10.3389/fgene.2019.00070

Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach
Cited by: 5
Author(s): Md. Facihul Azam, Aliyu Musa, Matthias Dehmer, Olli Yli‐Harja, Frank Emmert‐Streib
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2019.00951

Perinatal Bisphenol A Exposure and Reprogramming of Imprinted Gene Expression in the Adult Mouse Brain
Cited by: 11
Author(s): Maureen A. Malloy, Joseph Kochmanski, Tamara R. Jones, Justin A. Colacino, Jaclyn M. Goodrich, Dana C. Dolinoy, Laurie K. Svoboda
Software Mentions: 4
Published: almost 7 years ago

10.1074/mcp.RA120.002275

On the Robustness of Graph-Based Clustering to Random Network Alterations
Cited by: 7
Author(s): R. Greg Stacey, Michael A. Skinnider, Leonard J. Foster
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.102459

Multi-omics analysis reveals epithelial-mesenchymal transition-related gene FOXM1 as a novel prognostic biomarker in clear cell renal carcinoma
Cited by: 13
Author(s): Song Jing, Fangzhou Song, Kun Liu, Wanfeng Zhang, Ruihan Luo, Yongyao Tang
Software Mentions: 4
Published: over 6 years ago

10.3389/fgene.2019.00217

Genomic, Transcriptomic, and Epigenomic Features Differentiate Genes That Are Relevant for Muscular Polyunsaturated Fatty Acids in the Common Carp
Cited by: 18
Author(s): Hanyuan Zhang, Peng Xu, Yanliang Jiang, Zixia Zhao, Jianxin Feng, Ruyu Tai, Chuanju Dong, Jian Xu
Software Mentions: 4
Published: over 7 years ago

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in <i>Drosophila melanogaster</i>
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: almost 10 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: about 5 years ago

10.18632/aging.102579

Discovering master regulators in hepatocellular carcinoma: one novel MR, SEC14L2 inhibits cancer cells
Cited by: 14
Author(s): Zhihui Li, Yi Liu, Guoyan Tian, Jianyue Wu, Anqian Lu, Jin Chen, Beibei Xu, Junping Shi, Jin Yang
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-14-862

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
Cited by: 51
Author(s): Peter J.P. Croucher, Michael S. Brewer, Christopher J. Winchell, Geoff Oxford, Rosemary G. Gillespie
Software Mentions: 4
Published: over 13 years ago

10.3390/microorganisms9081737

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli
Cited by: 8
Author(s): Karla Vasco, Brian Nohomovich, Pallavi Singh, Cristina Venegas-Vargas, Rebekah E. Mosci, S. R. Rust, Paul C. Bartlett, Bo Norby, Daniel L. Grooms, Lixin Zhang, Shannon D. Manning
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13075-020-02195-y

Increased serum calpain activity is associated with HMGB1 levels in systemic sclerosis
Cited by: 9
Author(s): Ji-Na Zheng, Yang Li, Yue-Mei Yan, Yong Yu, Wenqi Shao, Qiang Wang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-6121-3

Genome-wide characterization and evolutionary analysis of heat shock transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)
Cited by: 22
Author(s): Mingjia Tang, Liang Xu, Yan Wang, Wanwan Cheng, Xiaobo Luo, Yang Xie, Lu Fan, Liwang Liu
Software Mentions: 4
Published: almost 7 years ago

10.3390/microorganisms9040787

Gut Microbiota Dynamics, Growth Performance, and Gut Morphology in Broiler Chickens Fed Diets Varying in Energy Density with or without Bacitracin Methylene Disalicylate (BMD)
Cited by: 13
Author(s): Deborah Adewole, Fisayo Akinyemi
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms8121954

The Limits and Avoidance of Biases in Metagenomic Analyses of Human Fecal Microbiota
Cited by: 8
Author(s): Emma Bergsten, Denis Mestivier, Iradj Sobhani
Software Mentions: 4
Published: over 5 years ago

10.3390/microorganisms8101506

Microbiome Management by Biological and Chemical Treatments in Maize Is Linked to Plant Health
Cited by: 16
Author(s): Peter Kusstatscher, Wisnu Adi Wicaksono, Dhivya Priya Thenappan, Eveline Adam, Henry Müller, Gabriele Berg
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.4535

Reference gene selection for qRT-PCR assays in<i>Stellera chamaejasme</i>subjected to abiotic stresses and hormone treatments based on transcriptome datasets
Cited by: 18
Author(s): Xin Liu, Hongwei Guan, Min Jae Song, Yànpíng Fù, Xiao Han, Lei Meng, Jingyu Ren, Bin Guo, Wei He, Yahui Wei
Software Mentions: 4
Published: over 8 years ago

10.3389/fbioe.2021.666582

nZVI Impacts Substrate Conversion and Microbiome Composition in Chain Elongation From D- and L-Lactate Substrates
Cited by: 6
Author(s): Carlos A. Contreras-Dávila, Johan Esveld, Cees J.N. Buisman, D.P.B.T.B. Strik
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-15-155

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses
Cited by: 36
Author(s): Xin Luo, Minho Chae, Raga Krishnakumar, Charles G. Danko, W. Lee Kraus
Software Mentions: 4
Published: over 12 years ago

10.3390/vaccines9060664

In Vitro Characterization of the Innate Immune Pathways Engaged by Live and Inactivated Tick-Borne Encephalitis Virus
Cited by: 3
Author(s): Aurora Signorazzi, Jeroen L. A. Pennings, Marilena P. Etna, Malou Noya, Eliana M. Coccia, Anke Huckriede
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-3442-3

Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening
Cited by: 65
Author(s): Qianglong Zhu, Shi Liu, Zhu Zhang, Sikandar Amanullah, Angela R. Davis, Feishi Luan
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.27488

MAGE-A inhibit apoptosis and promote proliferation in multiple myeloma through regulation of BIM and p21Cip1
Cited by: 10
Author(s): Anna Mei, Kaity Tung, Jessie Han, Deepak Perumal, Alessandro Laganà, Jonathan J. Keats, Daniel Auclair, Ajai Chari, Sundar Jagannath, Samir Parekh, Hearn Jay Cho
Software Mentions: 4
Published: over 6 years ago

10.1080/21505594.2017.1342910

<i>Pseudogymnoascus destructans</i> transcriptome changes during white-nose syndrome infections
Cited by: 22
Author(s): Sophia Reeder, Jonathan M. Palmer, Jenni M. Prokkola, Thomas M. Lilley, DeeAnn M. Reeder, Kenneth A. Field
Software Mentions: 4
Published: about 9 years ago

10.1080/21505594.2020.1768018

Transcriptional host–pathogen responses of <i>Pseudogymnoascus destructans</i> and three species of bats with white-nose syndrome
Cited by: 19
Author(s): Christina M. Davy, Michael E. Donaldson, Hana Banďouchová, Ana M. Breit, Nicole Dorville, Yvonne A. Dzal, Veronika Kováčová, Emma L. Kunkel, Natália Martínková, Kaleigh J. O. Norquay, James E. Paterson, Jan Zukal, Jiří Pikula, Craig K. R. Willis, Christopher J. Kyle
Software Mentions: 4
Published: about 6 years ago

10.1080/21505594.2021.1958057

Transcriptional response of <i>Aspergillus fumigatus</i> to copper and the role of the Cu chaperones
Cited by: 6
Author(s): Duaa Anabosi, Zohar Meir, Yana Shadkchan, Mariana Handelman, Ammar Abou-Kandil, Annie Yap, Daniel Urlings, Morgan Gold, Sven Krappmann, Hubertus Haas, Nir Osherov
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-015-1660-8

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
Cited by: 59
Author(s): Michael H. Perlin, Joëlle Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan M. Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Hélène Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E. Hood, David J. Schultz, Christina A. Cuomo
Software Mentions: 4
Published: about 11 years ago

10.3390/foods10081826

Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences
Cited by: 6
Author(s): Miriam Zago, Lia Rossetti, Tommaso Bardelli, Domenico Carminati, Nelson Espinoza N., Giorgio Giraffa
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-07091-y

Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning
Cited by: 10
Author(s): Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernando Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert J. Henry, Monalisa Sampaio Carneiro, Gabriel Rodrigues Alves Margarido
Software Mentions: 4
Published: almost 6 years ago

10.3390/v12080817

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain
Cited by: 6
Author(s): Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M. Workman, Jean-Jack M. Riethoven, David Steffen, Sarah Sillman, Hiep L.X. Vu
Software Mentions: 4
Published: about 6 years ago

10.1002/2211-5463.13130

<i>CCR7</i> and its related molecules may be potential biomarkers of pulmonary arterial hypertension
Cited by: 5
Author(s): Mengsi Cai, Xiuchun Li, Haoru Dong, Ying Wang, Xiaoying Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/v13040593

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes
Cited by: 23
Author(s): Yashu Song, Robert Hanner, Bin Meng
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2407-14-977

Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer
Cited by: 41
Author(s): Prabhakar Rajan, Jacqueline Stockley, Ian Sudbery, Janis Fleming, Ann Hedley, Gabriela Kalna, David Sims, Chris P. Ponting, Andreas Heger, Craig Robson, R. McMenemin, Ian Pedley, Hing Y. Leung
Software Mentions: 4
Published: over 11 years ago

10.3389/fgene.2020.612840

Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data
Cited by: 3
Author(s): Phillipe Loher, Nestoras Karathanasis
Software Mentions: 4
Published: over 5 years ago

10.1186/s12915-018-0569-5

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance
Cited by: 16
Author(s): Jessica M Stringer, Samuel C. Forster, Zhibo Qu, Lexie Prokopuk, Moira K O'Bryan, David K. Gardner, Stefan J. White, David L. Adelson, Patrick Western
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12915-019-0646-4

Enabling cell-type-specific behavioral epigenetics in Drosophila: a modified high-yield INTACT method reveals the impact of social environment on the epigenetic landscape in dopaminergic neurons
Cited by: 15
Author(s): Pavan Agrawal, Phuong Chung, Ulrike Heberlein, Clement F. Kent
Software Mentions: 4
Published: over 7 years ago

10.1002/ece3.4842

Studying the microbiota of bats: Accuracy of direct and indirect samplings
Cited by: 9
Author(s): Muriel Dietrich, Wanda Markotter
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.24898

Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets
Cited by: 17
Author(s): Rosemarie Weikard, Frieder Hadlich, H.M. Hammon, D. Frieten, C. Gerbert, Christian Koch, G. Dusel, Christa Kühn
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.4029

Changes in intestinal microbiota across an altitudinal gradient in the lizard <i>Phrynocephalus vlangalii</i>
Cited by: 44
Author(s): Wenya Zhang, Na Li, Xiaolong Tang, Naifa Liu, Zhao Wang
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.3671

The Groot Effect: Plant facilitation and desert shrub regrowth following extensive damage
Cited by: 21
Author(s): Christopher J. Lortie, Éva Gruber, Alessandro Filazzola, Taylor Noble, Michael F. Westphal
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.7500

Hatching date influences winter habitat occupancy: Examining seasonal interactions across the full annual cycle in a migratory songbird
Cited by: 4
Author(s): Michael E. Akresh, David I. King, Peter P. Marra
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2191-5

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
Cited by: 54
Author(s): Shilin Zhao, Chung I. Li, Yan Guo, Quanhu Sheng, Yu Shyr
Software Mentions: 4
Published: about 8 years ago

10.1186/s13071-021-04859-3

Blastocystis in the faeces of children from six distant countries: prevalence, quantity, subtypes and the relation to the gut bacteriome
Cited by: 11
Author(s): Ondřej Cinek, Katerina Polackova, Rasha Odeh, Abeer Alassaf, Lenka Kramná, Mary Ann Ugochi Ibekwe, Edna Majaliwa, Gunduz Ahmadov, Bashir Mukhtar Elwasila Elmahi, Hanan Mekki, Sami Oikarinen, Jan Lebl, Mohammed A. Abdullah
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2734-4

Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data
Cited by: 73
Author(s): Hao Yang, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, Guangrong Qin
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-019-2916-0

A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data
Cited by: 26
Author(s): Anjali Silva, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi
Software Mentions: 4
Published: about 7 years ago

10.18632/oncotarget.22878

Identification of cancer prognosis-associated functional modules using differential co-expression networks
Cited by: 10
Author(s): Wenshuai Yu, Shengjie Zhao, Yongcui Wang, Brian Nlong Zhao, Weiling Zhao, Xiaobo Zhou
Software Mentions: 4
Published: over 8 years ago

10.1002/ece3.6989

Effects of maternal genotypic identity and genetic diversity of the red mangrove <i>Rhizophora mangle</i> on associated soil bacterial communities: A field‐based experiment
Cited by: 9
Author(s): Hayley Craig, John Paul Kennedy, Donna J. Devlin, Richard D. Bardgett, Jennifer K. Rowntree
Software Mentions: 4
Published: almost 6 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: about 15 years ago

10.1002/ece3.6529

In the foothill zone—<i>Sabanejewia balcanica</i>(Karaman 1922), in the lowland zone—<i>Sabanejewia bulgarica</i>(Drensky, 1928): Myth or reality?
Cited by: 6
Author(s): Peter Križek, Jan Mendel, Jakub Fedorčák, Ján Koščo
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-015-0859-7

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Cited by: 9
Author(s): Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D’Esposito
Software Mentions: 4
Published: over 10 years ago

10.1002/ece3.5464

Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association
Cited by: 18
Author(s): Juliane Hartke, Philipp P. Sprenger, Jacqueline Sahm, Helena Winterberg, Jérôme Orivel, Hannes Baur, Till Beuerle, Thomas Schmitt, Barbara Feldmeyer, Florian Menzel
Software Mentions: 4
Published: about 7 years ago

10.1002/ece3.2863

A gradient of nutrient enrichment reveals nonlinear impacts of fertilization on Arctic plant diversity and ecosystem function
Cited by: 21
Author(s): Case M. Prager, Shahid Naeem, Natalie T. Boelman, Jan U. H. Eitel, Heather E. Greaves, Mary A. Heskel, Troy S. Magney, Duncan N. L. Menge, Lee A. Vierling, Kevin L. Griffin
Software Mentions: 4
Published: over 9 years ago

10.1002/ece3.4421

Sex-specific prey partitioning in breeding piscivorous birds examined via a novel, noninvasive approach
Cited by: 10
Author(s): Bettina Thalinger, Johannes Oehm, Christiane Zeisler, Julia Vorhauser, Michael Traugott
Software Mentions: 4
Published: almost 8 years ago

10.1002/eco.1827

The effects of catchment and riparian forest quality on stream environmental conditions across a tropical rainforest and oil palm landscape in Malaysian Borneo
Cited by: 55
Author(s): Sarah H. Luke, Holly Barclay, Kawi Bidin, Chey Vun Khen, Robert M. Ewers, William A. Foster, Anand Nainar, Marion Pfeifer, Glen Reynolds, Edgar C. Turner, R. P. D. Walsh, David C. Aldridge
Software Mentions: 4
Published: over 9 years ago

10.1155/2021/4582082

Identification of a Two-m6A RNA Methylation Regulator Risk Signature as an Independent Prognostic Biomarker in Papillary Renal Cell Carcinoma by Bioinformatic Analysis
Cited by: 5
Author(s): Fusheng Yang, Guojiang Zhao, Liyuan Ge, Yimeng Song, Kai Hong, Hongxian Zhang, Cheng Liu, Hong Peng, Lulin Ma
Software Mentions: 4
Published: over 5 years ago

10.1039/c9sc04090k

Is there a gender gap in chemical sciences scholarly communication?
Cited by: 34
Author(s): Aileen Day, Peter Corbett, J. Boyle
Software Mentions: 4
Published: over 6 years ago

10.3390/cells9061523

Potential Prognostic Role of SPARC Methylation in Non-Small-Cell Lung Cancer
Cited by: 9
Author(s): Federico Pio Fabrizio, Angelo Sparaneo, Andrea Fontana, Tommaso Mazza, Paolo Graziano, Angela Pantalone, Paola Parente, Flavia Centra, Natalizia Orlando, Domenico Trombetta, Annamaria la Torre, Gian Maria Ferretti, Marco Taurchini, Concetta Martina Di Micco, Evaristo Maiello, Vito Michele Fazio, Antonio Rossi, Lucia Anna Muscarella
Software Mentions: 4
Published: about 6 years ago

10.3390/cells9102320

Single Cell ADNP Predictive of Human Muscle Disorders: Mouse Knockdown Results in Muscle Wasting
Cited by: 7
Author(s): Oxana Kapitansky, Gidon Karmon, Shlomo Sragovich, Adva Hadar, Meishar Shahoha, Iman Jaljuli, Lior Bikovski, Eliezer Giladi, Róbert Pálovics, Tal Iram, Illana Gozes
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.15807

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease
Cited by: 39
Author(s): Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Annick De Paepe, Mohsen Karimi, Kaarel Krjutškov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström‐Lindberg, Johanna Ungerstedt
Software Mentions: 4
Published: over 9 years ago

10.3390/cells9020387

Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types
Cited by: 7
Author(s): Marianna Penzo, Rosanna Clima, Davide Treré, Lorenzo Montanaro
Software Mentions: 4
Published: over 6 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 Cancer
Cited 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

10.1038/s41422-019-0251-7

Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors
Cited by: 39
Author(s): Rong Guo, Fang Hu, Qitong Weng, Chen Lv, Hongling Wu, Lijuan Liu, Zongcheng Li, Yang Zeng, Zhijie Bai, Mengyun Zhang, Yuting Liu, Xiaofei Liu, Chengxiang Xia, Tongjie Wang, Pingwei Zhou, Kaitao Wang, Yong Dong, Yuxuan Luo, Xiangzhong Zhang, Yuxian Guan, Geng Yang, Juan Du, Yangqiu Li, Yu Lan, Jiekai Chen, Bing Liu, Jinyong Wang
Software Mentions: 4
Published: over 6 years ago

10.1016/j.celrep.2019.12.034

Mouse Ovarian Cancer Models Recapitulate the Human Tumor Microenvironment and Patient Response to Treatment
Cited by: 56
Author(s): Eleni Maniati, Chiara Berlato, Ganga Gopinathan, Owen Heath, Panoraia Kotantaki, Anissa Lakhani, Jacqueline McDermott, Colin Pegrum, Robin Delaine-Smith, Oliver M.T. Pearce, Priyanka Hirani, Joash D. Joy, Ludmila Szabova, Ruth Perets, Owen J. Sansom, Ronny Drapkin, Peter J. Bailey, Frances R. Balkwill
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.3133

Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides <i>Odontesthes argentinensis</i> and <i>O. bonariensis</i> (Atheriniformes)
Cited by: 17
Author(s): Lily C. Hughes, Gustavo M. Somoza, Bryan Nguyen, James P. Bernot, Mariano González‐Castro, Juan Martín Díaz de Astarloa, Guillermo Ortı́
Software Mentions: 4
Published: about 9 years ago

10.1016/j.celrep.2017.08.010

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
Cited by: 92
Author(s): Theodoros I. Roumeliotis, Steven P. Williams, Emanuel Gonçalvès, Clara Alsinet, Martín Del Castillo Velasco-Herrera, Nanne Aben, Fatemeh Zamanzad Ghavidel, Magali Michaut, Michaël Schubert, Stacey Price, James C. Wright, Lu Yu, Meizhu Yang, Rodrigo Dienstmann, Justin Guinney, Pedro Beltrão, Alvis Brāzma, Mercedes Pardo, Oliver Stegle, David J. Adams, Lodewyk Wessels, Julio Sáez-Rodríguez, Ultan McDermott, Jyoti S. Choudhary
Software Mentions: 4
Published: about 9 years ago

10.1038/celldisc.2017.13

Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation
Cited by: 7
Author(s): Miriam Landfors, Jostein Johansen, Jan Magnus Aronsen, Cathrine Broberg Vågbø, Louis C. Doré, Chuan He, Ivar Sjaastad, Pål Sætrom, Péter Fedorcsák, John Arne Dahl, Håvard Aanes, Markus Fußer, Arne Klungland
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2019.00493

Genome-Wide Analysis of Lung Adenocarcinoma Identifies Novel Prognostic Factors and a Prognostic Score
Cited 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

10.7554/eLife.61965

Sustained TNF-α stimulation leads to transcriptional memory that greatly enhances signal sensitivity and robustness
Cited by: 15
Author(s): Zuodong Zhao, Zhuqiang Zhang, Jingjing Li, Qiang Dong, Jun Xiong, Yingfeng Li, Mengying Lan, Gang Li, Bing Zhu
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.39658

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome
Cited by: 33
Author(s): Srivarsha Rajshekar, Jun Yao, Paige K. Arnold, Sara G. Payne, Yinwen Zhang, Teresa V. Bowman, Robert J. Schmitz, John Edwards, Mary Goll
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0186973

Monthly variations in aneurysmal subarachnoid hemorrhage incidence and mortality: Correlation with weather and pollution
Cited by: 11
Author(s): Myung Hoon Han, Jinhee Kim, Kyu Sun Choi, Choong Hyun Kim, Jae Min Kim, Jin Hwan Cheong, Hyeong Joong Yi, Seon Heui Lee
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0240322

Evaluating socio-economic and conservation impacts of management: A case study of time-area closures on Georges Bank
Cited by: 5
Author(s): David M. Keith, Jessica A. Sameoto, Freya Keyser, Christine A. Ward-Paige
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pbio.2006249

Insulin signaling and reduced glucocorticoid receptor activity attenuate postprandial gene expression in liver
Cited by: 35
Author(s): Adrija Kalviša, Majken Siersbæk, Stine M. Præstholm, Line Julie Lindorf Christensen, Ronni Nielsen, Oliver Stöhr, Sabine Vettorazzi, Jan Tuckermann, Morris F. White, Susanne Mandrup, Lars Grøntved
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-64514-2

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype
Cited by: 12
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Kathryn A. Helmin, Basil Khuder, Cynthia Rothblum-Oviatt, Joseph M. Collaco, Jonathan H. Wright, Paul A. Reyfman, Howard M. Lederman, Benjamin D. Singer
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-32448-5

The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis
Cited by: 51
Author(s): Joost H. M. Stassen, Ana López, Ritushree Jain, David Pascual-Pardo, Estrella Luna, Lisa M. Smith, Jurriaan Ton
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0172423

Generalist dispersers promote germination of an alien fleshy-fruited tree invading natural grasslands
Cited by: 14
Author(s): Martín Raúl Amodeo, María Belén Vázquez, Sergio Martín Zalba
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1008464

CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing
Cited by: 13
Author(s): Xènia Serrat, Dmytro Kukhtar, Eric Cornes, Anna Esteve‐Codina, Helena Benlloch, Germano Cecere, Julián Cerón
Software Mentions: 4
Published: almost 7 years ago

10.18632/aging.103753

Eight immune-related genes predict survival outcomes and immune characteristics in breast cancer
Cited by: 2
Author(s): Xu Han, Gangjian Wang, Lili Zhu, Liu Hong, Bingjie Li
Software Mentions: 4
Published: about 6 years ago

10.18632/oncotarget.12180

The transcriptional signature of human ovarian carcinoma macrophages is associated with extracellular matrix reorganization
Cited by: 72
Author(s): Florian Finkernagel, Silke Reinartz, Sonja Lieber, Till Adhikary, Annika Wortmann, Nathalie Hoffmann, Tim Bieringer, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0187079

Immune related gene expression in worker honey bee (Apis mellifera carnica) pupae exposed to neonicotinoid thiamethoxam and Varroa mites (Varroa destructor)
Cited by: 36
Author(s): Tanja Tesovnik, Ivanka Cizelj, Minja Zorc, Manuela Čitar, Janko Božič, Gordana Glavan, Mojca Narat
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0098115

Escherichia coli O157:H7 Super-Shedder and Non-Shedder Feedlot Steers Harbour Distinct Fecal Bacterial Communities
Cited by: 44
Author(s): Yong Xu, Éric Dugat-Bony, Rahat Zaheer, L.B. Selinger, Ruth Barbieri, Krysty Munns, Tim A. McAllister, L. Brent Selinger
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.pone.0236464

Estimation of time-varying reproduction numbers underlying epidemiological processes: A new statistical tool for the COVID-19 pandemic
Cited by: 71
Author(s): Hyokyoung Grace Hong, Yang Li
Software Mentions: 4
Published: about 6 years ago

10.3389/fgene.2016.00225

Extending the R Library PROPER to Enable Power Calculations for Isoform-Level Analysis with EBSeq
Cited by: 2
Author(s): Amadou Thierno Gaye
Software Mentions: 4
Published: over 9 years ago

10.1002/2211-5463.12982

Metabolomic analysis of fibrotic mice combined with public RNA‐Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis
Cited by: 8
Author(s): Yosui Nojima, Yoshito Takeda, Yohei Maeda, Takeshi Bamba, Eiichiro Fukusaki, Mari Itoh, Kenji Mizuguchi, Atsushi Kumanogoh
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0217600

Exploration of antibiotic resistance risks in a veterinary teaching hospital with Oxford Nanopore long read sequencing
Cited by: 15
Author(s): Kanishka Indiwari Kamathewatta, Rhys N. Bushell, Neil D. Young, Mark Stevenson, Helen Billman‐Jacobe, Glenn F. Browning, Marc S. Marenda
Software Mentions: 4
Published: about 7 years ago

10.18632/oncotarget.11788

Identification of candidate anti-cancer molecular mechanisms of Compound Kushen Injection using functional genomics
Cited by: 64
Author(s): Zhibo Qu, Jingang Cui, Yuka Harata-Lee, Thazin Nwe Aung, Qi Feng, Joy M. Raison, R. Daniel Kortschak, David L. Adelson
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0159392

Towards a Collaborative Research: A Case Study on Linking Science to Farmers’ Perceptions and Knowledge on Arabica Coffee Pests and Diseases and Its Management
Cited by: 30
Author(s): Theresa Liebig, Laurence Jassogne, Eric Rahn, Peter Läderach, Hans‐Michael Poehling, Patrick Kucel, Piet J.A. van Asten, Jacques Avelino
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pntd.0007743

Transcriptome of the parasitic flatworm Schistosoma mansoni during intra-mammalian development
Cited by: 19
Author(s): Arporn Wangwiwatsin, Anna V. Protasio, Shona Wilson, Christian Owusu, Nancy Holroyd, Mandy Sanders, Jacqueline A. Keane, Michael J. Doenhoff, Gabriel Rinaldi, Matthew Berriman
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0199664

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients
Cited by: 32
Author(s): Bahtiyar Yılmaz, Marianne R. Spalinger, Luc Biedermann, Yannick Franc, Nicolas Fournier, Jean‐Benoît Rossel, Pascal Juillerat, Gerhard Rogler, Andrew J. Macpherson, Michael Scharl
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pntd.0007640

Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice
Cited by: 11
Author(s): Ghalia Boubaker, Sebastian Strempel, Andrew Hemphill, Norbert Müller, Junhua Wang, Bruno Gottstein, Markus Spiliotis
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0237775

Diet type influences the gut microbiome and nutrient assimilation of Genetically Improved Farmed Tilapia (Oreochromis niloticus)
Cited by: 30
Author(s): Lara Parata, Debashish Mazumder, Jesmond Sammut, Suhelen Egan
Software Mentions: 4
Published: almost 6 years ago

10.18632/oncotarget.8239

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
Cited by: 13
Author(s): Su‐Jin Baek, Mirang Kim, Donghyuck Bae, Jeong‐Hwan Kim, Hee‐Jin Kim, Myoung‐Eun Han, Sae‐Ock Oh, Yong‐Sung Kim, Seon‐Young Kim
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0216834

TCGA based integrated genomic analyses of ceRNA network and novel subtypes revealing potential biomarkers for the prognosis and target therapy of tongue squamous cell carcinoma
Cited by: 19
Author(s): Zaiye Li, Canhua Jiang, Yongxiang Yuan
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0238420

Construction and analysis of a competing endogenous RNA network to reveal potential prognostic biomarkers for Oral Floor Squamous Cell Carcinoma
Cited by: 1
Author(s): Wenjing Zhang, Shuai Xu, Laner Shi, Zhangzhi Zhu, Xinying Xie
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0230566

Genetic compensation in a stable slc25a46 mutant zebrafish: A case for using F0 CRISPR mutagenesis to study phenotypes caused by inherited disease
Cited by: 35
Author(s): Elena Buglo, Evan Sarmiento, Nicole Belliard Martuscelli, David W. Sant, Matt C. Danzi, A. Jeanine Abrams, Julia E. Dallman, Stephan Züchner
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0249860

The successful reintroduction of African wild dogs (Lycaon pictus) to Gorongosa National Park, Mozambique
Cited by: 15
Author(s): Paola Bouley, António Paulo, Mercia Angela, Cole du Plessis, David G. Marneweck
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-016-0945-9

Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma
Cited by: 163
Author(s): Kyu‐Tae Kim, Hye Won Lee, Hae‐Ock Lee, Hye Jin Song, Da Eun Jeong, Sang Hyun Shin, Hyunho Kim, Yoojin Shin, Do‐Hyun Nam, Byong Chang Jeong, David G. Kirsch, Kyeung Min Joo, Woong-Yang Park
Software Mentions: 4
Published: over 10 years ago

10.12688/f1000research.9682.1

CELL5M: A geospatial database of agricultural indicators for Africa South of the Sahara
Cited by: 5
Author(s): Jawoo Koo, Cindy M. Cox, Melanie Bacou, Carlo Azzarri, Zhe Guo, Ulrike Wood‐Sichra, Queenie Gong, Liangzhi You
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0164121

Abundance and Diversity of Crypto- and Necto-Benthic Coastal Fish Are Higher in Marine Forests than in Structurally Less Complex Macroalgal Assemblages
Cited by: 38
Author(s): Pierre Thiriet, Antonio Franco, Adrien Cheminée, Paolo Guidetti, Olivier Bianchimani, Solène Basthard‐Bogain, Jean-Michel Cottalorda, Hazel O. Arceo, Joan Moranta, Pierre Lejeune, Patrice Francour, Luisa Mangialajo
Software Mentions: 4
Published: almost 10 years ago