhang, Linquan Wu, Qian Feng
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.3001230

Adipose triglyceride lipase protects renal cell endocytosis in a Drosophila dietary model of chronic kidney disease
Cited by: 23
Author(s): Aleksandra Lubojemska, M. Irina Stefana, Sebastian Sorge, Andrew P. Bailey, Lena Lampe, Azumi Yoshimura, Alana Burrell, Lucy Collinson, Alex P. Gould
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2019.00994

Bacterial Community Diversity and Screening of Growth-Affecting Bacteria From Isochrysis galbana Following Antibiotic Treatment
Cited by: 7
Author(s): Jiasheng Cao, Z.-P. Kong, Yufan Zhang, Ting Ling, Jilin Xu, Kai Liao, Chengxu Zhou, Xiaojun Yan
Software Mentions: 4
Published: about 7 years ago

10.1186/s12920-020-0682-5

A pan-cancer study of class-3 semaphorins as therapeutic targets in cancer
Cited by: 37
Author(s): Xiaoli Zhang, Brett Klamer, Jin Li, Soledad Fernández, Lang Li
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pbio.3000358

Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen
Cited by: 30
Author(s): Teresa R. O’Meara, Matthew J. O’Meara, Elizabeth J. Polvi, Mohammad Reza Pourhaghighi, Sean D. Liston, Zhen‐Yuan Lin, Amanda O. Veri, Andrew Emili, Anne‐Claude Gingras, Leah E. Cowen
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-89366-2

Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes
Cited by: 9
Author(s): Cecília Ártico Banho, Vincent Mérel, Thiago Y. Oliveira, Claudia M. A. Carareto, Cristina Vieira
Software Mentions: 4
Published: about 5 years ago

10.1002/ajh.25994

The prognostic value of additional copies of <scp>1q21</scp> in multiple myeloma depends on the primary genetic event
Cited by: 20
Author(s): Maurus Locher, Michael Steurer, Emina Jukic, Markus A. Keller, Friedrich Fresser, Carmen Ruepp, Ewald Wöll, Irmgard Verdorfer, Günther Gastl, Wolfgang Willenbacher, Roman Weger, David Nachbaur, Dominik Wolf, Eberhard Gunsilius, Johannes Zschocke, Normann Steiner
Software Mentions: 4
Published: almost 6 years ago

10.1080/19490976.2021.1875797

Early life environmental exposures have a minor impact on the gut ecosystem following a natural birth
Cited by: 6
Author(s): Nishat Tasnim, Candice Quin, S K Gill, Chunping Dai, Miranda M. Hart, Deanna L. Gibson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1002533

Quality of Computationally Inferred Gene Ontology Annotations
Cited by: 107
Author(s): Nives Škunca, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 4
Published: about 14 years ago

10.1136/gutjnl-2016-313681

A novel prognostic model for transplant-free survival in primary sclerosing cholangitis
Cited by: 74
Author(s): E M de Vries, Junfeng Wang, Kate D. Williamson, Mariska Leeflang, Kirsten Boonstra, Rinse K. Weersma, Ulrich Beuers, Roger W. Chapman, Ronald B. Geskus, Cyriel Y. Ponsioen
Software Mentions: 4
Published: almost 9 years ago

10.5334/gh.347

Health Education about Rheumatic Heart Disease: A Community-Based Cluster Randomized Trial
Cited by: 4
Author(s): Kaciane K.B. Oliveira, Bruno Ramos Nascimento, Andrea Beaton, Maria Carmo P. Nunes, José Luiz P. Silva, Lara C Rabelo, Márcia M. Barbosa, Carolina Soares Viana de Oliveira, Mariana D.O. Mata, Waydder Antônio A. Costa, Andréa Franco Pereira, Craig Sable, Antônio Luiz Pinho Ribeiro
Software Mentions: 4
Published: over 6 years ago

10.1186/s12968-017-0387-x

A novel multiparametric imaging approach to acute myocarditis using T2-mapping and CMR feature tracking
Cited by: 30
Author(s): Bettina Baeßler, Melanie Treutlein, Frank Schaarschmidt, Christian Stehning, Bernhard Schnackenburg, Guido Michels, David Maintz, Alexander C. Bunck
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pcbi.1009144

PEDF, a pleiotropic WTC-LI biomarker: Machine learning biomarker identification and validation
Cited by: 5
Author(s): George Crowley, James Kim, Sophia Kwon, Rachel Lam, David J. Prezant, Mengling Liu, Anna Nolan
Software Mentions: 4
Published: almost 5 years ago

10.1111/geb.13197

Simulating forest resilience: A review
Cited by: 41
Author(s): Katharina Albrich, Werner Rammer, Monica G. Turner, Zak Ratajczak, Kristin H. Braziunas, Winslow D. Hansen, Rupert Seidl
Software Mentions: 4
Published: over 5 years ago

10.1083/jcb.201711048

A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo
Cited by: 54
Author(s): David Bending, Paz Prieto Martín, Alina Paduraru, Catherine Ducker, Erik Marzaganov, Marie Laviron, Satsuki Kitano, Hitoshi Miyachi, Tessa Crompton, M. Ono
Software Mentions: 4
Published: about 8 years ago

10.3389/fgene.2021.745277

Chromobox Homolog 8 (CBX8) in Human Tumor Carcinogenesis and Prognosis: A Pancancer Analysis Using Multiple Databases
Cited by: 4
Author(s): Dongjie Shi, Lei Ao, Hua Yu, Yongzhi Xia, Juan Li, Wenjie Zhong, Haijian Xia
Software Mentions: 4
Published: almost 5 years ago

10.1002/gch2.202100002

Formulation and Characterization of Formaldehyde‐Free Chemically Modified Bone‐Based Adhesive for Lignocellulosic Composite Products
Cited by: 5
Author(s): Nazrul Islam, Afroza Akter Liza, Mst. Liza Khatun, Omar Faruk, Atanu Kumar Das, Moutusi Dey, Jahurul Haque Akanda
Software Mentions: 4
Published: about 5 years ago

10.1002/gch2.202000044

Preparation and Evaluation of Rice Bran‐Modified Urea Formaldehyde as Environmental Friendly Wood Adhesive
Cited by: 5
Author(s): Nazrul Islam, Omar Faruk, Nasim Rana, Atanu Kumar Das, Ahsan Habib
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1003031

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
Cited by: 255
Author(s): Lauren M. Bragg, Graham N. Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson
Software Mentions: 4
Published: about 13 years ago

10.1038/s41598-021-88363-9

Transcriptional signatures in prefrontal cortex confer vulnerability versus resilience to food and cocaine addiction-like behavior
Cited by: 11
Author(s): Mohit Navandar, Elena Martín‐García, Rafaël Maldonado, Beat Lutz, Susanne Gerber, Iñigo Ruı́z de Azúa
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2371-3

Integrating omics datasets with the OmicsPLS package
Cited by: 48
Author(s): Said el Bouhaddani, Hae‐Won Uh, Geurt Jongbloed, Caroline Hayward, Lucija Klarić, Szymon M. Kiełbasa, Jeanine J. Houwing‐Duistermaat
Software Mentions: 4
Published: over 7 years ago

10.1093/gigascience/giz102

Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field
Cited by: 13
Author(s): Lovely Mae F Lawas, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Ellen Zuther, Dirk K. Hincha
Software Mentions: 4
Published: almost 7 years ago

10.3389/fgene.2021.700489

Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds
Cited by: 4
Author(s): Sofia Michailidou, Athanasios Ι. Gelasakis, Georgios Banos, G. Arsenos, Anagnostis Argiriou
Software Mentions: 4
Published: almost 5 years ago

10.1093/gigascience/giz052

Accumulating computational resource usage of genomic data analysis workflow to optimize cloud computing instance selection
Cited by: 8
Author(s): Toshio Ohta, Tomoya Tanjo, Osamu Ogasawara
Software Mentions: 4
Published: about 7 years ago

10.3389/fmicb.2017.01943

An Investigation into Rumen Fungal and Protozoal Diversity in Three Rumen Fractions, during High-Fiber or Grain-Induced Sub-Acute Ruminal Acidosis Conditions, with or without Active Dry Yeast Supplementation
Cited by: 38
Author(s): Suzanne L. Ishaq, Ousama AlZahal, Nicola Walker, B.W. McBride
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-11-45

NeatMap - non-clustering heat map alternatives in R
Cited by: 77
Author(s): Satwik Rajaram, Yoshitsugu Oono
Software Mentions: 4
Published: over 16 years ago

10.1007/s00401-020-02217-8

Extrinsic immune cell-derived, but not intrinsic oligodendroglial factors contribute to oligodendroglial differentiation block in multiple sclerosis
Cited by: 47
Author(s): Laura Starost, Maren Lindner, Martin Herold, Yu Xu, Hannes C.A. Drexler, Katharina Heß, Marc Ehrlich, Linda Ottoboni, Francesca Ruffini, Martin Stehling, Albrecht Röpke, Christian Thomas, Hans R. Schöler, Jack Antel, Jürgen Winkler, Gianvito Martino, Luisa Klotz, Tanja Kuhlmann
Software Mentions: 4
Published: almost 6 years ago

10.1093/gigascience/giy140

NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
Cited by: 79
Author(s): Szymon T. Calus, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2019.00232

Central and Peripheral Changes in FOS Expression in Schizophrenia Based on Genome-Wide Gene Expression
Cited by: 10
Author(s): Jing Huang, Fangkun Liu, Bolun Wang, Hui Tang, Ziwei Teng, Lehua Li, Yan Qiu, Haishan Wu, Jindong Chen
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-019-3201-y

Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
Cited by: 4
Author(s): Christopher Grace, Martin Farrall, Hugh Watkins, Anuj Goel
Software Mentions: 4
Published: over 6 years ago

10.1007/s12079-020-00575-2

Spermatozoa induce transcriptomic alterations in bovine oviductal epithelial cells prior to initial contact
Cited by: 7
Author(s): Qurat Ul Ain Reshi, Janeli Viil, James Ord, Freddy Lättekivi, Kasun Godakumara, Mohammad Mehedi Hasan, Monika Nõmm, Kersti Jääger, Agne Velthut-Meikas, Ülle Jaakma, Andres Salumets, Alireza Fazeli
Software Mentions: 4
Published: almost 6 years ago

10.1093/gigascience/giy034

Improving the annotation of the Heterorhabditis bacteriophora genome
Cited by: 15
Author(s): Florence McLean, Duncan Berger, Dominik R. Laetsch, Hillel T. Schwartz, Mark Blaxter
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1007357

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti
Cited by: 48
Author(s): George C. diCenzo, Alex B. Benedict, Marco Fondi, Graham C. Walker, Turlough M. Finan, Alessio Mengoni, Joel S. Griffitts
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1002604

Gene Reactivation by 5-Aza-2′-Deoxycytidine–Induced Demethylation Requires SRCAP–Mediated H2A.Z Insertion to Establish Nucleosome Depleted Regions
Cited by: 52
Author(s): Xiaojing Yang, Houtan Noushmehr, Han Han, Claudia Andreu-Vieyra, Gangning Liang, Peter A. Jones
Software Mentions: 4
Published: about 14 years ago

10.1371/journal.pgen.1008385

Distinct genetic variation and heterogeneity of the Iranian population
Cited by: 30
Author(s): Zohreh Mehrjoo, Zohreh Fattahi, Maryam Beheshtian, Marzieh Mohseni, Hossein Poustchi, Fariba Ardalani, Khadijeh Jalalvand, Sanaz Arzhangi, Zahra Mohammadi, Shahrouz Khoshbakht, Farid Najafi, Pooneh Nikuei, Mohammad Haddadi, Elham Zohrehvand, Morteza Oladnabi, Akbar Mohammadzadeh, Mandana Hadi Jafari, Tara Akhtarkhavari, Ehsan Shamsi Gooshki, Ali-Akbar Haghdoost, Reza Najafipour, Lisa‐Marie Niestroj, Barbara Helwing, Yasmina Gossmann, Mohammad Reza Toliat, Reza Malekzadeh, Peter Nürnberg, Kimia Kahrizi, Hossein Najmabadi, Michael Nothnagel
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1007978

Fast and flexible linear mixed models for genome-wide genetics
Cited by: 46
Author(s): Daniel E. Runcie, Lorin Crawford
Software Mentions: 4
Published: over 7 years ago

10.1111/jcmm.14045

Inhibition of miR-148a-3p resists hepatocellular carcinoma progress of hepatitis C virus infection through suppressingc-Junand MAPK pathway
Cited by: 27
Author(s): Yibin Deng, Jianchu Wang, Meijin Huang, Guidan Xu, Wujun Wei, Houji Qin
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-88516-w

Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB
Cited by: 11
Author(s): Roza Berhanu Lemma, Marit Ledsaak, Bettina M. Fuglerud, Geir Kjetil Sandve, Ragnhild Eskeland, Odd S. Gabrielsen
Software Mentions: 4
Published: about 5 years ago

10.1093/gigascience/gix058

Connections between the human gut microbiome and gestational diabetes mellitus
Cited by: 178
Author(s): Yashu Kuang, Jinhua Lu, Shenghui Li, Junhua Li, Mingyang Yuan, Jianxing He, Niannian Chen, Wan-Qing Xiao, Shi‐Li Shen, Lan Qiu, Yongming Wu, Cui-Yue Hu, Yanyan Wu, Weidong Li, Qiaozhu Chen, Hong‐Wen Deng, Christopher J. Papasian, Huimin Xia, Xiu Qiu
Software Mentions: 4
Published: almost 9 years ago

10.1186/s13742-016-0150-5

The preprocessed connectomes project repository of manually corrected skull-stripped T1-weighted anatomical MRI data
Cited by: 35
Author(s): Benjamin Puccio, James Pooley, John Pellman, Elise C. Taverna, R. Cameron Craddock
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1008348

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon
Cited by: 35
Author(s): Quentin Rougemont, Jean‐Sébastien Moore, Thibault Leroy, Éric Normandeau, Eric B. Rondeau, Ruth E. Withler, Donald M. Van Doornik, Penelope A. Crane, Kerry A. Naish, John Carlos Garza, Terry D. Beacham, Ben F. Koop, Louis Bernatchez
Software Mentions: 4
Published: almost 6 years ago

10.1016/j.gpb.2020.06.004

The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells
Cited by: 4
Author(s): Monika Hiller, M Geissler, George M.C. Janssen, Peter A. van Veelen, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008326

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome
Cited by: 31
Author(s): Paja Sijacic, Dylan H Holder, Marko Bajic, Roger B. Deal
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1004137

Accurate and Robust Genomic Prediction of Celiac Disease Using Statistical Learning
Cited by: 97
Author(s): Gad Abraham, Jason A. Tye‐Din, Oneil G. Bhalala, Adam Kowalczyk, Justin Zobel, Michael Inouye
Software Mentions: 4
Published: over 12 years ago

10.5808/GI.2020.18.1.e6

Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples
Cited by: 2
Author(s): Sonali P. Barwe, Anilkumar Gopalakrisnapillai, Nitin Mahajan, Todd E. Druley, E. Anders Kolb, Erin L. Crowgey
Software Mentions: 4
Published: about 6 years ago

10.1186/s13073-021-00948-1

An epigenetic and transcriptomic signature of immune tolerance in human monocytes through multi-omics integration
Cited by: 9
Author(s): Xanthe Brands, Bastiaan W. Haak, Augustijn M. Klarenbeek, Joe Butler, Fabrice Uhel, Wanhai Qin, Natasja A. Otto, Marja E. Jakobs, Daniel Faber, René Lutter, W. Joost Wiersinga, Tom van der Poll, Brendon P. Scicluna
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-86821-y

Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach
Cited by: 3
Author(s): Momoko Hamano, Seitaro Nomura, Midori Iida, Issei Komuro, Yoshihiro Yamanishi
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1007807

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay
Cited by: 79
Author(s): Michael J. Roach, Daniel L. Johnson, Jöerg Bohlmann, H. J. J. Van Vuuren, Steven J.M. Jones, Isak S. Pretorius, Simon A. Schmidt, Anthony R. Borneman
Software Mentions: 4
Published: over 7 years ago

10.1186/s13073-021-00826-w

Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trial
Cited by: 16
Author(s): Seung Tae Kim, K. Jason, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Jeeyun Lee
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-87588-y

In situ novel environment assay reveals acoustic exploration as a repeatable behavioral response in migratory bats
Cited by: 3
Author(s): Theresa Schabacker, Oliver Lindecke, Sofia Rizzi, Lara Marggraf, Gunārs Pētersons, Christian C. Voigt, Lysanne Snijders
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1008076

Heterogeneous pathway activation and drug response modelled in colorectal-tumor-derived 3D cultures
Cited by: 57
Author(s): Dirk Schumacher, Geoffroy Andrieux, Karsten Boehnke, Marlen Keil, Alessandra Silvestri, Maxine Silvestrov, Ulrich Keilholz, Johannes Haybaeck, Gerrit Erdmann, Christoph Sachse, Markus F. Templin, Jens Hoffmann, Melanie Boerries, Reinhold Schäfer, Christian Regenbrecht
Software Mentions: 4
Published: about 7 years ago

10.1186/s13073-020-00824-4

The identification of novel immunogenic antigens as potential Shigella vaccine components
Cited by: 8
Author(s): Ruklanthi de Alwis, Li Liang, Omid Taghavian, Emma Werner, Trang Nguyen Hoang Thu, Vu Thuy Duong, D. Huw Davies, Philip L. Felgner, Stephen Baker
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-021-07646-7

Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzzii
Cited by: 18
Author(s): Victoria A. Ingham, Faye Brown, Hilary Ranson
Software Mentions: 4
Published: about 5 years ago

10.1111/jcmm.15505

Asiaticoside might attenuate bleomycin‐induced pulmonary fibrosis by activating cAMP and Rap1 signalling pathway assisted by A2AR
Cited by: 18
Author(s): Jing Luo, Ting Zhang, Ce Zhu, Junwei Sun, Wenjing Zhu, Wenxiu Ai, Xiaoying Huang, Xiaobing Wang
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pmed.1002338

Prehospital immune responses and development of multiple organ dysfunction syndrome following traumatic injury: A prospective cohort study
Cited by: 89
Author(s): Jon Hazeldine, David N Naumann, Emma Toman, David Davies, Jonathan Bishop, Zhangjie Su, Peter Hampson, Robert J. Dinsdale, Nicholas Crombie, Niharika Arora Duggal, Paul Harrison, Antonio Belli, Janet M. Lord
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pmed.1003656

SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants
Cited by: 100
Author(s): Marc Charabati, Alberto Ospina Stella, Anupriya Aggarwal, D.R. Darley, Deepti Pilli, Daniele Vitale, Vera Merheb, Fiona X Z Lee, Philip Cunningham, G. J. Walker, Christina Fichter, David A. Brown, William D. Rawlinson, Sonia R Isaacs, Vennila Mathivanan, Markus Hoffmann, Stefan Pöhlman, Ohan Mazigi, Daniel Christ, Dominic E. Dwyer, Rebecca Rockett, Vitali Sintchenko, Veronica C. Hoad, David O. Irving, Gregory J. Dore, Iain B Gosbell, Anthony D. Kelleher, Gail V. Matthews, Fabienne Brilot, Stuart Turville
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-017-01126-3

Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments
Cited by: 106
Author(s): Arghya Mukherjee, Bobby Chettri, James S. Langpoklakpam, Pijush Basak, Aravind Prasad, Ashis K. Mukherjee, Maitree Bhattacharyya, Arvind Singh, Dhrubajyoti Chattopadhyay
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-021-87069-2

White matter abnormalities in adults with bipolar disorder type-II and unipolar depression
Cited by: 6
Author(s): Anna Manelis, Adriane M. Soehner, Yaroslav Halchenko, Skye Satz, Rachel Ragozzino, Mora M. Lucero, Holly A. Swartz, Mary L. Phillips, Amelia Versace
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pmed.1002722

Airway obstruction and bronchial reactivity from age 1 month until 13 years in children with asthma: A prospective birth cohort study
Cited by: 33
Author(s): Henrik Wegener Hallas, Bo Chawes, Morten Arendt Rasmussen, Lambang Arianto, Jakob Stokholm, Klaus Bønnelykke, Hans Bisgaard
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pntd.0006236

Forecasting the spatial and seasonal dynamic of Aedes albopictus oviposition activity in Albania and Balkan countries
Cited by: 18
Author(s): Clément Tisseuil, Enkelejda Velo, Silvia Bino, Përparim Kadriaj, Kujtim Mersini, Ada Shukullari, Artan Simaku, Elton Rogozi, Beniamino Caputo, Els Ducheyne, Alessandra della Torre, Paul L. Reiter, Marius Gilbert
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pntd.0007332

Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil
Cited by: 19
Author(s): Laís Ceschini Machado, Mariana C. Morais-Sobral, Túlio de Lima Campos, Mylena Ribeiro Pereira, Maria de Fátima Pessoa Militão de Albuquerque, Clément Gilbert, Rafael Freitas Oliveira Franca, Gabriel Luz Wallau
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pntd.0009357

Mark-release-recapture of male Aedes aegypti (Diptera: Culicidae): Use of rhodamine B to estimate movement, mating and population parameters in preparation for an incompatible male program
Cited by: 10
Author(s): Brendan J Trewin, Dan Pagendam, Brian J. Johnson, Chris Paton, Nigel Snoad, Scott A. Ritchie, Kyran M. Staunton, Bradley J. White, Sara N. Mitchell, Nigel W. Beebe
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.59390

Gap junction-mediated glycinergic inhibition ensures precise temporal patterning in vocal behavior
Cited by: 8
Author(s): Boris P. Chagnaud, Jonathan T. Perelmuter, Paul M. Forlano, Andrew H. Bass
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0007921

Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection
Cited by: 18
Author(s): Amin Addetia, Lauren C. Tantalo, Michelle J. Lin, Hong Xie, Meei‐Li Huang, Christina M. Marra, Alexander L. Greninger
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2020.01092

Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics
Cited by: 8
Author(s): Balázs Brankovics, A.D. van Diepeningen, G. Sybren de Hoog, Theo A. J. van der Lee, C. Waalwijk
Software Mentions: 4
Published: about 6 years ago

10.1111/jcmm.16133

Identification of Smad3‐related transcriptomes in type‐2 diabetic nephropathy by whole transcriptome RNA sequencing
Cited by: 3
Author(s): Qin Zhou, Hong-Hong Guo, Chaolun Yu, Xiao‐Ru Huang, Lijun Liang, Puhua Zhang, Jia-Kuo Yu, Jizhou Zhang, Ting‐Fung Chan, Rong Ma, Hui‐Yao Lan
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-86504-8

Identification and external validation of a prognostic signature associated with DNA repair genes in gastric cancer
Cited by: 5
Author(s): Shimin Chen, Wenbo Liu, Haojun Yu
Software Mentions: 4
Published: about 5 years ago

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