cran: fdrtool | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1007792

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research
Cited by: 38
Author(s): Augusto Anguita‐Ruiz, Alberto Segura‐Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá‐Fdez
Software Mentions: 23
Published: over 4 years ago

10.3389/fmicb.2019.01726

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System
Cited by: 66
Author(s): Hai-Zhen Zhu, Z.F. Zhang, Nan Zhou, Cheng‐Ying Jiang, Baojun Wang, Lei Cai, Shuang‐Jiang Liu
Software Mentions: 17
Published: over 5 years ago

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: almost 10 years ago

10.12688/f1000research.8967.2

An end to end workflow for differential gene expression using Affymetrix microarrays
Cited by: 16
Author(s): Bernd Klaus, Stefanie Reisenauer
Software Mentions: 13
Published: over 6 years ago

10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Cited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 8 years ago

10.1002/sim.8116

Correlation‐adjusted regression survival scores for high‐dimensional variable selection
Cited by: 10
Author(s): Thomas Welchowski, Verena Zuber, Matthias Schmid
Software Mentions: 11
Published: almost 6 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 5 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: over 9 years ago

10.3389/fmicb.2018.02452

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Cited by: 52
Author(s): Umer Zeeshan Ijaz, Lojika Sivaloganathan, Aaron McKenna, Anne Richmond, Carmel Kelly, Mark Linton, Alexandros Ch. Stratakos, Ursula Lavery, Abdi Elmi, Brendan W. Wren, Nick Dorrell, Nicolae Corcionivoschi, Ozan Gundogdu
Software Mentions: 9
Published: about 6 years ago

10.1186/1471-2164-15-139

Unique features of the transcriptional response to model aneuploidy in human cells
Cited by: 85
Author(s): Milena Dürrbaum, Anastasia Yurievna Kuznetsova, Verena Passerini, Silvia Stingele, Gabriele Stoehr, Zuzana Storchová
Software Mentions: 9
Published: almost 11 years ago

10.3390/ijerph17197127

Relationship between Quality of Life and the Complexity of Default Mode Network in Resting State Functional Magnetic Resonance Image in Down Syndrome
Cited by: 6
Author(s): María Carbó‐Carreté, Cristina Cañete‐Massé, María Dolores Figueroa-Jiménez, Maribel Peró‐Cebollero, Joan Guàrdia‐Olmos
Software Mentions: 9
Published: about 4 years ago

10.1172/jci.insight.141683

CD84 is a regulator of the immunosuppressive microenvironment in Multiple Myeloma
Cited by: 15
Author(s): Hadas Lewinsky, Emine Gulsen Gunes, Keren David, Lihi Radomir, Matthias P. Kramer, Bianca Pellegrino, Michal Perpinial, Jing Chen, Ting He, Anthony G. Mansour, Kun yu Teng, Supriyo Bhattacharya, Enrico Caserta, Estelle Troadec, Peter Lee, Mingye Feng, Jonathan J. Keats, Amrita Krishnan, Michael Rosenzweig, Jianhua Yu, Michael A. Caligiuri, Yosef Cohen, Olga Shevetz, Shirly Becker-Herman, Flavia Pichiorri, Steven T. Rosen, Idit Shachar
Software Mentions: 9
Published: almost 4 years ago

10.1038/s41598-020-66865-2

Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys
Cited by: 37
Author(s): Elizabeth K. Mallott, Carola Borries, Andreas Koenig, Katherine R. Amato, Amy Lu
Software Mentions: 8
Published: over 4 years ago

10.1093/bib/bbaa290

NetCoMi: network construction and comparison for microbiome data in R
Cited by: 165
Author(s): Stefanie Peschel, Christian L. Müller, Erika von Mutius, Anne‐Laure Boulesteix, Martin Depner
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pgen.1009253

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus
Cited by: 22
Author(s): Xavier Grau‐Bové, Eric R. Lucas, Dimitra Pipini, Emily J. Rippon, Arjèn Emiel van 't Hof, Constant Edi, Samuel Dadzie, Alexander Egyir-Yawson, John Essandoh, Joseph Chabi, Luc Djogbénou, Nicholas J. Harding, Alistair Miles, Dominic P. Kwiatkowski, Martin J. Donnelly, David Weetman
Software Mentions: 8
Published: almost 4 years ago

10.3389/fvets.2019.00499

Developing Diagnostic Frameworks in Veterinary Behavioral Medicine: Disambiguating Separation Related Problems in Dogs
Cited by: 25
Author(s): Luciana Santos de Assis, Raquel Matos, Thomas W. Pike, Ohp Burman, Daniel S. Mills
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0183933

Tensor decomposition-based unsupervised feature extraction applied to matrix products for multi-view data processing
Cited by: 24
Author(s): Y-h. Taguchi
Software Mentions: 7
Published: over 7 years ago

10.1186/s13059-020-02081-5

The Tug1 lncRNA locus is essential for male fertility
Cited by: 59
Author(s): Jordan P. Lewandowski, Gabrijela Dumbović, Audrey Watson, Tae-Young Hwang, Emily Jacobs-Palmer, Nydia P Chang, Christian Much, Kyle M. Turner, Christopher Kirby, Nimrod D. Rubinstein, Abigail F. Groff, Steve C. Liapis, Chiara Gerhardinger, Assaf C. Bester, Pier Paolo Pandolfi, John G. Clohessy, Hopi E. Hoekstra, Martin Sauvageau, John L. Rinn
Software Mentions: 6
Published: over 4 years ago

10.1128/mSystems.00163-21

Oral Epithelial Cells Distinguish between Candida Species with High or Low Pathogenic Potential through MicroRNA Regulation
Cited by: 5
Author(s): Márton Horváth, Gábor Nagy, Nóra Zsindely, László Bodai, Péter Horváth, Csaba Vágvölgyi, Joshua D. Nosanchuk, Renáta Tóth, Attila Gácser
Software Mentions: 6
Published: over 3 years ago

10.1073/pnas.1914491116

BMP signaling inhibition in Drosophila secondary cells remodels the seminal proteome and self and rival ejaculate functions
Cited by: 28
Author(s): Ben R. Hopkins, Irem Sepil, Sarah Bonham, Thomas D. Miller, P. David Charles, Román Fischer, Benedikt M. Kessler, Clive Wilson, Stuart Wigby
Software Mentions: 6
Published: about 5 years ago

10.1073/pnas.1906149116

Divergent allocation of sperm and the seminal proteome along a competition gradient in Drosophila melanogaster
Cited by: 70
Author(s): Ben R. Hopkins, Irem Sepil, Thézénas M-L., Jo Craig, Thomas D. Miller, P. David Charles, Román Fischer, Benedikt M. Kessler, Amanda Bretman, Tommaso Pizzari, Stuart Wigby
Software Mentions: 6
Published: over 5 years ago

10.15252/msb.202110253

Model‐guided development of an evolutionarily stable yeast chassis
Cited by: 5
Author(s): Filipa Pereira, Helena Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, D. Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R. Patil
Software Mentions: 6
Published: over 3 years ago

10.15252/msb.20145776

A high‐throughput <scp>C</scp> h <scp>IP</scp> ‐ <scp>S</scp> eq for large‐scale chromatin studies
Cited by: 28
Author(s): Christophe D. Chabbert, Sophie H. Adjalley, Bernd Klaus, E. Fritsch, Ishaan Gupta, Vicent Pelechano, Lars M. Steinmetz
Software Mentions: 5
Published: almost 10 years ago

10.3389/fcell.2014.00040

Quantifying periodicity in omics data
Cited by: 7
Author(s): Cornelia Amariei, Masaru Tomita, Douglas B. Murray
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2105-9-303

A unified approach to false discovery rate estimation
Cited by: 343
Author(s): Korbinian Strimmer
Software Mentions: 5
Published: over 16 years ago

10.1371/journal.ppat.1006699

The yeast form of the fungus Candida albicans promotes persistence in the gut of gnotobiotic mice
Cited by: 70
Author(s): Lena Böhm, Sanda Torsin, Su Hlaing Tint, Marie Therese Eckstein, Tobias Ludwig, J. Christian Pérez
Software Mentions: 5
Published: about 7 years ago

10.1186/s40168-020-00995-7

Characterization of the human skin resistome and identification of two microbiota cutotypes
Cited by: 30
Author(s): Zhiming Li, Jingjing Xia, Liuyiqi Jiang, Yimei Tan, Yitai An, Xiaodong Zhu, Jie Ruan, Zhihua Chen, Hefu Zhen, Yanyun Ma, Zhuye Jie, Liang Xiao, Huanming Yang, Jian Wang, Karsten Kristiansen, Xun Xu, Li Jin, Chao Nie, Jean Krutmann, Xiao Liu, Jiucun Wang
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.47214

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Cited by: 15
Author(s): Daniel Andergassen, Zachary D. Smith, Jordan P. Lewandowski, Chiara Gerhardinger, Alexander Meissner, John L. Rinn
Software Mentions: 5
Published: about 5 years ago

10.1098/rstb.2013.0342

Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation
Cited by: 44
Author(s): Alexander S. T. Papadopulos, Maria Kaye, Céline Devaux, Helen Hipperson, Jackie Lighten, Luke T. Dunning, I. Hutton, William J. Baker, Roger K. Butlin, Vincent Savolainen
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0104947

Voxel-Wise Motion Artifacts in Population-Level Whole-Brain Connectivity Analysis of Resting-State fMRI
Cited by: 22
Author(s): Tamás Spisák, András Jakab, Sándor Attila Kis, Gábor Opposits, Csaba Aranyi, Ervin Berényi, Miklós Emri
Software Mentions: 5
Published: over 10 years ago

10.1128/mSystems.00130-17

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
Cited by: 284
Author(s): Marius Vital, André Karch, Dietmar H. Pieper
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pntd.0008671

Novel small RNAs expressed by Bartonella bacilliformis under multiple conditions reveal potential mechanisms for persistence in the sand fly vector and human host
Cited by: 6
Author(s): Shaun Wachter, Linda D. Hicks, Rahul Raghavan, Michael F. Minnick
Software Mentions: 5
Published: about 4 years ago

10.1002/eji.201948432

CD73 contributes to anti‐inflammatory properties of afferent lymphatic endothelial cells in humans and mice
Cited by: 10
Author(s): Dominik Eichin, Alberto Pessia, Akiko Takeda, Joni Laakkonen, Lydia Bellmann, Matti Kankainen, Beat A. Imhof, Patrizia Stoitzner, Jing Tang, Marko Salmi, Sirpa Jalkanen
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0245824

MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction
Cited by: 51
Author(s): Otília Menyhárt, Boglárka Weltz, Balázs Győrffy
Software Mentions: 5
Published: over 3 years ago

10.3389/fmicb.2020.00641

Functional Analysis of Sugars in Modulating Bacterial Communities and Metabolomics Profiles of Medicago sativa Silage
Cited by: 14
Author(s): Bing Wang, Run Gao, Zhaohai Wu, Zhu Yu
Software Mentions: 4
Published: over 4 years ago

10.3389/fcell.2021.675438

Identification of Key Genes With Differential Correlations in Lung Adenocarcinoma
Cited by: 9
Author(s): You Zhou, Bin Xu, Yi Zhou, Jian Liu, Xiao Zheng, Yingting Liu, Hepu Deng, Ming Liu, Xiubao Ren, Jianchuan Xia, Xiangyin Kong, Tao Huang, Jingting Jiang
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0158247

Nonlinear Network Reconstruction from Gene Expression Data Using Marginal Dependencies Measured by DCOL
Cited by: 10
Author(s): Haodong Liu, Peng Li, Mengyao Zhu, Xiaofei Wang, Jianwei Lu, Tianwei Yu
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0234986

Molecular analyses of glioblastoma stem-like cells and glioblastoma tissue
Cited by: 7
Author(s): Marco Wallenborn, Leiming Xu, Holger Kirsten, Leili Rohani, Daniela Rudolf, Peter Ahnert, Christian Schmidt, R. Schulz, Mandy Richter, Wolfgang Krupp, Wolf Mueller, Adiv A. Johnson, Jürgen Meixensberger, Heidrun Holland
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12123786

Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures
Cited by: 9
Author(s): Sofia Karkampouna, Maria Rosaria De Filippo, Charlotte K.Y. Ng, Irena Klima, Eugenio Zoni, Martin Spahn, Frank Stein, Per Haberkant, George N. Thalmann, Marianna Kruithof-de Julio
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-017-3944-7

Genome-wide signals of positive selection in strongylocentrotid sea urchins
Cited by: 11
Author(s): Kord M. Kober, Grant H. Pogson
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-92385-8

Genome-enabled discovery of evolutionary divergence in brains and behavior
Cited by: 4
Author(s): Chinar Patil, J. B. Sylvester, Kawther Abdilleh, Michael Norsworthy, Karen Pottin, Milan Malinsky, Ryan F. Bloomquist, Zachary V. Johnson, Patrick T. McGrath, J. Todd Streelman
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-79704-1

Data-driven detection of subtype-specific differentially expressed genes
Cited by: 9
Author(s): Lulu Chen, Yingzhou Lu, Chiung Ting Wu, Robert Clarke, Guoqiang Yu, Jennifer E. Van Eyk, David M. Herrington, Yue Wang
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-65638-1

Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Cited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-020-02706-8

Molecular insights into the compatible and incompatible interactions between sugar beet and the beet cyst nematode
Cited by: 19
Author(s): Razieh Ghaemi, Ebrahim Pourjam, Naser Safaie, Bruno Verstraeten, S B Mahmoudi, Rahim Mehrabi, Tim De Meyer, Tina Kyndt
Software Mentions: 4
Published: about 4 years ago

10.1186/s13104-019-4471-1

Shiny-Seq: advanced guided transcriptome analysis
Cited by: 26
Author(s): Zenitha Sundararajan, Rainer Knoll, Peter Hombach, Matthias Becker, Joachim L. Schultze, Thomas Ulas
Software Mentions: 4
Published: over 5 years ago

10.1186/1752-0509-5-1

Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach
Cited by: 118
Author(s): Atsushi Fukushima, Miyako Kusano, Henning Redestig, Masanori Arita, Kazuki Saito
Software Mentions: 4
Published: almost 14 years ago

10.1186/s40246-019-0247-x

Transcriptomic analysis of monocytes from HIV-positive men on antiretroviral therapy reveals effects of tobacco smoking on interferon and stress response systems associated with depressive symptoms
Cited by: 6
Author(s): David R. Lorenz, Vikas Misra, Dana Gabuzda
Software Mentions: 4
Published: about 5 years ago

10.1186/s40168-018-0542-0

Pathogenic functions of host microbiota
Cited by: 64
Author(s): Silke Rath, Tatjana Rud, André Karch, Dietmar H. Pieper, Marius Vital
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-018-2081-x

Control procedures and estimators of the false discovery rate and their application in low-dimensional settings: an empirical investigation
Cited by: 18
Author(s): Regina Brinster, Anna Köttgen, Bamidele O. Tayo, Martin Schumacher, Peggy Sekula
Software Mentions: 4
Published: almost 7 years ago

10.1016/j.gpb.2016.04.004

Comparative Gene Expression Analysis of Mouse and Human Cardiac Maturation
Cited by: 38
Author(s): Hideki Uosaki, Y-h. Taguchi
Software Mentions: 4
Published: over 8 years ago

10.15252/msb.20177998

The relative resistance of children to sepsis mortality: from pathways to drug candidates
Cited by: 10
Author(s): Rose Bernadette Joachim, Gabriel Altschuler, John N. Hutchinson, Hector R. Wong, Winston Hide, Lester Kobzik
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.2478

Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
Cited by: 13
Author(s): Chien-Hung Huang, Jin-Shuei Ciou, Shun-Tsung Chen, Victor C. Kok, Yuan‐Chiang Chung, Jeffrey J. P. Tsai, Nilubon Kurubanjerdjit, Chi-Ying F. Huang, Ka-Lok Ng
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pcbi.1005700

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
Cited by: 15
Author(s): David Amar, Ron Shamir, Daniel Yekutieli
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1008518

Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis
Cited by: 10
Author(s): Alfredo Rago, John H. Werren, John K. Colbourne
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1008830

Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3′UTR intron-containing NMD targets
Cited by: 18
Author(s): Pooja Gangras, Thomas L. Gallagher, Michael A. Parthun, Zhongxia Yi, Robert D. Patton, Kiel T. Tietz, Natalie C. Deans, Ralf Bundschuh, Sharon L. Amacher, Guramrit Singh
Software Mentions: 4
Published: over 4 years ago

10.3389/fpsyg.2019.01893

Effects of Mortality Salience on Physiological Arousal
Cited by: 13
Author(s): Johannes Klackl, Eva Jonas
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.576661

Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments
Cited by: 14
Author(s): Hualong Wang, Raven L. Bier, Laura Zgleszewski, Marc Peipoch, Emmanuel C. Omondi, Atanu Mukherjee, Feng Chen, Chuanlun Zhang, Jinjun Kan
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2018.00696

A Comprehensive RNA Expression Signature for Cervical Squamous Cell Carcinoma Prognosis
Cited by: 5
Author(s): Jie Xiong, Shengyu Guo, Zhitong Bing, Yanlin Su, Le Guo
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.101027

Higher expression of somatic repair genes in long-lived ant queens than workers
Cited by: 28
Author(s): Eric R. Lucas, Eyal Privman, Laurent Keller
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-10-384

Regularized estimation of large-scale gene association networks using graphical Gaussian models
Cited by: 189
Author(s): Nicole Krämer, Juliane Schäfer, Anne‐Laure Boulesteix
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2105-10-161

GAGE: generally applicable gene set enrichment for pathway analysis
Cited by: 1,035
Author(s): Weijun Luo, Michael S. Friedman, Kerby Shedden, Kurt D. Hankenson, Peter J. Woolf
Software Mentions: 3
Published: over 15 years ago

10.1186/s12885-021-08681-z

Genome-wide profiling of alternative splicing in glioblastoma and their clinical value
Cited by: 3
Author(s): Youwei Li, Dongsheng Guo
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2164-15-S9-S6

Transcriptome alterations of mitochondrial and coagulation function in schizophrenia by cortical sequencing analysis
Cited by: 25
Author(s): Kuo-Chuan Huang, Ko-Chun Yang, Han Lin, Theresa Tsun-Hui Tsao, Sheng-An Lee
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-13-596

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells
Cited by: 1
Author(s): Maria Bro Kloster, Anders Ellern Bilgrau, María Rodrigo-Domingo, Kim Steve Bergkvist, Alexander Schmitz, Mads Sønderkær, Julie Støve Bødker, Steffen Falgreen, Mette Nyegaard, Hans Erik Johnsen, Kåre Lehmann Nielsen, Karen Dybkær, Martin Bøgsted
Software Mentions: 3
Published: about 12 years ago

10.1186/1752-0509-4-124

Molecular mechanistic associations of human diseases
Cited by: 11
Author(s): Philip Stegmaier, Mathias Krull, Nico Voss, Alexander Kel, Edgar Wingender
Software Mentions: 3
Published: over 14 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: over 10 years ago

10.3390/microorganisms8070981

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves
Cited by: 15
Author(s): Yaoyue Wang, Qingmiao Shen, Shu Zhong, Yulin Chen, Yuxin Yang
Software Mentions: 3
Published: over 4 years ago

10.1111/mec.13615

Rapid genome‐wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools
Cited by: 77
Author(s): Steven J. Franks, Nolan C. Kane, Niamh B. O’Hara, Silas Tittes, Joshua S. Rest
Software Mentions: 3
Published: over 8 years ago

10.15252/msb.202010188

SARS‐CoV‐2 infection remodels the host protein thermal stability landscape
Cited by: 15
Author(s): Joel Selkrig, Megan L. Stanifer, André Mateus, Karin Mitosch, Iñigo Barrio-Hernandez, Mandy Rettel, Heeyoung Kim, Carlos G.P. Voogdt, Philipp Walch, Carmon Kee, Nils Kurzawa, Frank Stein, Clement M Potel, Anna Jarząb, Bernhard Küster, Ralf Bartenschlager, Steeve Boulant, Pedro Beltrão, Athanasios Typas, Mikhail M. Savitski
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0003220

Fibrotic Myofibroblasts Manifest Genome-Wide Derangements of Translational Control
Cited by: 93
Author(s): Ola Larsson, Deanna Diebold, Danhua Fan, Mark S. Peterson, Richard Seonghun Nho, Peter B. Bitterman, Craig A. Henke
Software Mentions: 3
Published: over 16 years ago

10.3390/cancers13174468

Tumor Nonimmune-Microenvironment-Related Gene Expression Signature Predicts Brain Metastasis in Lung Adenocarcinoma Patients after Surgery: A Machine Learning Approach Using Gene Expression Profiling
Cited by: 4
Author(s): Seokjin Haam, Jae‐Ho Han, Hyun Woo Lee, Young Wha Koh
Software Mentions: 3
Published: over 3 years ago

10.1016/j.devcel.2020.11.010

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease
Cited by: 139
Author(s): Rasa Elmentaite, Alex Ross, Kenny Roberts, Kylie R. James, Daniel Ortmann, Tomás Gomes, Komal Nayak, Liz Tuck, Sophie Pritchard, Ömer Bayraktar, Robert Heuschkel, Ludovic Vallier, Sarah A. Teichmann, Matthias Zilbauer
Software Mentions: 3
Published: about 4 years ago

10.15252/embj.2021107913

Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol
Cited by: 15
Author(s): Anna M. Schlagowski, Katharina Knöringer, Sandrine Morlot, Ana Sánchez Vicente, Tamara Flohr, Lena Krämer, Felix Boos, Nabeel Khalid, Sheraz Ahmed, Jana Schramm, Lena Maria Murschall, Per Haberkant, Frank Stein, Jan Riemer, Benedikt Westermann, Ralf J. Braun, Konstanze F. Winklhofer, Gilles Charvin, Johannes M. Herrmann
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2019.01356

The Sole Mycobacterium smegmatis MazF Toxin Targets tRNALys to Impart Highly Selective, Codon-Dependent Proteome Reprogramming
Cited by: 7
Author(s): Valdir C. Barth, Nancy A. Woychik
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpsyg.2021.689304

Do Histories of Painful Life Experiences Affect the Expression of Empathy Among Young Adults? An Electroencephalography Study
Cited by: 5
Author(s): Parvaneh Yaghoubi Jami, Hyemin Han, Stephen J. Thoma, Behzad Mansouri, Rick Houser
Software Mentions: 3
Published: over 3 years ago

10.1242/jcs.233783

Condensin II protein dysfunction impacts mitochondrial respiration and stress response
Cited by: 7
Author(s): Emily Deutschman, Jacqueline R. Ward, Avinash Kumar, Greeshma Ray, Nicole Welch, Madeleine E. Lemieux, S. Dasarathy, Michelle S. Longworth
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.ppat.1000154

Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis
Cited by: 227
Author(s): Andrew McDonagh, Natalie D. Fedorova, Jonathan Crabtree, Yu Yan, Heenam Stanley Kim, Dan Chen, Omar Loss, Timothy C. Cairns, Gustavo H. Goldman, Darius Armstrong‐James, Ken Haynes, Hubertus Haas, Markus Schrettl, Gregory S. May, William C. Nierman, Elaine Bignell
Software Mentions: 3
Published: over 16 years ago

10.3390/ijms17050696

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Cited by: 31
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 8 years ago

10.1186/1752-0509-7-134

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways
Cited by: 8
Author(s): Jon Pey, Kaspar Valgepea, Ángel Rubio, John E. Beasley, Francisco J. Planes
Software Mentions: 2
Published: about 11 years ago

10.1038/srep11953

Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs
Cited by: 91
Author(s): Jing Lü, Ye Hou, Hui Wu, Yuanxin Miao, Xinyun Li, Jianhua Cao, John M. Brameld, Tim Parr, Zhao Song
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0048289

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen
Cited by: 230
Author(s): Derrick E. Fouts, Sebastian Szpakowski, Janaki Purushe, Manolito Torralba, R. C. Waterman, M. D. MacNeil, L. J. Alexander, Karen E. Nelson
Software Mentions: 2
Published: about 12 years ago

10.3389/fgene.2014.00011

Exploring the potential benefits of stratified false discovery rates for region-based testing of association with rare genetic variation
Cited by: 4
Author(s): Changjiang Xu, Antonio Ciampi, Celia M.T. Greenwood
Software Mentions: 2
Published: almost 11 years ago

10.3389/fgene.2012.00301

The Utility of Mitochondrial and Y Chromosome Phylogenetic Data to Improve Correction for Population Stratification
Cited by: 6
Author(s): Robert Makowsky, Qi Yan, Howard W. Wiener, Michael J. Sandel, Brahim Aı̈ssani, Hemant K. Tiwari, Sadeep Shrestha
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12920-016-0229-y

Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia
Cited by: 31
Author(s): Sheng-An Lee, Kuo-Chuan Huang
Software Mentions: 2
Published: about 8 years ago

10.1186/gb-2014-15-7-r89

Host lifestyle affects human microbiota on daily timescales
Cited by: 707
Author(s): Lawrence A. David, Arne Materna, Jonathan Friedman, Maria I Campos-Baptista, Matthew Blackburn, Alessandra Perrotta, Susan E. Erdman, Eric J. Alm
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-021-83520-6

Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza
Cited by: 18
Author(s): Mei Jiang, Haimei Chen, Jingting Liu, Qing Du, Shanfa Lu, Chang Liu
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0147027

Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates
Cited by: 8
Author(s): Richard Laughlin, Kenneth L. Drake, John C. Morrill, L. Garry Adams
Software Mentions: 2
Published: almost 9 years ago

10.6064/2012/519394

A Comparison of Two Classes of Methods for Estimating False Discovery Rates in Microarray Studies
Cited by: 3
Author(s): Emily Hansen, Kathleen F. Kerr
Software Mentions: 2
Published: almost 13 years ago

10.15252/msb.20178131

Quantifying compartment‐associated variations of protein abundance in proteomics data
Cited by: 10
Author(s): Luca Parca, Martin Beck, Peer Bork, Alessandro Ori
Software Mentions: 2
Published: over 6 years ago

10.1186/1744-8069-5-7

Correlational Analysis for Identifying Genes whose Regulation Contributes to Chronic Neuropathic Pain
Cited by: 40
Author(s): Annina H. Persson, Mathias Gebauer, Suzana Jordan, Christiane Metz-Weidmann, Anke M. Schulte, Hans‐Christoph Schneider, Danping Ding‐Pfennigdorff, Jonas Thun, Xiao‐Jun Xu, Zsuzsanna Wiesenfeld‐Hallin, Ariel Darvasi, Kaj Fried, Marshall Devor
Software Mentions: 2
Published: almost 16 years ago

10.3390/cancers13164157

The Fatty Acid and Protein Profiles of Circulating CD81-Positive Small Extracellular Vesicles Are Associated with Disease Stage in Melanoma Patients
Cited by: 14
Author(s): Giovanni Paolino, Veronica Huber, Serena Camerini, Marialuisa Casella, Alberto Macone, Lucia Bertuccini, Francesca Iosi, Elisa Moliterni, Serena Cecchetti, Irene Ruspantini, Flavia Chiarotti, Elisabetta Vergani, Luca Lalli, Carla Raggi, Antonella Di Biase, Stefano Calvieri, Santo Raffaele Mercuri, Luana Lugini, Cristina Federici
Software Mentions: 2
Published: over 3 years ago

10.1093/molbev/msu135

How the Mountain Pine Beetle (Dendroctonus ponderosae) Breached the Canadian Rocky Mountains
Cited by: 69
Author(s): Jasmine K. Janes, Yisu Li, Christopher I. Keeling, Macaire Man Saint Yuen, Celia K. Boone, Janice E. K. Cooke, Jöerg Bohlmann, Dezene P. W. Huber, Brent W. Murray, David W. Coltman, Felix A. H. Sperling
Software Mentions: 2
Published: over 10 years ago

10.1016/j.cell.2018.03.053

Pervasive Protein Thermal Stability Variation during the Cell Cycle
Cited by: 173
Author(s): Isabelle Becher, Amparo Andrés-Pons, Natalie Romanov, Frank Stein, Maike Schramm, Florence Baudin, Dominic Helm, Nils Kurzawa, André Mateus, Marie Therese Mackmull, Athanasios Typas, Christoph W. Müller, Peer Bork, Martin Beck, Mikhail M. Savitski
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2019.00356

Saponin-Induced Shifts in the Rumen Microbiome and Metabolome of Young Cattle
Cited by: 68
Author(s): Bing Wang, Man Peng, Qi Yu Diao, Tiebin Yan
Software Mentions: 2
Published: almost 6 years ago

10.1098/rsob.150262

Primate-specific oestrogen-responsive long non-coding RNAs regulate proliferation and viability of human breast cancer cells
Cited by: 10
Author(s): Chin-Yo Lin, Erica L. Kleinbrink, Fabien Dachet, Juan Cai, Donghong Ju, Amanda Goldstone, Emily J. Wood, Liu Ka, Hui Jia, Anton Scott Goustin, Mary A. Kosir, Pattaraporn Thepsuwan, Leonard Lipovich
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0200694

Assessing genetic architecture and signatures of selection of dual purpose Gir cattle populations using genomic information
Cited by: 50
Author(s): Amanda Marchi Maiorano, Daniela Lourenco, S. Tsuruta, Alejandra Maria Toro Ospina, Nedenia Bonvino Stafuzza, Yutaka Masuda, Aníbal Eugênio Vercesi Filho, Joslaine Noely dos Santos Gonçalves Cyrillo, Rogério Abdallah Curi, Josineudson Augusto Ii Vasconcelos Silva
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.112.003194

Microarray-Based Capture of Novel Expressed Cell Type–Specific Transfrags (CoNECT) to Annotate Tissue-Specific Transcription in Drosophila melanogaster
Cited by: 0
Author(s): Xiaojing Hong, Harshavardhan Doddapaneni, Josep M. Comeron, Matthew J. Rodesch, Heather A. Halvensleben, Chung Yi Nien, F. Bolei, Raghu Metpally, Todd Richmond, Thomas Albert, J. Robert Manak
Software Mentions: 2
Published: over 12 years ago

10.1186/1756-0381-5-18

Mining SOM expression portraits: feature selection and integrating concepts of molecular function
Cited by: 51
Author(s): Henry Wirth, Martin von Bergen, Hans Binder
Software Mentions: 2
Published: about 12 years ago

10.1186/1472-6785-14-20

High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid
Cited by: 28
Author(s): An Vanden Broeck, Wouter Van Landuyt, Karen Cox, Luc De Bruyn, Ralf Gyselings, Gerard Oostermeijer, Bertille Valentin, Gregor Božič, Branko Dolinar, Zoltán Illyés, Joachim Mergeay
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12872-019-01320-3

Total iron binding capacity (TIBC) is a potential biomarker of left ventricular remodelling for patients with iron deficiency anaemia
Cited by: 3
Author(s): Yan Chen, Jing Wan, Haidan Xia, LI Ya, Yufeng Xu, Haiyan Lin, Hassah Batool Iftikhar
Software Mentions: 1
Published: almost 5 years ago

Projects: cran: fdrtool

Papers Mentioning fdrtool 124