10.1186/s12859-021-04120-9

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
Cited by: 15
Author(s): Sagnik Banerjee, Priyanka Bhandary, Margaret R. Woodhouse, Taner Z. Sen, Roger P. Wise, Carson M. Andorf
Software Mentions: 4
Published: over 5 years ago

10.1186/s12936-021-03848-2

MALBoost: a web-based application for gene regulatory network analysis in Plasmodium falciparum
Cited by: 0
Author(s): Roelof van Wyk, Riëtte van Biljon, Lyn-Marié Birkholtz
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-016-1276-2

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Cited by: 87
Author(s): Sergi Sayols, Denise Scherzinger, H. Klein
Software Mentions: 4
Published: almost 10 years ago

10.3389/fcimb.2016.00193

Genome-Wide Transcriptional and Post-transcriptional Regulation of Innate Immune and Defense Responses of Bovine Mammary Gland to Staphylococcus aureus
Cited by: 41
Author(s): Lingzhao Fang, Yali Hou, Jinpeng An, Bingjie Li, Mengyuan Song, Xiao Wang, Peter Sørensen, Yichun Dong, Chao Liu, Yachun Wang, Huabin Zhu, Shengli Zhang, Ying Yu
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-019-2668-x

Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction
Cited by: 21
Author(s): Vu Viet Hoang Pham, Junpeng Zhang, Lin Liu, Buu Truong, Taosheng Xu, Trung Tin Nguyen, Jiuyong Li, Thuc Duy Le
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.5726

Strategies to optimize modeling habitat suitability of<i>Bertholletia excelsa</i>in the Pan‐Amazonia
Cited by: 16
Author(s): Daiana Carolina Monteiro Tourne, Maria Victória Ramos Ballester, Patrick M. A. James, L. G. Martorano, Marcelino Carneiro Guedes, Evert Thomas
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-45364-z

Disease-free monoculture farming by fungus-growing termites
Cited by: 31
Author(s): Saria Otani, Victoria L. Challinor, Nina B. Kreuzenbeck, Sara Kildgaard, Søren Krath Christensen, Louise Lee Munk Larsen, Duur K. Aanen, Silas Anselm Rasmussen, Christine Beemelmanns, Michael Poulsen
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2021.640266

DNA Methylation and Expression Profiles of Whole Blood in Parkinson’s Disease
Cited by: 28
Author(s): Adrienne Henderson, Qi Wang, Bessie Meechoovet, Ashley L. Siniard, Marcus Naymik, Matthew De Both, Matthew J. Huentelman, Richard J. Caselli, Erika Driver‐Dunckley, Travis Dunckley
Software Mentions: 4
Published: about 5 years ago

10.1038/s41437-019-0252-9

Conservation of the genome-wide recombination rate in white-footed mice
Cited by: 8
Author(s): April Peterson, Nathan D. Miller, Bret A. Payseur
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-019-6142-y

DNA methylation profiles capturing breast cancer heterogeneity
Cited by: 19
Author(s): Xiao Chen, Jianying Zhang, Xiaofeng Dai
Software Mentions: 4
Published: over 6 years ago

10.1080/19336896.2021.1924557

Transcriptomic analysis of zebrafish prion protein mutants supports conserved cross-species function of the cellular prion protein
Cited by: 1
Author(s): Niall M. Pollock, Patricia L.A. Leighton, Gavin J. Neil, W. Ted Allison
Software Mentions: 4
Published: over 5 years ago

10.3389/fphys.2019.00917

Integrated Analysis of DNA Methylation and Biochemical/Metabolic Parameter During the Long-Term Isolation Environment
Cited by: 2
Author(s): Quan Yuan, Feng Liang, Yuexing Zhu, Ying Chen, Xu Zi, Fang Du, Ke Lv, Hailong Chen, Lei Qu, Ruifeng Xu, Hongyu Zhang, Jianghui Xiong, Yinghui Li
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-25604-4

Transcriptomic integration of D4R and MOR signaling in the rat caudate putamen
Cited by: 8
Author(s): Alejandra Valderrama-Carvajal, Haritz Irizar, Belén Gago, Haritz Jiménez-Urbieta, Kjell Fuxé, María C. Rodríguez‐Oroz, David Otaegui, Alicia Rivera
Software Mentions: 4
Published: about 8 years ago

10.1186/gb-2014-15-2-r30

Using high-density DNA methylation arrays to profile copy number alterations
Cited by: 109
Author(s): Andrew Feber, Paul Guilhamon, Matthias Lechner, Tim R. Fenton, Gareth A. Wilson, Christina Thirlwell, Tiffany Morris, Adrienne M. Flanagan, Andrew E. Teschendorff, John D. Kelly, Stephan Beck
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pbio.1002112

Natural Selection Constrains Neutral Diversity across A Wide Range of Species
Cited by: 270
Author(s): Russell Corbett-Detig, Daniel L. Hartl, Timothy B. Sackton
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0180647

Assessment of circulating copy number variant detection for cancer screening
Cited by: 30
Author(s): Bhuvan Molparia, Eshaan Nichani, Ali Torkamani
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0111637

miR-27 Negatively Regulates Pluripotency-Associated Genes in Human Embryonal Carcinoma Cells
Cited by: 14
Author(s): Heiko Fuchs, Matthias Theuser, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: over 11 years ago

10.1186/s12866-020-02052-7

MALDI-TOF mass spectrometry for sub-typing of Streptococcus pneumoniae
Cited by: 6
Author(s): Sivkheng Kann, Sena Sao, Chanleakhena Phoeung, Youlet By, Juliet E. Bryant, Florence Komurian-Pradel, Vonthanak Saphonn, Monidarin Chou, Paul Turner
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-32930-0

Social and nutritional factors shape larval aggregation, foraging, and body mass in a polyphagous fly
Cited by: 17
Author(s): Juliano Morimoto, Binh Nguyen, Shabnam Tarahi Tabrizi, Fleur Ponton, Phillip W. Taylor
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12903-018-0591-6

Predicting oral malodour based on the microbiota in saliva samples using a deep learning approach
Cited by: 24
Author(s): Yoshio Nakano, Nao Suzuki, Fumiyuki Kuwata
Software Mentions: 4
Published: almost 8 years ago

10.3389/fgene.2021.630215

Comparing Statistical Tests for Differential Network Analysis of Gene Modules
Cited by: 2
Author(s): Jaron Arbet, Yaxu Zhuang, Elizabeth Litkowski, Laura Saba, Katerina Kechris
Software Mentions: 4
Published: about 5 years ago

10.1002/advs.202003504

Cytosolic Delivery of Thiolated Neoantigen Nano‐Vaccine Combined with Immune Checkpoint Blockade to Boost Anti‐Cancer T Cell Immunity
Cited by: 28
Author(s): Da Zhang, Zongming Lin, Ming Wu, Zhixiong Cai, Youshi Zheng, Lei He, Zhenli Li, Jie Zhou, Liqin Sun, Geng Chen, Yongyi Zeng, Juan Li, Jingfeng Liu, Huanghao Yang, Xiaolong Liu
Software Mentions: 4
Published: over 5 years ago

10.3390/biomedicines9020215

Reclassification of Kidney Clear Cell Carcinoma Based on Immune Cell Gene-Related DNA CpG Pairs
Cited by: 1
Author(s): Qizhan Luo, Thomas-Alexander Vögeli
Software Mentions: 4
Published: over 5 years ago

10.1002/2211-5463.12747

Prediction of a miRNA‐mRNA functional synergistic network for cervical squamous cell carcinoma
Cited by: 5
Author(s): Dan Sun, Lu Han, Rui Cao, Huali Wang, Jiyong Jiang, Yue Deng, Xiaohui Yu
Software Mentions: 4
Published: over 6 years ago

10.1093/bib/bbaa014

Regression on imperfect class labels derived by unsupervised clustering
Cited by: 1
Author(s): Rasmus Froberg Brøndum, Thomas Yssing Michaelsen, Martin Bøgsted
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.203030

Downregulation of USP18 reduces tumor-infiltrating activated dendritic cells in extranodal diffuse large B cell lymphoma patients
Cited by: 5
Author(s): Chong Zhao, Runzhi Huang, Zhiwei Zeng, Siqi Yang, Wei Lü, Jiali Liu, Yanyu Wei, Hong Guo, Yanjie Zhang, Penghui Yan, Zongqiang Huang, Jun Shi
Software Mentions: 4
Published: about 5 years ago

10.3390/ma10121365

Optimization and Characterization of Paper-Made Surface Enhanced Raman Scattering (SERS) Substrates with Au and Ag NPs for Quantitative Analysis
Cited by: 27
Author(s): Silvia Dalla Marta, Chiara Novara, Fabrizio Giorgis, Alois Bonifacio, Valter Sergo
Software Mentions: 4
Published: over 8 years ago

10.18632/aging.202558

ENAM gene associated with T classification and inhibits proliferation in renal clear cell carcinoma
Cited by: 8
Author(s): Xiaohan Ren, Shengjie Liang, Yang Li, Yisheng Ji, Lin Li, Chao Qin, Kai Fang
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2019.00473

Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease
Cited by: 44
Author(s): William L. King, Nachshon Siboni, Nathan L. R. Williams, Tim Kahlke, Khue Viet Nguyen, Cheryl Jenkins, Michael Dove, Wayne A. O’Connor, Justin R. Seymour, Maurizio Labbate
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2019.02474

Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment
Cited by: 7
Author(s): Yufan Wu, Peng Xing, Shuang‐Jiang Liu, Qinglong L. Wu
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2014.00352

Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus
Cited by: 5
Author(s): Jinyuan Yan, Michael D. Bradley, Jannice Friedman, Roy D. Welch
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pcbi.1007496

Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer
Cited by: 15
Author(s): Miranda D. Stobbe, Gian Andri Thun, Andrea Diéguez-Docampo, Meritxell Oliva, Justin P. Whalley, Emanuele Raineri, Marta Gut
Software Mentions: 4
Published: over 6 years ago

10.3389/fphys.2021.707116

Transcriptional Time Course After Rotator Cuff Tear
Cited by: 3
Author(s): Laura S Vasquez-Bolanos, Michael C. Gibbons, Severin Ruoss, Isabella T. Wu, Mario Vargas-Vila, Sydnee A Hyman, Mary C. Esparza, Donald C. Fithian, Joseph R. Lane, Anshuman Singh, Chanond A. Nasamran, Kathleen M. Fisch, Samuel R. Ward
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2017.02499

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium
Cited by: 36
Author(s): Elham Karimi, Maria João Ramos, Jorge M. S. Gonçalves, Joana R. Xavier, Margarida Reis, Rodrigo Costa
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2018.00945

Lactation Stage-Dependency of the Sow Milk Microbiota
Cited by: 47
Author(s): Wei Chen, Jiandui Mi, Ning Lv, Jin‐Ming Gao, Jun Cheng, Ruizhu Wu, Jingyun Ma, Tian Lan, Xindi Liao
Software Mentions: 4
Published: about 8 years ago

10.3389/fmicb.2018.00149

Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses
Cited by: 81
Author(s): Michael Hemkemeyer, Anja B. Dohrmann, Bent T. Christensen, Christoph C. Tebbe
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0023628

Rhythmic Diel Pattern of Gene Expression in Juvenile Maize Leaf
Cited by: 12
Author(s): Maciej Jończyk, Alicja Sobkowiak, Paweł Siedlecki, Przemysław Biecek, Joanna Trzcińska-Danielewicz, Jerzy Tiuryn, Jan Fronk, Paweł Sowiński
Software Mentions: 4
Published: almost 15 years ago

10.1038/s41598-019-40495-9

Differential gene expression induced by Verteporfin in endometrial cancer cells
Cited by: 8
Author(s): Lisa Bang, Venkata Ramesh Dasari, Dokyoon Kim, Radhika Gogoi
Software Mentions: 4
Published: over 7 years ago

10.1186/s12935-020-1116-3

Multi-dimensional omics characterization in glioblastoma identifies the purity-associated pattern and prognostic gene signatures
Cited by: 12
Author(s): Yi Xiong, Zujian Xiong, Hang Cao, Chang Li, Siyi Wanggou, Xuejun Li
Software Mentions: 4
Published: over 6 years ago

10.1002/cam4.3388

A methylomics‐associated nomogram predicts recurrence‐free survival of thyroid papillary carcinoma
Cited by: 7
Author(s): Hengyu Chen, Xianxiong Ma, Ming Yang, Mengyi Wang, Lei Li, Tao Huang
Software Mentions: 4
Published: almost 6 years ago

10.3389/pore.2021.601693

Identification of Biomarkers Related to Immune Cell Infiltration in Hepatocellular Carcinoma Using Gene Co-Expression Network
Cited by: 2
Author(s): Wanbang Zhou, Yiyang Chen, Ruixing Luo, Zifan Li, Guanwei Jiang, Xi Ou
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0084955

Clustering Gene Expression Regulators: New Approach to Disease Subtyping
Cited by: 30
Author(s): Mikhail A. Pyatnitskiy, Ilya Mazo, Maria Shkrob, Elena Schwartz, Ekaterina Kotelnikova
Software Mentions: 4
Published: over 12 years ago

10.3389/fmicb.2018.00699

Tillage Changes Vertical Distribution of Soil Bacterial and Fungal Communities
Cited by: 112
Author(s): Run‐Cang Sun, Wenyan Li, Wenxu Dong, Yinping Tian, Chunsheng Hu, Binbin Liu
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-42560-9

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats
Cited by: 22
Author(s): Diana D. Moreno-Santillán, Carlos Machaín-Williams, Georgina Hernández-Montes, Jorge Ortega
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-47046-2

SMAC, a computational system to link literature, biomedical and expression data
Cited by: 2
Author(s): S. Pirro, Emanuela Gadaleta, Andrea Galgani, Vittorio Colizzi, Claude Chelala
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0192704

Immune checkpoint inhibitor PD-1 pathway is down-regulated in synovium at various stages of rheumatoid arthritis disease progression
Cited by: 71
Author(s): Yanxia Guo, Alice M. Walsh, Mary Canavan, Mihir D. Wechalekar, Suzanne Cole, Xiaoli Yin, Brian Scott, Matthew J. Loza, Carl Orr, Trudy McGarry, Michèle Bombardieri, Frances Humby, Susanna Proudman, Costantino Pitzalis, Malcolm D. Smith, Joshua R. Friedman, I.E. Anderson, Loui Madakamutil, Douglas J. Veale, Ursula Fearon, Sunil Nagpal
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-45432-4

Neighbourhood socioeconomic deprivation and allostatic load: a multi-cohort study
Cited by: 28
Author(s): Ana Isabel Ribeiro, Sílvia Fraga, Michelle Kelly-Irving, Cyrille Delpierre, Silvia Stringhini, Mika Kivimäki, Stéphane Joost, Idris Guessous, Martina Gandini, Paolo Víneis, Henrique Barros
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-019-46018-w

Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost
Cited by: 66
Author(s): Jorge Domínguez, Manuel Aira, Allison R. Kolbe, María Gómez-Brandòn, Marcos Pérez‐Losada
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0229687

Expanding radiogenic strontium isotope baseline data for central Mexican paleomobility studies
Cited by: 16
Author(s): Sofía I. Pacheco‐Forés, Gwyneth W. Gordon, Kelly J. Knudson
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-021-07615-0

Identification of the conserved long non-coding RNAs in myogenesis
Cited by: 0
Author(s): Anupam Bhattacharya, Simang Champramary, Tanya Tripathi, Debajit Thakur, Ilya Ioshikhes, Satyendra Kumar Singh, Soumyadeep Nandi
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0251502

“Know your epidemic, know your response”: Epidemiological assessment of the substance use disorder crisis in the United States
Cited by: 8
Author(s): Andrés Hernández, Minxuan Lan, Neil J. MacKinnon, Adam J. Branscum, Diego F. Cuadros
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2013-14-5-r42

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance
Cited by: 174
Author(s): David Martino, Yuk Jing Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M. Craig
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pcbi.1007390

Sequence specificity despite intrinsic disorder: How a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
Cited by: 11
Author(s): Ruchi Lohia, Reza Salari, Grace Brannigan
Software Mentions: 4
Published: almost 7 years ago

10.1002/ctm2.364

Clinical and functional significance of a novel ferroptosis‐related prognosis signature in lung adenocarcinoma
Cited by: 9
Author(s): Ziqi Wang, Jie Diao, Xingru Zhao, Zhiwei Xu, Xiaoju Zhang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41597-019-0205-4

The Personal Genome Project-UK, an open access resource of human multi-omics data
Cited by: 18
Author(s): Olga Chervova, Lucía Conde, José Afonso Guerra-Assunção, Ismail Moghul, A. D. B. Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan Tian, Vitaly Voloshin, Tiago S. Jesus, Rifat Hamoudi, Javier Herrero, Stephan Beck
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-017-16520-0

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis
Cited by: 130
Author(s): Thomas P. Quinn, Mark F. Richardson, David Lovell, Tamsyn M. Crowley
Software Mentions: 4
Published: over 8 years ago

10.1002/hep.26414

Proteome‐wide analyses of human hepatocytes during differentiation and dedifferentiation
Cited by: 108
Author(s): Cliff Rowe, Dave T. Gerrard, Roz Jenkins, Andrew Berry, Kesta Durkin, Lars Sundström, Chris Goldring, B. Kevin Park, Neil R. Kitteringham, Karen Piper Hanley, Neil A. Hanley
Software Mentions: 4
Published: about 13 years ago

10.1155/2021/3766659

Multiomics Differences in Lung Squamous Cell Carcinoma Patients with High Radiosensitivity Index Compared with Those with Low Radiosensitivity Index
Cited by: 2
Author(s): You Wei Du, Shengtao Yuan, Xibing Zhuang, Qi Zhang, Tiankui Qiao
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2019.00235

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs
Cited by: 49
Author(s): Cristiane P. G. Calixto, Nikoleta A. Τzioutziou, Allan B. James, Csaba Hornyik, Wenbin Guo, Runxuan Zhang, Hugh G. Nimmo, John W. Brown
Software Mentions: 4
Published: over 7 years ago

10.1136/jitc-2020-001610

Neoadjuvant chemoradiation alters biomarkers of anticancer immunotherapy responses in locally advanced rectal cancer
Cited by: 17
Author(s): Incheol Seo, Hye Won Lee, Sang Jun Byun, Jee Young Park, Hyeonji Min, Sung Hwan Lee, Ju-Seog Lee, Shin Kim, Sung Uk Bae
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1005698

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
Cited by: 19
Author(s): Maike Kathrin Aurich, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.53127

Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity
Cited by: 23
Author(s): Nairita Maitra, Chi He, Heidi M. Blank, Mitsuhiro Tsuchiya, Birgit Schilling, Matt Kaeberlein, Rodolfo Aramayo, Brian K. Kennedy, Michael Polymenis
Software Mentions: 4
Published: about 6 years ago

10.3390/insects9040185

Differential Gene Expression in Red Imported Fire Ant (Solenopsis invicta) (Hymenoptera: Formicidae) Larval and Pupal Stages
Cited by: 11
Author(s): Margaret L. Allen, Joshua H. Rhoades, Michael E. Sparks, Michael J. Grodowitz
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-018-4946-9

Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower
Cited by: 61
Author(s): Chen Jiang, Xiaohui Tang, Chaoxiang Ren, Bin Wei, Yingliang Wu, Qinghua Wu, Jin Pei
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2018.00049

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen
Cited by: 28
Author(s): Coraline R. Praz, Fabrizio Menardo, Mark D. Robinson, Marion Müller, Thomas Wicker, Salim Bourras, Beat Keller
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2017.01430

Transcriptomic Analysis Reveals Candidate Genes for Female Sterility in Pomegranate Flowers
Cited by: 32
Author(s): Lina Chen, Jie Zhang, Haoxian Li, Juan Niu, Hui Xue, Beibei Liu, Qi Wang, Xiang Luo, Fuhong Zhang, Dan Zhao, Shangyin Cao
Software Mentions: 4
Published: almost 9 years ago

10.3389/fimmu.2021.724541

Scoring System Based on RNA Modification Writer-Related Genes to Predict Overall Survival and Therapeutic Response in Bladder Cancer
Cited by: 3
Author(s): Pu Zhang, Zijian Liu, Decai Wang, Yunxue Li, Yifei Xing, Yajun Xiao
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmolb.2021.633951

Identification of Epithelial-Mesenchymal Transition-Related lncRNAs that Associated With the Prognosis and Immune Microenvironment in Colorectal Cancer
Cited by: 6
Author(s): Chuan Liu, Chuan Hu, Jianyi Li, Liqing Jiang, Chengliang Zhao
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.541479

Identification and Validation of Novel Biomarkers for Diagnosis and Prognosis of Hepatocellular Carcinoma
Cited by: 26
Author(s): Xiaoyi Hu, Mingyang Bao, Jiacheng Huang, Lin Zhou, Shusen Zheng
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0212473

Nasal microbial composition and chronic otitis media with effusion: A case-control study
Cited by: 18
Author(s): Rebecca E. Walker, Caroline Walker, Carlos A. Camargo, Jim Bartley, David Flint, John M. D. Thompson, Edwin A. Mitchell
Software Mentions: 4
Published: over 7 years ago

10.3389/fonc.2021.724655

Super-Enhancer Induced IL-20RA Promotes Proliferation/Metastasis and Immune Evasion in Colorectal Cancer
Cited by: 12
Author(s): Du Yu, Xiao Yang, Jia Wei Lin, Zichao Cao, Chenghao Lu, Zheyu Yang, Minhua Zheng, Ruijun Pan, Wei Cai
Software Mentions: 4
Published: about 5 years ago

10.3389/fsurg.2021.717084

Identification of a Novel Signature Predicting Overall Survival in Head and Neck Squamous Cell Carcinoma
Cited by: 4
Author(s): Haige Zheng, Huixian Liu, Yumin Lu, Li Hengguo
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmed.2021.654635

Multi-Omics Integrative Analysis Uncovers Molecular Subtypes and mRNAs as Therapeutic Targets for Liver Cancer
Cited by: 4
Author(s): Yi Shen, Wei Xiong, Qi Gu, Qin Zhang, Yue Jia, Changsong Liu, Duan Wang
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.114.013508

<i>De Novo</i> Assembly and Annotation of the Transcriptome of the Agricultural Weed <i>Ipomoea purpurea</i> Uncovers Gene Expression Changes Associated with Herbicide Resistance
Cited by: 41
Author(s): Trent A Leslie, Regina S. Baucom
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2164-14-331

Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish
Cited by: 32
Author(s): Håvard Aanes, Oľga Østrup, Ingrid S. Andersen, Lars Fredrik Moen, Sinnakaruppan Mathavan, Philippe Collas, Peter Aleström
Software Mentions: 4
Published: about 13 years ago

10.1038/s41598-020-59549-4

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii
Cited by: 7
Author(s): Katrine Højholt Iversen, Louise Rasmussen, Kosai Al-Nakeeb, José Juan Almagro Armenteros, Christian Salgård Jensen, Rimtas Dargis, Oksana Lukjancenko, Ulrik Stenz Justesen, Claus Moser, Flemming Schønning Rosenvinge, Xiaohui Chen Nielsen, Jens Jørgen Christensen, Simon Rasmussen
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.118.200880

Activation of the Bile Acid Pathway and No Observed Antimicrobial Peptide Sequences in the Skin of a Poison Frog
Cited by: 1
Author(s): Megan L. Civitello, Robert D. Denton, Michael Zasloff, John H. Malone
Software Mentions: 4
Published: over 7 years ago

10.1534/g3.119.400757

Machine Learning Enables High-Throughput Phenotyping for Analyses of the Genetic Architecture of Bulliform Cell Patterning in Maize
Cited by: 9
Author(s): Pengfei Qiao, Lin Meng, Miguel Vasquez, Susanne Matschi, James Chamness, Matheus Baseggio, Laurie G. Smith, Mert R. Sabuncu, Michael A. Gore, Michael J. Scanlon
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2377-11-33

Health-related quality of life in adults with epilepsy: the effect of age, age at onset and duration of epilepsy in a multicentre Italian study
Cited by: 41
Author(s): Valeria Edefonti, Francesca Bravi, Katherine Turner, Ettore Beghi, Maria Paola Canevini, Monica Ferraroni, A. Piazzini
Software Mentions: 4
Published: over 15 years ago

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in <i>Arabidopsis thaliana</i>
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-90607-7

Defining the combined stress response in wild Arachis
Cited by: 12
Author(s): Ana Paula Zotta Mota, Ana Cristina Miranda Brasileiro, Bruna Vidigal, Thais Nicolini Oliveira, Andressa da Cunha Quintana Martins, Mario Alfredo de Passos Saraiva, Ana Cláudia Guerra Araújo, Roberto Coiti Togawa, Maria Fátima Grossi-de-Sá, P. M. Guimarães
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-3691-9

Normalized long read RNA sequencing in chicken reveals transcriptome complexity similar to human
Cited by: 106
Author(s): Richard Kuo, Elizabeth Tseng, Lél Eöry, Ian R. Paton, Alan Archibald, David W. Burt
Software Mentions: 4
Published: over 9 years ago

10.1128/mBio.03348-19

An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during <i>Salmonella</i> Infection
Cited by: 21
Author(s): Leon N. Schulte, Matthias Schweinlin, Alexander J. Westermann, Harshavardhan Janga, Sara Correia Santos, Silke Appenzeller, Heike Walles, Jörg Vogel, Marco Metzger
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0248320

Plant structural diversity alters sediment retention on and underneath herbaceous vegetation in a flume experiment
Cited by: 6
Author(s): Lena Kretz, Katinka Koll, Carolin Seele‐Dilbat, Fons van der Plas, Alexandra Weigelt, Christian Wirth
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0118808

Prediction of Chemical Respiratory Sensitizers Using GARD, a Novel In Vitro Assay Based on a Genomic Biomarker Signature
Cited by: 31
Author(s): Andy Forreryd, Henrik Johansson, Ann-Sofie Albrekt, Carl Borrebaeck, Malin Lindstedt
Software Mentions: 4
Published: over 11 years ago

10.1038/s41380-020-0767-8

AP-1 controls the p11-dependent antidepressant response
Cited by: 25
Author(s): Revathy U. Chottekalapanda, Salina Kalik, Jodi Gresack, Alyssa Ayala, Melanie Gao, Wei Wang, Sarah J. Meller, Ammar Aly, Anne Schaefer, Paul Greengard
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-94045-3

Landscape transformations produce favorable roosting conditions for turkey vultures and black vultures
Cited by: 9
Author(s): J. E. Hill, Kenneth F. Kellner, Bryan M. Kluever, Michael L. Avery, John S. Humphrey, Eric A. Tillman, Travis L. DeVault, Jerrold L. Belant
Software Mentions: 4
Published: about 5 years ago

10.1534/g3.113.009431

gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images
Cited by: 99
Author(s): Omar Wagih, Leopold Parts
Software Mentions: 4
Published: over 12 years ago

10.3390/metabo11040232

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
Cited by: 7
Author(s): Alina Renz, Lina Widerspick, Andreas Dräger
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.00431

MetaPhat: Detecting and Decomposing Multivariate Associations From Univariate Genome-Wide Association Statistics
Cited by: 10
Author(s): Jake Lin, Rubina Tabassum, Samuli Ripatti, Matti Pirinen
Software Mentions: 4
Published: about 6 years ago

10.15252/msb.20177656

Toward an integrated map of genetic interactions in cancer cells
Cited by: 65
Author(s): Benedikt Rauscher, Florian Heigwer, Luisa Henkel, Thomas Hielscher, Oksana Voloshanenko, Michael Boutros
Software Mentions: 4
Published: over 8 years ago

10.1093/bioinformatics/btw390

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Cited by: 106
Author(s): David Dao, Adam Fraser, Jia‐Jang Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter
Software Mentions: 4
Published: about 10 years ago

10.3389/fpls.2016.01145

Evolution of Epiphytism and Fruit Traits Act Unevenly on the Diversification of the Species-Rich Genus Peperomia (Piperaceae)
Cited by: 9
Author(s): Lena Frenzke, Paul Goetghebeur, Christoph Neinhuis, Marie‐Stéphanie Samain, Stefan Wanke
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.ppat.1006302

Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Cited by: 87
Author(s): Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M. Barros, J. G. Baldwin, A Mortazavi, Adler R. Dillman
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.ppat.1009552

Intraspecific variation in immune gene expression and heritable symbiont density
Cited by: 8
Author(s): Holly L. Nichols, Elliott B. Goldstein, Omid Saleh Ziabari, Benjamin J. Parker
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-015-0857-9

Methods for the integration of multi-omics data: mathematical aspects
Cited by: 272
Author(s): Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone Castellani, Luciano Milanesi
Software Mentions: 4
Published: over 10 years ago

10.1155/2021/6656622

Profiles of Innate Immune Cell Infiltration and Related Core Genes in Psoriasis
Cited by: 11
Author(s): Xiaoting Gong, Wei Wang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-021-04110-x

Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis
Cited by: 0
Author(s): Xueyuan Cao, Stan Pounds
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-015-2277-7

Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome
Cited by: 42
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma T. Steenkmap, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: over 10 years ago