10.1038/s41598-017-05949-y
Enhanced differential expression statistics for data-independent acquisition proteomicsCited by: 29
Author(s): Tomi Suomi, Laura L. Elo
Software Mentions: 4
Published: about 9 years ago
10.3390/microorganisms8111663
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected GutCited by: 11
Author(s): Hiroki Nishiyama, Hisashi Endo, Romain Blanc-Mathieu, Hiroyuki Ogata
Software Mentions: 4
Published: over 5 years ago
10.1097/MD.0000000000023153
Identification of candidate biomarkers correlated with the pathogenesis and prognosis of breast cancer via integrated bioinformatics analysisCited by: 8
Author(s): Shuyu Liu, Xinkui Liu, Jiarui Wu, Wei Zhou, Mengwei Ni, Ziqi Meng, Shanshan Jia, Jingyuan Zhang, Siyu Guo, Shan Lu, Yingfei Li
Software Mentions: 4
Published: over 5 years ago
10.1289/EHP172
A Systematic Comparison of Linear Regression–Based Statistical Methods to Assess Exposome-Health AssociationsCited by: 143
Author(s): Lydiane Agier, Lützen Portengen, Marc Chadeau‐Hyam, Xavier Basagaña, Lise Giorgis-Allemand, Valérie Siroux, Oliver Robinson, Jelle Vlaanderen, Juan R. González, Mark Nieuwenhuijsen, Paolo Víneis, Martine Vrijheid, Rémy Slama, Roel Vermeulen
Software Mentions: 4
Published: over 9 years ago
10.3389/fonc.2020.613333
Construction of Bone Metastasis-Specific Regulation Network Based on Prognostic Stemness-Related Signatures in Breast Invasive CarcinomaCited by: 2
Author(s): Runzhi Huang, Zhenyu Li, Jiayao Zhang, Zhiwei Zeng, Jiaqi Zhang, Mingxiao Li, Siqao Wang, Shuyuan Xian, Yuna Xue, Xi Chen, Jie Li, Wing Yan Elizabeth Cheng, Bin Wang, Penghui Yan, Daoke Yang, Zongqiang Huang
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0245756
Birds of a feather moult together: Differences in moulting distribution of four species of storm-petrelsCited by: 4
Author(s): Anne N. M. A. Ausems, Grzegorz Skrzypek, Katarzyna Wojczulanis‐Jakubas, Dariusz Jakubas
Software Mentions: 4
Published: over 5 years ago
10.1038/s41597-019-0263-7
The Empusa code generator and its application to GBOL, an extendable ontology for genome annotationCited by: 9
Author(s): Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vítor A. P. Martins dos Santos, Peter J. Schaap, María Suárez-Diez
Software Mentions: 4
Published: over 6 years ago
10.1007/s11356-019-05689-8
Acute effect of daily fine particulate matter pollution on cerebrovascular mortality in Shanghai, China: a population-based time series studyCited by: 12
Author(s): Khadija Akter Leepe, Mei Li, Xin Fang, Ayako Hiyoshi, Yang Cao
Software Mentions: 4
Published: about 7 years ago
10.1186/s12864-020-06789-3
Distinctions between sex and time in patterns of DNA methylation across pubertyCited by: 11
Author(s): Sarah R. Moore, Kathryn L. Humphreys, Natalie L. Colich, Elena Goetz Davis, David Lin, Julia L. MacIsaac, Michæl S. Kobor, Ian H. Gotlib
Software Mentions: 4
Published: about 6 years ago
10.1186/1471-2105-12-61
A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelinesCited by: 10
Author(s): Marcin Cieślik, Cameron Mura
Software Mentions: 4
Published: over 15 years ago
10.3389/fgene.2021.628192
KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-β Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan PigsCited by: 7
Author(s): Tao Wang, Yuanyuan Guo, Shengwei Liu, Chaoxin Zhang, Tongyan Cui, Kun Ding, Peng Wang, Xibiao Wang, Zhipeng Wang
Software Mentions: 4
Published: over 5 years ago
10.1007/s00259-020-04814-x
Individual brain metabolic connectome indicator based on Kullback-Leibler Divergence Similarity Estimation predicts progression from mild cognitive impairment to Alzheimer’s dementiaCited by: 45
Author(s): Min Wang, Jiehui Jiang, Zhuangzhi Yan, Ian Alberts, Jingjie Ge, Huiwei Zhang, Chuantao Zuo, Jin‐Tai Yu, Axel Rominger, Kuangyu Shi, Alzheimer’s Disease Neuroimaging Initiative
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-018-22629-7
A Lachnospiraceae-dominated bacterial signature in the fecal microbiota of HIV-infected individuals from Colombia, South AmericaCited by: 33
Author(s): Homero San‐Juan‐Vergara, Eduardo Zurek, Nadim J. Ajami, Christian Mogollon, Mario Peña, Iván Portnoy, Jorge I. Vélez, Christian Cadena-Cruz, Yirys Díaz-Olmos, Leidy Hurtado-Gómez, Silvana Sanchez-Sit, Danitza Hernández, Irina Urruchurtu, Pierina Di-Ruggiero, Ella Guardo-García, Nury Torres, Oscar M. Vidal, Diego Viasus, Joseph F. Petrosino, Guillermo Cervantes-Acosta
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-018-35230-9
Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin womenCited by: 35
Author(s): Lara R. Dugas, Beatriz Peñalver Bernabé, Medha Priyadarshini, Na Fei, Seo Jin Park, Laquita Brown, Jacob Plange‐Rhule, David E. Nelson, Evelyn Toh, Xiang Gao, Qunfeng Dong, Jun Sun, Stephanie Kliethermes, Neil Gottel, Amy Luke, Jack A. Gilbert, Brian T. Layden
Software Mentions: 4
Published: over 7 years ago
10.1371/journal.pone.0243532
Captivated by thought: “Sticky” thinking leaves traces of perceptual decoupling in task-evoked pupil sizeCited by: 3
Author(s): Stefan Huijser, Mathanja Verkaik, Marieke K. van Vugt, Niels Taatgen
Software Mentions: 4
Published: over 5 years ago
10.3390/ijms21175990
Peripheral Cytokine Levels Differ by HPV Status and Change Treatment-Dependently in Patients with Head and Neck Squamous Cell CarcinomaCited by: 14
Author(s): D Mytilineos, Jasmin Ezić, Adrian von Witzleben, Joannis Mytilineos, Ramin Lotfi, Daniel E. Fürst, Chrysanthi Tsamadou, Marie‐Nicole Theodoraki, Angelika Oster, Gunnar Völkel, Hans A. Kestler, Cornelia Brunner, Patrick J. Schuler, Johannes Doescher, Thomas Hoffmann, Simon Laban
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pcbi.1002753
Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence DataCited by: 44
Author(s): Art F. Y. Poon, Luke C. Swenson, Evelien M. Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B. van 't Wout, P. Richard Harrigan
Software Mentions: 4
Published: over 13 years ago
10.3390/nu10050576
Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science ProjectCited by: 92
Author(s): Natalia Klimenko, Alexander V. Tyakht, Anna Popenko, Anatoly S. Vasiliev, Ilya Altukhov, Dimitry D Ischenko, Tatiana I. Shashkova, Daria Efimova, Dimitri A. Nikogosov, Dmitrii A. Osipenko, Sergey Musienko, Kseniya S. Selezneva, Ancha Baranova, Alexander Kurilshikov, Stepan V. Toshchakov, Aleksei A. Korzhenkov, Nazar I. Samarov, Margarita Shevchenko, A.V. Tepliuk, Dmitry Alexeev
Software Mentions: 4
Published: about 8 years ago
10.1007/s00330-020-07624-9
A PET/CT nomogram incorporating SUVmax and CT radiomics for preoperative nodal staging in non-small cell lung cancerCited by: 20
Author(s): Yunming Xie, Hongguang Zhao, Yan Guo, Fanyang Meng, Xiangchun Liu, Yiying Zhang, Xiaochen Huai, Qianting Wong, Yu Fu, Huimao Zhang
Software Mentions: 4
Published: over 5 years ago
10.3389/fphar.2021.678256
Dysregulated lncRNAs are Involved in the Progress of Sepsis by Constructing Regulatory Networks in Whole Blood CellsCited by: 5
Author(s): Yanwei Cheng, Xue Cao, Jiange Zhang, Dong Chen, Juan Zhu, Lijun Xu, Lijie Qin
Software Mentions: 4
Published: almost 5 years ago
10.1038/s41598-018-23746-z
Local oceanographic variability influences the performance of juvenile abalone under climate changeCited by: 26
Author(s): Charles A. Boch, Fiorenza Micheli, Maha W. Alnajjar, Stephen G. Monismith, Jody M. Beers, Juan Carlos Bonilla, Antonio Espinoza, Leonardo Vázquez‐Vera, C. Brock Woodson
Software Mentions: 4
Published: over 8 years ago
10.3389/fonc.2020.560229
A Molecular Subtype Model for Liver HBV-Related Hepatocellular Carcinoma Patients Based on Immune-Related GenesCited by: 5
Author(s): Qiyao Zhang, Xiao Yu, Qingyuan Zheng, Yuting He, Wenzhi Guo
Software Mentions: 4
Published: almost 6 years ago
10.1186/1471-2164-11-50
Integrating multiple genome annotation databases improves the interpretation of microarray gene expression dataCited by: 17
Author(s): Jun Yin, Sarah McLoughlin, Ian B. Jeffery, Antonino Glaviano, Breandán N. Kennedy, Desmond G. Higgins
Software Mentions: 4
Published: over 16 years ago
10.1371/journal.pntd.0009062
Exploring the influence of different habitats and their volatile chemistry in modulating sand fly population structure in a leishmaniasis endemic foci, KenyaCited by: 2
Author(s): Iman B. Hassaballa, Baldwyn Torto, Catherine L. Sole, David P. Tchouassi
Software Mentions: 4
Published: over 5 years ago
10.1186/s40303-016-0017-9
αT-catenin in restricted brain cell types and its potential connection to autismCited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: about 10 years ago
10.1186/s13040-017-0149-1
Genetically improved BarraCUDACited by: 7
Author(s): William B. Langdon, Brian Y.H. Lam
Software Mentions: 4
Published: almost 9 years ago
10.7554/eLife.53237
Rapid sex-specific adaptation to high temperature in DrosophilaCited by: 20
Author(s): Sheng‐Kai Hsu, Ana Marija Jakšić, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schlötterer
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0070387
Link between Epigenomic Alterations and Genome-Wide Aberrant Transcriptional Response to Allergen in Dendritic Cells Conveying Maternal Asthma RiskCited by: 31
Author(s): Lyudmila Mikhaylova, Yiming Zhang, Lester Kobzik, Alexey V. Fedulov
Software Mentions: 4
Published: almost 13 years ago
10.1038/s41598-017-11327-5
Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpeaCited by: 26
Author(s): Vikash Singh, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Software Mentions: 4
Published: almost 9 years ago
10.1111/jcmm.14779
Four transcription profile–based models identify novel prognostic signatures in oesophageal cancerCited by: 9
Author(s): Tongyan Liu, Panqi Fang, Chencheng Han, Zhongliang Ma, Weizhang Xu, Wenjia Xia, Jingwen Hu, Yongming Xu, Lin Xu, Rong Yin, Siwei Wang, Qin Zhang
Software Mentions: 4
Published: over 6 years ago
10.3390/ijms22041811
Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial GenomesCited by: 15
Author(s): Liina Kinkar, Robin B. Gasser, Bonnie L. Webster, David Rollinson, D. Timothy J. Littlewood, Bill C.H. Chang, Andreas J. Stroehlein, Pasi K. Korhonen, Neil D. Young
Software Mentions: 4
Published: over 5 years ago
10.3389/fpsyg.2019.00124
Toward a New Approach to Cross-Cultural Distinctiveness and Typicality of Human Faces: The Cross-Group Typicality/ Distinctiveness MetricCited by: 12
Author(s): Karel Kleisner, Šimon Pokorný, S. Adil Sarıbay
Software Mentions: 4
Published: over 7 years ago
10.1038/s41598-020-66475-y
Wave exposure reduces herbivory in post-disturbed reefs by filtering species composition, abundance and behaviour of key fish herbivoresCited by: 10
Author(s): Rucha Karkarey, Pooja Rathod, Rohan Arthur, Shreya Yadav, Anne Heloise Theo, Teresa Alcoverro
Software Mentions: 4
Published: about 6 years ago
10.7554/eLife.21052
Embryonic origin of adult stem cells required for tissue homeostasis and regenerationCited by: 66
Author(s): Erin L. Davies, Kai Y. Lei, Christopher Seidel, Amanda E Kroesen, Sean A. McKinney, Longhua Guo, Sofia Robb, E. J. Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Software Mentions: 4
Published: over 9 years ago
10.3389/fgene.2020.00845
Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During AdipogenesisCited by: 3
Author(s): Jinwei Zhang, Jideng Ma, Xiankun Zhou, Silu Hu, Liangpeng Ge, Jing Sun, Penghao Li, Keren Long, Long Jin, Qianzi Tang, Lingyan Liu, Xuewei Li, Surong Shuai, Mingzhou Li
Software Mentions: 4
Published: almost 6 years ago
10.3389/fcell.2021.699212
A Novel Six Metastasis-Related Prognostic Gene Signature for Patients With OsteosarcomaCited by: 12
Author(s): Di Zheng, Kezhou Xia, Ling Yu, Changtian Gong, Yubo Shi, Wěi Li, Yonglong Qiu, Jian Yang, Weichun Guo
Software Mentions: 4
Published: about 5 years ago
10.7554/eLife.55102
The S-phase-induced lncRNA SUNO1 promotes cell proliferation by controlling YAP1/Hippo signaling pathwayCited by: 17
Author(s): Qinyu Hao, Xinying Zong, Qinyu Sun, Yo Chuen Lin, You Shang, Seyedsasan Hashemikhabir, Rosaline Y.C. Hsu, Mohammad Kamran, Ritu Chaudhary, Vidisha Tripathi, Deepak Kumar Singh, Arindam Chakraborty, Xiao Ling Li, Yoonjung Kim, Arturo V. Orjalo, Maria Polycarpou‐Schwarz, Branden S. Moriarity, Lisa M. Miller Jenkins, Hans Johansson, Yuelin J. Zhu, Sven Diederichs, Anindya Bagchi, Tae Hoon Kim, Sarath Chandra Janga, Ashish Lal, Supriya G. Prasanth, Kannanganattu V. Prasanth
Software Mentions: 4
Published: over 5 years ago
10.3389/fonc.2021.705547
Construction of Novel Methylation-Driven Gene Model and Investigation of PARVB Function in GlioblastomaCited by: 3
Author(s): Wanli Yu, Pengfei Wu, Fang Wang, Miao Li, Bo Han, Zhiqun Jiang
Software Mentions: 4
Published: almost 5 years ago
10.1155/2018/1243858
Characterization of Transcription Termination-Associated RNAs: New Insights into their Biogenesis, Tailing, and Expression in Primary TumorsCited by: 4
Author(s): Ilaria Laudadio, Sara Formichetti, Silvia Gioiosa, Filippos Klironomos, Nikolaus Rajewsky, Giuseppe Macino, Claudia Carissimi, Valerio Fulci
Software Mentions: 4
Published: over 8 years ago
10.3390/metabo8030041
Unbiased Lipidomic Profiling of Triple-Negative Breast Cancer Tissues Reveals the Association of Sphingomyelin Levels with Patient Disease-Free SurvivalCited by: 27
Author(s): Preeti Purwaha, Franklin Gu, Danthasinghe Waduge Badrajee Piyarathna, Theckelnaycke Rajendiran, Anindita Ravindran, Angela R. Omilian, Sao Jiralerspong, Gokul M. Das, Carl Morrison, Christine B. Ambrosone, Cristian Coarfa, Nagireddy Putluri, Arun Sreekumar
Software Mentions: 4
Published: about 8 years ago
10.1002/ece3.4122
A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum settingCited by: 13
Author(s): Elisabeth Fitzek, Adline Delcamp, Erwan Guichoux, Marlene Hahn, Matthew S. Lobdell, Andrew L. Hipp
Software Mentions: 4
Published: about 8 years ago
10.3390/ijms22084267
smartPARE: An R Package for Efficient Identification of True mRNA Cleavage SitesCited by: 4
Author(s): Kristian Persson Hodén, Xinyi Hu, Gabriel García Martínez, Christina Dixelius
Software Mentions: 4
Published: over 5 years ago
10.1371/journal.pone.0131274
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic DataCited by: 51
Author(s): Natalja Kurbatova, Justin C. Mason, Hugh W. Morgan, Terrence F. Meehan, Natasha A. Karp
Software Mentions: 4
Published: about 11 years ago
10.3389/fonc.2021.701500
Development and Validation of a Radiosensitivity Prediction Model for Lower Grade Glioma Based on Spike-and-Slab LassoCited by: 3
Author(s): Zixuan Du, Shang Cai, Derui Yan, Huijun Li, Xinyan Zhang, Wei Yang, Jianping Cao, Nengjun Yi, Zaixiang Tang
Software Mentions: 4
Published: almost 5 years ago
10.1534/g3.118.200677
Genotype-by-Environment-by-Environment Interactions in the <i>Saccharomyces cerevisiae</i> Transcriptomic Response to Alcohols and AnaerobiosisCited by: 5
Author(s): Maria Sardi, Molly Krause, Justin Heilberger, Audrey P. Gasch
Software Mentions: 4
Published: over 7 years ago
10.7554/eLife.38432
Immune-mediated hookworm clearance and survival of a marine mammal decrease with warmer ocean temperaturesCited by: 13
Author(s): Mauricio Seguel, Felipe Montalva, Diego Pérez-Venegas, Josefina Gutiérrez, Héctor Pavés, Ananda Müller, Carola Valencia-Soto, Elizabeth W. Howerth, Victoria C Mendiola, Nicole L. Gottdenker
Software Mentions: 4
Published: over 7 years ago
10.3390/ani10112123
Social Network Analysis of Agonistic Behaviour and Its Association with Economically Important Traits in PigsCited by: 8
Author(s): Saif Agha, E. Fábrega, Raquel Quintanilla, Juan Pablo Sánchez
Software Mentions: 4
Published: over 5 years ago
10.3390/ani10010144
Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan PlateauCited by: 16
Author(s): Wei Guo, Weiwei Wang, Sisi Bi, Ruijun Long, Farman Ullah, Muhammad Shafiq, Mi Zhou, Ying Zhang
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-020-71889-9
Gene expression is stable in a complete CIB1 knockout keratinocyte modelCited by: 2
Author(s): Elias Imahorn, Magomet Aushev, Stefan Herms, Per Hoffmann, Sven Cichon, Julia Reichelt, Peter Itin, Bettina Burger
Software Mentions: 4
Published: almost 6 years ago
10.1111/jcmm.15271
Systematic prediction of key genes for ovarian cancer by co‐expression network analysisCited by: 12
Author(s): Mingyuan Wang, Jinjin Wang, Jinglan Liu, Lili Zhu, Heng Ma, Jian Zou, Wei Wu, Kangkai Wang
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0017080
The Light Responsive Transcriptome of the Zebrafish: Function and RegulationCited by: 92
Author(s): Benjamin D. Weger, Meltem Sahinbas, G. Otto, Philipp Mracek, Olivier Armant, Dirk Dolle, Kajori Lahiri, Daniela Vallone, Laurence Ettwiller, Robert Geisler, Nicholas S. Foulkes, Thomas Dickmeis
Software Mentions: 4
Published: over 15 years ago
10.1016/j.artmed.2020.101930
Using topological data analysis and pseudo time series to infer temporal phenotypes from electronic health recordsCited by: 14
Author(s): Arianna Dagliati, Nophar Geifman, Niels Peek, John H. Holmes, Lucia Sacchi, Riccardo Bellazzi, Seyed Erfan Sajjadi, Allan Tucker
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0163491
LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector MachinesCited by: 3
Author(s): Jingting Xu, Hong Hu, Yang Dai
Software Mentions: 4
Published: almost 10 years ago
10.7554/eLife.45310
A cis-carotene derived apocarotenoid regulates etioplast and chloroplast developmentCited by: 45
Author(s): Christopher I. Cazzonelli, Xin Hou, Yağiz Alagöz, John Rivers, Namraj Dhami, Jiwon Lee, Shashikanth Marri, Barry J. Pogson
Software Mentions: 4
Published: over 6 years ago
10.3389/fgene.2019.00493
Genome-Wide Analysis of Lung Adenocarcinoma Identifies Novel Prognostic Factors and a Prognostic ScoreCited by: 10
Author(s): Donglai Chen, Yueqiang Song, Fuquan Zhang, Xiaofan Wang, Erjia Zhu, Xi Zhang, Gening Jiang, Siguang Li, Chang Chen, Yongbing Chen
Software Mentions: 4
Published: about 7 years ago
10.1093/gigascience/giaa027
Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-CCited by: 43
Author(s): Matthew A. Field, Benjamin D. Rosen, Olga Dudchenko, Eva Chan, André E. Minoche, Richard J. Edwards, Kirston Barton, Ruth J. Lyons, Daniel Enosi Tuipulotu, Vanessa M. Hayes, Arina D. Omer, Zane Colaric, Jens Keilwagen, Ksenia Skvortsova, Ozren Bogdanović, Martin A. Smith, E Aiden, Timothy P. L. Smith, Robert A. Zammit, J. William O. Ballard
Software Mentions: 4
Published: over 6 years ago
10.7554/eLife.67740
Bacterial–fungal interactions in the neonatal gut influence asthma outcomes later in lifeCited by: 16
Author(s): Rozlyn C.T. Boutin, Charisse Petersen, Sarah E. Woodward, Antonio Serapio-Palacios, Tahereh Bozorgmehr, Rachelle Loo, Alina Chalanuchpong, Mihai Cirstea, Bernard C. Lo, Kelsey E. Huus, Weronika Barcik, Meghan B. Azad, Allan B. Becker, Piush J. Mandhane, Theo J. Moraes, Malcolm R. Sears, Padmaja Subbarao, Kelly M. McNagny, Stuart E. Turvey, B. Brett Finlay
Software Mentions: 4
Published: over 5 years ago
10.1186/1471-2105-13-294
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target predictionCited by: 25
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 4
Published: over 13 years ago
10.3390/ijms22157939
Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture ConditionsCited by: 5
Author(s): Byung Chul Kim, Kyu Hwan Kwack, Jeewan Chun, Jae Hyung Lee
Software Mentions: 4
Published: almost 5 years ago
10.3389/fgene.2021.736423
Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast CancerCited by: 4
Author(s): He Zhang, Baoai Han, Xingxing Han, Yuying Zhu, Hui Liu, Zhiyong Wang, Yanfen Cui, Ran Tian, Zicong Gao, Ruinan Tian, Sixin Ren, Xiaoyan Zuo, Jianfei Tian, Fei Zhang, Ruifang Niu
Software Mentions: 4
Published: almost 5 years ago
10.3389/fgene.2020.612840
Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics DataCited by: 3
Author(s): Phillipe Loher, Nestoras Karathanasis
Software Mentions: 4
Published: over 5 years ago
10.3390/ijms22179413
The Multi-Elemental Composition of the Aqueous Humor of Patients Undergoing Cataract Surgery, Suffering from Coexisting Diabetes, Hypertension, or Diabetic RetinopathyCited by: 7
Author(s): Jolanta Flieger, Joanna Dolar-Szczasny, Robert Ręjdak, Dariusz Majerek, Małgorzata Tatarczak-Michalewska, Jędrzej Proch, Eliza Blicharska, Wojciech Flieger, Jacek Baj, Przemysław Niedzielski
Software Mentions: 4
Published: almost 5 years ago
10.3390/genes12020203
Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in AustraliaCited by: 8
Author(s): Marnie J. Hodge, Sara de las Heras‐Saldana, Sally J. Rindfleish, Cyril Stephen, Sameer D. Pant
Software Mentions: 4
Published: over 5 years ago
10.1186/s12864-019-6088-0
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifsCited by: 10
Author(s): Jonas Ibn-Salem, Miguel A. Andrade‐Navarro
Software Mentions: 4
Published: over 6 years ago
10.7554/eLife.41641
IFNγ induces epigenetic programming of human T-bethi B cells and promotes TLR7/8 and IL-21 induced differentiationCited by: 104
Author(s): Esther Zumaquero, Sara L Stone, Christopher D. Scharer, Scott A. Jenks, Anoma Nellore, Betty Mousseau, Antonio Rosal-Vela, Davide Botta, John E. Bradley, Wojciech Wojciechowski, Travis Ptacek, Maria I. Danila, Jeffrey C. Edberg, S. Louis Bridges, Robert P. Kimberly, W. Winn Chatham, Trenton R. Schoeb, Alexander F. Rosenberg, Jeremy M. Boss, Igñacio Sanz, Frances E. Lund
Software Mentions: 4
Published: about 7 years ago
10.1186/gb-2013-14-11-r131
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAsCited by: 162
Author(s): Ana C. Marques, Jim R. Hughes, Bryony Graham, Monika S. Kowalczyk, Douglas R. Higgs, Chris P. Ponting
Software Mentions: 4
Published: over 13 years ago
10.3390/metabo10060220
Non-Targeted Metabolite Profiles and Sensory Properties Elucidate Commonalities and Differences of Wines Made with the Same Variety but Different Cultivar ClonesCited by: 6
Author(s): Álvaro Cuadros-Inostroza, Claudio Verdugo-Alegría, Lothar Willmitzer, Yerko Moreno-Simunovic, José G. Vallarino
Software Mentions: 4
Published: about 6 years ago
10.1128/mSystems.00327-19
Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City SewageCited by: 19
Author(s): Susan Joseph, Thomas Battaglia, Julia M. Maritz, Jane M. Carlton, Martin J. Blaser
Software Mentions: 4
Published: almost 7 years ago
10.1371/journal.pcbi.1004809
QuIN: A Web Server for Querying and Visualizing Chromatin Interaction NetworksCited by: 11
Author(s): Asa Thibodeau, Eladio J. Márquez, Oscar Junhong Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar
Software Mentions: 4
Published: about 10 years ago
10.18632/aging.202170
A three-gene signature based on tumour microenvironment predicts overall survival of osteosarcoma in adolescents and young adultsCited by: 10
Author(s): Chun-Kai Wen, Hongxue Wang, Han Wang, Hao Yuan Mo, Weiying Zhong, Jing Tang, Yuefeng Lu, Wenxian Zhou, Aihua Tan, Yan Liu, Weimin Xie
Software Mentions: 4
Published: over 5 years ago
10.3389/fgene.2020.01017
Identification of a Novel Signature and Construction of a Nomogram Predicting Overall Survival in Clear Cell Renal Cell CarcinomaCited by: 5
Author(s): Xiangkun Wu, Zhijian Zhao, Aisha Khan, Chao Cai, Daojun Lv, Danan Gu, Yongda Liu
Software Mentions: 4
Published: almost 6 years ago
10.1186/1471-2164-12-110
Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1Cited by: 16
Author(s): Zen H. Lu, Alex di Domenico, Steven H. Wright, Pamela Knight, Bruce Whitelaw, Alan D. Pemberton
Software Mentions: 4
Published: over 15 years ago
10.1099/mgen.0.000108
A population genomics approach to exploiting the accessory 'resistome' of Escherichia coliCited by: 18
Author(s): Robert Goldstone, David George Emslie Smith
Software Mentions: 4
Published: over 9 years ago
10.18632/aging.104134
The value of a metabolic reprogramming-related gene signature for pancreatic adenocarcinoma prognosis predictionCited by: 12
Author(s): Zhen Tan, Yubin Lei, Jin Xu, Si Shi, Jie Hua, Bo Zhang, Qingcai Meng, Jiang Liu, Yiyin Zhang, Miaoyan Wei, Xianjun Yu, Chen Liang
Software Mentions: 4
Published: over 5 years ago
10.1186/s12859-016-1158-7
DISMISS: detection of stranded methylation in MeDIP-Seq dataCited by: 6
Author(s): Umar Niazi, Kathrin K. Geyer, Martin Vickers, Karl F. Hoffmann, Martin Swain
Software Mentions: 4
Published: almost 10 years ago
10.1007/s00204-021-03132-x
The diarrhetic shellfish-poisoning toxin, okadaic acid, provokes gastropathy, dysbiosis and susceptibility to bacterial infection in a non-rodent bioassay, Galleria mellonellaCited by: 13
Author(s): Helena Emery, William Traves, Andrew F. Rowley, Christopher J. Coates
Software Mentions: 4
Published: almost 5 years ago
10.7554/eLife.36828
Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptorCited by: 12
Author(s): Corinne L Pender, H. Robert Horvitz
Software Mentions: 4
Published: about 8 years ago
10.3390/biomedicines9030266
Dysbiosis and Enhanced Beta-Defensin Production in Hair Follicles of Patients with Lichen Planopilaris and Frontal Fibrosing AlopeciaCited by: 6
Author(s): Andria Constantinou, Katarzyna Polak-Witka, Marios Tomazou, Anastasis Oulas, Varvara Kanti, Rolf Schwarzer, Johannes Helmuth, Anke Edelmann, Ulrike Blume-Peytavi, George M. Spyrou, Annika Vogt
Software Mentions: 4
Published: over 5 years ago
10.1186/s40168-019-0721-7
Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteriaCited by: 231
Author(s): Xiaofan Wang, Tsung Cheng Tsai, Feilong Deng, Xiaoyuan Wei, Jianmin Chai, J. S. Knapp, J. K. Apple, C. V. Maxwell, Jung Ae Lee, Ying Liu, Jiangchao Zhao
Software Mentions: 4
Published: almost 7 years ago
10.3389/fpls.2018.00272
Ethylene-Related Gene Expression Networks in Wood FormationCited by: 34
Author(s): Carolin Seyfferth, Bernard A. Wessels, Soile Jokipii-Lukkari, Björn Sundberg, Nicolas Delhomme, Judith Felten, Hannele Tuominen
Software Mentions: 4
Published: over 8 years ago
10.18632/aging.102556
Robust immunoscore model to predict the response to anti-PD1 therapy in melanomaCited by: 14
Author(s): Run‐Cong Nie, Shu Qiang Yuan, Yun Wang, Yan Yu Cai, Shi Chen, Shu Man Li, Jie Zhou, Guo Ming Chen, Tian Qi Luo, Zhi Wei Zhou, Yuan Fang Li
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0237556
Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiotaCited by: 4
Author(s): Takeo Shibata, Mayumi Nakagawa, Hannah N. Coleman, Sarah M. Owens, William W. Greenfield, Toshiyuki Sasagawa, Michael S. Robeson
Software Mentions: 4
Published: almost 5 years ago
10.3389/fgene.2020.614160
An Eight-CpG-based Methylation Classifier for Preoperative Discriminating Early and Advanced-Late Stage of Colorectal CancerCited by: 1
Author(s): Ji Hu, Fu-Ying Zhao, Bin Huang, Ran Jing, Meiyuan Chen, Hailin Liu, You-Song Deng, Xia Zhao, Xiaofan Han
Software Mentions: 4
Published: over 5 years ago
10.1186/s40168-020-00799-9
Rhizosphere protists are key determinants of plant healthCited by: 123
Author(s): Wu Xiong, Yuqi Song, Kun Yang, Yian Gu, Zhong Wei, George A. Kowalchuk, Yangchun Xu, Alexandre Jousset, Qirong Shen, Stefan Geisen
Software Mentions: 4
Published: over 6 years ago
10.3389/fvets.2020.00438
Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy CatsCited by: 2
Author(s): Andrea Balboni, Giovanni Franzo, Luca Bano, Stefano Arcangeli, Alessia Rizzardi, Lorenza Urbani, Sofia Segatore, Federica Serafini, Francesco Dondi, Mara Battilani
Software Mentions: 4
Published: almost 6 years ago
10.3390/microorganisms8020190
Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule MiningCited by: 5
Author(s): Florian Centler, Sarah Günnigmann, Ingo Fetzer, Annelie Wendeberg
Software Mentions: 4
Published: over 6 years ago
10.3390/microorganisms9030549
Lake Ecosystem Robustness and Resilience Inferred from a Climate-Stressed Protistan Plankton NetworkCited by: 16
Author(s): Dominik Forster, Zhishuai Qu, Gianna Pitsch, Estelle P. Bruni, Barbara Kammerlander, Thomas Pröschold, Bettina Sonntag, Thomas Posch, Thorsten Stoeck
Software Mentions: 4
Published: over 5 years ago
10.3389/fmicb.2018.00093
Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic MethodCited by: 17
Author(s): Yonggang Yan, Qin Jiang, Jian-Gong Wang, Ting Zhu, Bin Zou, Qiongfen Qiu, Zhe‐Xue Quan
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-019-54855-y
Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assaysCited by: 51
Author(s): Stephanie M. Rosales, Margaret W. Miller, Dana E. Williams, Nikki Traylor-Knowles, Benjamin Young, Xaymara M. Serrano
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-020-59955-8
Vaginal microbiota diverges in sows with low and high reproductive performance after porcine reproductive and respiratory syndrome vaccinationCited by: 14
Author(s): Letícia P Sanglard, Stephan Schmitz‐Esser, Kent Gray, Daniel Linhares, Carl J. Yeoman, Jack C. M. Dekkers, Megan C. Niederwerder, Nick V. L. Serão
Software Mentions: 4
Published: over 6 years ago
10.2196/jmir.6342
Methods for Evaluating Respondent Attrition in Web-Based SurveysCited 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
10.3389/fimmu.2017.01351
Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16Cited by: 11
Author(s): Xi Yang, Niamh M. Troy, Denise Anderson, Olga M. Pena, Jason P. Lynch, Simon Phipps, Anthony Bosco, John W. Upham
Software Mentions: 4
Published: over 8 years ago
10.7717/peerj.3334
<i>pathVar:</i>a new method for pathway-based interpretation of gene expression variabilityCited by: 6
Author(s): Laurence de Torrenté, Stephanie M. Zimmerman, Deanne Taylor, Yu Hasegawa, Christine A. Wells, Jessica C. Mar
Software Mentions: 4
Published: about 9 years ago
10.1038/s41598-021-97790-7
Glycosaminoglycan biosynthesis pathway in host genome is associated with Helicobacter pylori infectionCited by: 0
Author(s): Dingxue Hu, Yueqi Lu, Daoming Wang, Chao Nie, Yan Li
Software Mentions: 4
Published: almost 5 years ago
10.1186/1471-2156-15-24
A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate riskCited by: 21
Author(s): Samuel G. Younkin, Robert B. Scharpf, Holger Schwender, Margaret M. Parker, Alan F. Scott, Mary L. Marazita, Terri H. Beaty, Ingo Ruczinski
Software Mentions: 4
Published: over 12 years ago
10.1186/1471-2105-9-461
minet: A R/Bioconductor Package for Inferring Large Transcriptional Networks Using Mutual InformationCited by: 469
Author(s): Patrick Meyer, Frédéric Lafitte, Gianluca Bontempi
Software Mentions: 4
Published: over 17 years ago
10.1186/s12864-017-4186-4
The gene SMART study: method, study design, and preliminary findingsCited by: 45
Author(s): Xu Yan, Nir Eynon, Ioannis Papadimitriou, Jujiao Kuang, Fiona Munson, Oren Tirosh, Lannie O’Keefe, Lyn R. Griffiths, Kevin J. Ashton, Nuala M. Byrne, Yannis Pitsiladis, David Bishop
Software Mentions: 4
Published: over 8 years ago
10.18632/aging.103945
Single-cell transcriptome analysis demonstrates inter-patient and intra-tumor heterogeneity in primary and metastatic lung adenocarcinomaCited by: 20
Author(s): Yafei Liu, Guanchao Ye, Lan Huang, Chunyang Zhang, Yinliang Sheng, Bin Wu, Lu Han, Chunli Wu, Bo Dong, Yu Qi
Software Mentions: 4
Published: over 5 years ago
10.3389/fimmu.2021.695806
An Unbiased Machine Learning Exploration Reveals Gene Sets Predictive of Allograft Tolerance After Kidney TransplantationCited by: 7
Author(s): Qiang Fu, Divyansh Agarwal, Kevin Deng, Rudy Matheson, Hongji Yang, Wei Liang, Ran Qing, Shaoping Deng, James F. Markmann
Software Mentions: 4
Published: about 5 years ago
10.1371/journal.pone.0228206
Mixed evidence for the relationship between periodontitis and Alzheimer’s disease: A bidirectional Mendelian randomization studyCited by: 20
Author(s): Yi‐Qian Sun, Rebecca C Richmond, Yue Chen, Xiao-Mei Mai
Software Mentions: 4
Published: over 6 years ago