Ecosyste.ms: Papers

10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: over 5 years ago

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.1186/s13072-020-00342-y

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
Cited by: 39
Author(s): Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
Software Mentions: 14
Published: over 4 years ago

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: about 9 years ago

10.1038/s42003-019-0415-5

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
Cited by: 137
Author(s): Lukas M. Weber, Małgorzata Nowicka, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 5 years ago

10.1186/s12859-016-1386-x

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Cited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: almost 8 years ago

10.1016/j.csbj.2021.05.040

Robustness of differential gene expression analysis of RNA-seq
Cited by: 31
Author(s): Alexey Stupnikov, Caitríona E. McInerney, Kienan I. Savage, Stuart McIntosh, Frank Emmert‐Streib, Richard D. Kennedy, Manuel Salto-Tellez, Kevin M. Prise, Darragh G. McArt
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12859-017-1847-x

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Cited by: 42
Author(s): Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes‐Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush
Software Mentions: 10
Published: about 7 years ago

10.1186/gb-2014-15-2-r29

voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Cited by: 4,221
Author(s): Charity W. Law, Yunshun Chen, Wei Shi, Gordon K. Smyth
Software Mentions: 10
Published: almost 11 years ago

10.1186/s12859-017-1539-6

Model based heritability scores for high-throughput sequencing data
Cited by: 9
Author(s): Pratyaydipta Rudra, Wenmei Shi, Brian Vestal, Pamela Russell, Aaron Odell, Robin D. Dowell, Richard A. Radcliffe, Laura Saba, Katerina Kechris
Software Mentions: 10
Published: over 7 years ago

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: over 6 years ago

10.1186/s12859-017-1498-y

Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysis
Cited by: 15
Author(s): Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano
Software Mentions: 10
Published: almost 8 years ago

10.7554/eLife.58178

16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development
Cited by: 24
Author(s): Julien G. Roth, Kristin Muench, Aditya Asokan, Victoria M Mallett, Hongwei Gai, Yogendra Verma, Stephen G. Weber, Carol Charlton, Jonas L. Fowler, Kyle M. Loh, Ricardo E. Dolmetsch, Theo Palmer
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pone.0220518

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne)
Cited by: 4
Author(s): Albert Fradera-Sola, Ann Thomas, Dagmara Gasior, John A. Harper, Matthew J. Hegarty, Ian Armstead, Narcís Fernández-Fuentes
Software Mentions: 9
Published: over 5 years ago

10.1186/s12859-016-0994-9

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments
Cited by: 79
Author(s): Ran Bi, Peng Liu
Software Mentions: 9
Published: over 8 years ago

10.1186/s13059-016-1000-6

Blood lipids influence DNA methylation in circulating cells
Cited by: 149
Author(s): Koen F. Dekkers, Maarten van Iterson, Roderick C. Slieker, Matthijs Moed, Marc Jan Bonder, M.A. van Galen, Hailiang Mei, Daria V. Zhernakova, Leonard H van den Berg, Joris Deelen, Jenny van Dongen, Diana van Heemst, Albert Hofman, Jouke Jan Hottenga, Carla Kallen, Casper G. Schalkwijk, Coen D. A. Stehouwer, Ettje F. Tigchelaar, André G. Uitterlinden, Gonneke Willemsen, Alexandra Zhernakova, Lude Franke, Peter A.C. ’t Hoen, Ritsert C. Jansen, Joyce B. J. van Meurs, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M.J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Erik W. van Zwet, P. Eline Slagboom, J. Wouter Jukema, Bastiaan T. Heijmans
Software Mentions: 9
Published: over 8 years ago

10.1002/jia2.25148

Oral abstracts of the 22nd International AIDS Conference, 23-27 July 2018, Amsterdam, the Netherlands
Cited by: 9
Author(s):
Software Mentions: 9
Published: over 6 years ago

10.1186/s40246-019-0242-2

Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis
Cited by: 4
Author(s): Carlos Ruiz‐Arenas, Alejandro Cáceres, Vı́ctor Moreno, Juan R. González
Software Mentions: 9
Published: about 5 years ago

10.1038/s41598-020-60336-4

Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 nephrectomy
Cited by: 18
Author(s): Denis Delić, Franziska Wiech, Richard Urquhart, Ogsen Gabrielyan, Kathrin Rieber, Marcel Rolser, Oleg Tsuprykov, Ahmed A. Hasan, Bernhard K. Krämer, Patrick Baum, A Köhler, Florian Gantner, Mark Michael, Berthold Hocher, Thomas Klein
Software Mentions: 9
Published: over 4 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: about 9 years ago

10.1186/s12859-020-3506-x

Negative binomial additive model for RNA-Seq data analysis
Cited by: 16
Author(s): Ruwei Xu, Pei Fen Kuan
Software Mentions: 8
Published: over 4 years ago

10.3389/fcimb.2018.00326

In Search of Biomarkers for Pathogenesis and Control of Leishmaniasis by Global Analyses of Leishmania-Infected Macrophages
Cited by: 16
Author(s): Patrícia Sampaio Tavares Veras, Pablo Ivan Pereira Ramos, Juliana Perrone Bezerra de Menezes
Software Mentions: 8
Published: about 6 years ago

10.1186/s12935-020-01661-6

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Cited by: 6
Author(s): R. Adam, Sanne M. van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E. de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen
Software Mentions: 8
Published: almost 4 years ago

10.17179/excli2015-168

Data- and knowledge-based modeling of gene regulatory networks: an update.
Cited by: 24
Author(s): Jörg Linde, Sylvie Schulze, Sebastian Henkel, Reinhard Guthke
Software Mentions: 8
Published: almost 10 years ago

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: over 4 years ago

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0201751

Pancreatic cancer survival analysis defines a signature that predicts outcome
Cited by: 52
Author(s): Pichai Raman, Ravikanth Maddipati, Kian Huat Lim, Aydın Tözeren
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.57843

Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in the HPA stress axis
Cited by: 17
Author(s): Arne Sahm, Matthias Platzer, Philipp Koch, Yoshiyuki Henning, Martin Bens, Marco Groth, Hynek Burda, Sabine Begall, Saskia Ting, Moritz Goetz, Paul Van Daele, Magdalena Staniszewska, Jasmin Klose, Pedro Fragoso Costa, Steve Hoffmann, Karol Szafranski, Philip Dammann
Software Mentions: 7
Published: over 3 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single <i>Ctena orbiculata</i> (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: about 5 years ago

10.1186/s12864-016-2816-x

EventPointer: an effective identification of alternative splicing events using junction arrays
Cited by: 28
Author(s): Juan Pablo Romero, Ander Muniategui, Fernando J. de Miguel, Ander Aramburu, Luis M. Montuenga, Rubén Pı́o, Ángel Rubio
Software Mentions: 7
Published: over 8 years ago

10.1186/s13059-021-02466-0

Acute depletion of CTCF rewires genome-wide chromatin accessibility
Cited by: 26
Author(s): Beisi Xu, Hong Wang, Shaela Wright, Judith Hyle, Yang Zhang, Ying Shao, Mingming Niu, Yiping Fan, Wojciech Rosikiewicz, Mohamed Nadhir Djekidel, Junmin Peng, Rui Lu, Chunliang Li
Software Mentions: 7
Published: about 3 years ago

10.1186/s13040-017-0150-8

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
Cited by: 15
Author(s): Bork A. Berghoff, Torgny Karlsson, Thomas Källman, E. Gerhart H. Wagner, Manfred Grabherr
Software Mentions: 7
Published: about 7 years ago

10.1155/2020/2837906

Integrative Analysis of Three Novel Competing Endogenous RNA Biomarkers with a Prognostic Value in Lung Adenocarcinoma
Cited by: 7
Author(s): Juan Tan, Weimin Wang, Bin Song, Yawei Song, Zili Meng
Software Mentions: 7
Published: over 4 years ago

10.1016/j.ccell.2019.08.008

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer
Cited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: about 5 years ago

10.3390/genes11040400

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant
Cited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.8206

consensusDE: an R package for assessing consensus of multiple RNA-seq algorithms with RUV correction
Cited by: 24
Author(s): Ashley J. Waardenberg, Matthew A. Field
Software Mentions: 7
Published: almost 5 years ago

10.12688/f1000research.9005.3

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
Cited by: 297
Author(s): Charity W. Law, Monther Alhamdoosh, Shian Su, Xueyi Dong, Tian Li, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 7
Published: almost 6 years ago

10.1186/1471-2105-14-91

A comparison of methods for differential expression analysis of RNA-seq data
Cited by: 725
Author(s): Charlotte Soneson, Mauro Delorenzi
Software Mentions: 7
Published: over 11 years ago

10.1186/s12864-020-6502-7

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Cited by: 23
Author(s): Xiaohong Li, Nigel G. F. Cooper, Timothy E. O’Toole, Eric C. Rouchka
Software Mentions: 6
Published: almost 5 years ago

10.3389/fpls.2017.01926

A Pectin Methylesterase ZmPme3 Is Expressed in Gametophyte factor1-s (Ga1-s) Silks and Maps to that Locus in Maize (Zea mays L.)
Cited by: 28
Author(s): Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott
Software Mentions: 6
Published: about 7 years ago

10.12688/wellcomeopenres.15115.1

Single-cell transcriptome analysis of CD8+ T-cell memory inflation
Cited by: 7
Author(s): Andrew J. Highton, Madeleine E Zinser, Lian Ni Lee, Claire Hutchings, Catherine de Lara, Chansavath Phetsouphanh, Christian Willberg, Claire L. Gordon, Paul Klenerman, Emanuele Marchi
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.09800

Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss
Cited by: 177
Author(s): Fredrick E. Henry, Ken Sugino, Adam Tozer, Tiago Branco, Scott M. Sternson
Software Mentions: 6
Published: about 9 years ago

10.1186/s12864-019-5851-6

BALLI: Bartlett-adjusted likelihood-based linear model approach for identifying differentially expressed genes with RNA-seq data
Cited by: 3
Author(s): Kyungtaek Park, Jaehoon An, Jungsoo Gim, Minseok Seo, Woojoo Lee, Taesung Park, Sungho Won
Software Mentions: 6
Published: over 5 years ago

10.3389/fpls.2018.01212

A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant–Microbe Interactions
Cited by: 12
Author(s): Silvia Zanini, Ena Šečić, Lukas Jelonek, Karl-Heinz Kögel
Software Mentions: 6
Published: over 6 years ago

10.3389/fimmu.2020.628804

Transcriptomic Analysis of Long-Term Protective Immunity Induced by Vaccination With Mycoplasma gallisepticum Strain ts-304
Cited by: 5
Author(s): Sathya N Kulappu Arachchige, Neil D. Young, Anna Kanci Condello, Oluwadamilola S Omotainse, Amir H. Noormohammadi, Nadeeka K. Wawegama, Glenn F. Browning
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.65369

Surprising phenotypic diversity of cancer-associated mutations of Gly 34 in the histone H3 tail
Cited by: 18
Author(s): Brandon R Lowe, Rajesh K Yadav, Ryan A. Henry, Patrick Schreiner, Atsushi Matsuda, Alfonso G. Fernandez, David Finkelstein, Margaret Campbell, Satish Kallappagoudar, Carolyn M Jablonowski, Andrew J. Andrews, Yasushi Hiraoka, Janet F. Partridge
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1009095

Identifying the combinatorial control of signal-dependent transcription factors
Cited by: 15
Author(s): Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
Software Mentions: 6
Published: over 3 years ago

10.1093/biostatistics/kxw055

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Cited by: 112
Author(s): Aaron T. L. Lun, John C. Marioni
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0255139

De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage
Cited by: 2
Author(s): María Cárcamo de la Concepción, Daniel J. Sargent, Nada Šurbanovski, Richard Colgan, Marco Moretto
Software Mentions: 6
Published: over 3 years ago

10.1016/j.celrep.2020.108629

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide
Cited by: 10
Author(s): Kathrin Leppek, Gun Woo Byeon, Kotaro Fujii, Maria Barna
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13073-021-00939-2

Identification of TBX15 as an adipose master trans regulator of abdominal obesity genes
Cited by: 17
Author(s): David Z. Pan, Min‐Hua Zong, Caroline Comenho, Sandhya Rajkumar, Amogha Koka, Seung Hyuk Lee, Marcus Alvarez, Dorota Kaminska, Arthur Ko, Janet S. Sinsheimer, Karen L. Mohlke, Nicholas Mancuso, Linda Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Marı́a Teresa Tusié-Luna, Carlos A. Aguilar-Salinas, Kirsi H. Pietiläinen, Jussi Pihlajamäki, Markku Laakso, Kristina M. Garske, Päivi Pajukanta
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-016-2386-y

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics
Cited by: 103
Author(s): Viktor Jönsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12859-018-2019-3

Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12885-021-08362-x

Differential chromatin accessibility landscape of gain-of-function mutant p53 tumours
Cited by: 2
Author(s): Bhavya Dhaka, Radhakrishnan Sabarinathan
Software Mentions: 5
Published: over 3 years ago

10.1186/s13100-018-0138-z

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Cited by: 33
Author(s): Gavin Pereira, Laura Sánchez, Paul Schaughency, Alejandro Rubio-Roldán, Justin Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W. Ostrow, John Ravits, Haig H. Kazazian, Sarah J. Wheelan, Sara R. Heras, Jens Mayer, José L. García‐Pérez, John Goodier
Software Mentions: 5
Published: almost 6 years ago

10.15252/msb.20199012

Sex‐dependent and sex‐independent regulatory systems of size variation in natural populations
Cited by: 4
Author(s): Hirokazu Okada, Ryuta Yagi, Vincent Gardeux, Bart Deplancke, Ernst Hafen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1007431

Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development
Cited by: 18
Author(s): Timothy M. Johanson, Hannah D. Coughlan, Aaron T. L. Lun, Naiara G. Bediaga, Gaetano Naselli, Alexandra L. Garnham, Leonard C. Harrison, Rhys S. Allan
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1008367

Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development
Cited by: 15
Author(s): Robert L. Baker, Wen Fung Leong, Marcus T. Brock, Matthew J. Rubin, R. J. Cody Markelz, Stephen M. Welch, Julin Maloof, Cynthia Weinig
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0244439

The peptide symporter SLC15a4 is essential for the development of systemic lupus erythematosus in murine models
Cited by: 14
Author(s): Arna Katewa, Eric Suto, Jessica Hui, Jose Heredia, Jie Liang, Jason A. Hackney, Keith R. Anderson, Tuija Alcantar, Natasha Bacarro, Debra Dunlap, Jeffrey Eastham, Andrés Paler-Martı́nez, Xin Y. Rairdan, Zora Modrušan, Wyne P. Lee, Cary D. Austin, Daniel Lafkas, Nico Ghilardi
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.cell.2020.09.062

M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained Immunity
Cited by: 126
Author(s): Nargis Khan, Jeffrey Downey, Joaquín Sanz, Eva Kaufmann, Birte Blankenhaus, Alain Pacis, Erwan Pernet, Eisha Ahmed, Sílvia Cardoso, Anastasia Nijnik, Bruce Mazer, Christopher M. Sassetti, Marcel A. Behr, Miguel P. Soares, Luis B. Barreiro, Maziar Divangahi
Software Mentions: 5
Published: about 4 years ago

10.1016/j.celrep.2020.107843

Alzheimer’s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation
Cited by: 194
Author(s): Karpagam Srinivasan, Brad A. Friedman, Ainhoa Etxeberría, Melanie A. Huntley, Marcel P. van der Brug, Oded Foreman, Jonathan S. Paw, Zora Modrušan, Thomas G. Beach, Geidy E. Serrano, David V. Hansen
Software Mentions: 5
Published: over 4 years ago

10.15252/emmm.202013328

Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients
Cited by: 11
Author(s): Mirko Signorelli, Mitra Ebrahimpoor, Olga Veth, Kristina Hettne, Nisha Verwey, R. García-Rodríguez, Christa L Tanganyika-deWinter, Luz Berenice López-Hernández, Rosa Escobar Cedillo, Benjamín Gómez-D́iaz, Ólafur Þ. Magnússon, Hailiang Mei, Roula Tsonaka, Annemieke Aartsma‐Rus, Pietro Spitali
Software Mentions: 5
Published: over 3 years ago

10.15252/emmm.202013162

The NFIB‐ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cells
Cited by: 23
Author(s): Federica Zilli, Pedro Marques Ramos, Priska Auf der Maur, Charly Jehanno, Atul Sethi, Marie–May Coissieux, Tobias Eichlisberger, Loïc Sauteur, Adelin Rouchon, Laura Bonapace, Joana Couto, Roland Rad, Michael Rugaard Jensen, Andrea Banfi, Michael Stadler, Mohamed Bentires‐Alj
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2020.00552

Id Proteins Promote a Cancer Stem Cell Phenotype in Mouse Models of Triple Negative Breast Cancer via Negative Regulation of Robo1
Cited by: 15
Author(s): Wee Siang Teo, Holly Holliday, N. Karthikeyan, Aurélie Cazet, Daniel Roden, Kate Harvey, Christina Valbirk Konrad, Reshma Murali, Binitha Anu Varghese, Archana P. Thankamony, Chia-Ling Chan, Andrea McFarland, Simon Junankar, Sunny Ye, Jessica Yang, Iva Nikolić, Jaynish S. Shah, Laura A. Baker, Ewan K.A. Millar, Matthew J. Naylor, Christopher J. Ormandy, Sunil R. Lakhani, Warren Kaplan, Albert S. Mellick, Sandra A. O’Toole, Alexander Swarbrick, Radhika Nair
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-015-0781-3

Do count-based differential expression methods perform poorly when genes are expressed in only one condition?
Cited by: 5
Author(s): Xiaobei Zhou, Mark D. Robinson
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-021-02401-3

Detection of cell-free microbial DNA using a contaminant-controlled analysis framework
Cited by: 18
Author(s): Enrique Zozaya‐Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson, Sarah‐Jane Dawson
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-018-27027-7

Immunoprofiles of human Sertoli cells infected with Zika virus reveals unique insights into host-pathogen crosstalk
Cited by: 32
Author(s): Daniel P. Strange, Richard Green, Dietmar W. Siemann, Michael Gale, Saguna Verma
Software Mentions: 5
Published: over 6 years ago

10.1128/mBio.03202-19

Reducing Aspergillus fumigatus Virulence through Targeted Dysregulation of the Conidiation Pathway
Cited by: 18
Author(s): James I P Stewart, Vinicius M. Fava, Joshua D. Kerkaert, Adithya S. Subramanian, Fabrice N. Gravelat, Mélanie Lehoux, P. Lynne Howell, Robert A. Cramer, Donald C. Sheppard
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms22010382

Exosomal miRNAs as Potential Biomarkers to Monitor Phosphodiesterase 5 Inhibitor Induced Anti-Fibrotic Effects on CCl4 Treated Rats
Cited by: 9
Author(s): Andre Broermann, RM Schmid, Ogsen Gabrielyan, Marlene Sakowski, Claudia Eisele, Sascha Keller, Michael Wolff, Patrick Baum, Birgit Stierstorfer, J. Huber, Bernhard K. Krämer, Berthold Hocher, Ruediger Streicher, Denis Delić
Software Mentions: 5
Published: almost 4 years ago

10.1038/srep29477

Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis
Cited by: 18
Author(s): Lai-Ping Wong, Kaiyu Jiang, Yanmin Chen, Teresa Hennon, Lucy C Holmes, Carol A. Wallace, James N. Jarvis
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0143496

Human Breast Milk miRNA, Maternal Probiotic Supplementation and Atopic Dermatitis in Offspring
Cited by: 56
Author(s): Melanie Rae Simpson, Gaute Brede, Jostein Johansen, Roar Johnsen, Ola Storrø, Pål Sætrom, Torbjørn Øien
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12920-017-0295-9

RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking
Cited by: 46
Author(s): Margaret M. Parker, Robert Chase, Andrew Lamb, Alejandro Reyes, Aabida Saferali, Jeong H. Yun, Blanca E. Himes, Edwin K. Silverman, Craig P. Hersh, Peter J. Castaldi
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.ppat.1007290

Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance
Cited by: 33
Author(s): Brad R. Rosenberg, Marion Depla, Catherine A. Freije, Denis Gaucher, Sabrina Mazouz, Maude Boisvert, Nathalie Bédard, Julie Bruneau, Charles M. Rice, Naglaa H. Shoukry
Software Mentions: 4
Published: about 6 years ago

10.1186/s12902-021-00709-6

Identification of hub genes related to the progression of type 1 diabetes by computational analysis
Cited by: 10
Author(s): G Prashanth, Basavaraj Vastrad, Anandkumar Tengli, Chanabasayya Vastrad, Iranna Kotturshetti
Software Mentions: 4
Published: over 3 years ago

10.1200/CCI.19.00118

Statistical Assessment of Depth Normalization for Small RNA Sequencing
Cited by: 7
Author(s): Li‐Xuan Qin, Jian Zou, Jiejun Shi, Ann Lee, Aleksandra Mihailović, Thalia A. Farazi, Thomas Tuschl, Samuel Singer
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1008358

Multi-omics analysis identifies mitochondrial pathways associated with anxiety-related behavior
Cited by: 34
Author(s): R. Zuzanna Misiewicz, Stella Iurato, Natalia Kulesskaya, Laura Salminen, Luís Filipe Rodrigues, Giuseppina Maccarrone, Jade Martins, Darina Czamara, Mikaela Laine, Ewa Sokołowska, Kalevi Trontti, Christiane Rewerts, Božidar Novak, Naama Volk, Dong Ik Park, Eija Jokitalo, Lars Paulín, Petri Auvinen, Vootele Võikar, Alon Chen, Angelika Erhardt, Christoph W. Turck, Iiris Hovatta
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms20204983

Methionine Adenosyltransferase 1a (MAT1A) Enhances Cell Survival During Chemotherapy Treatment and is Associated with Drug Resistance in Bladder Cancer PDX Mice
Cited by: 10
Author(s): Kelly A. Martin, Nicholas R. Hum, Aimy Sebastian, Wei He, Salma Siddiqui, Paramita M. Ghosh, Chong Xian Pan, Ralph de Vere White, Gabriela G. Loots
Software Mentions: 4
Published: about 5 years ago

10.3389/fcell.2018.00164

The Transcriptome of Human Endometrial Mesenchymal Stem Cells Under TGFβR Inhibition Reveals Improved Potential for Cell-Based Therapies
Cited by: 31
Author(s): Shanti Gurung, Sarah Williams, James A. Deane, Jerome A. Werkmeister, Caroline E. Gargett
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0207952

RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns
Cited by: 8
Author(s): Gary P. Brennan, Dimitrios Vitsios, Sophie Casey, Ann-Marie Looney, Boubou Hallberg, David C. Henshall, Geraldine B. Boylan, Deirdre M. Murray, Catherine Mooney
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2014.00329

A comparison of control samples for ChIP-seq of histone modifications
Cited by: 24
Author(s): Christoffer Flensburg, Sarah Kinkel, Andrew Keniry, Marnie E. Blewitt, Alicia Oshlack
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0163344

Differing Alterations of Two Esca Associated Fungi, Phaeoacremonium aleophilum and Phaeomoniella chlamydospora on Transcriptomic Level, to Co-Cultured Vitis vinifera L. calli
Cited by: 6
Author(s): Jochen Fischer, Stéphane Compant, Romain Pierron, Markus Gorfer, Alban Jacques, Eckhard Thines, Harald Berger
Software Mentions: 4
Published: about 8 years ago

10.1038/s41419-018-1141-5

Plau and Tgfbr3 are YAP-regulated genes that promote keratinocyte proliferation
Cited by: 18
Author(s): Susan M. Corley, Veronica Mendoza-Reinoso, Nichole Giles, Emma Suwanun Singer, John E.A. Common, Marc R. Wilkins, Annemiek Beverdam
Software Mentions: 4
Published: about 6 years ago

10.1111/pbi.12898

A <i>Vitis vinifera</i> basic helix–loop–helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield
Cited by: 34
Author(s): Sung Don Lim, Won Cheol Yim, Degao Liu, Rongbin Hu, Xiaohan Yang, John C. Cushman
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-017-3797-0

Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols
Cited by: 20
Author(s): Susan M. Corley, Karen L. MacKenzie, Annemiek Beverdam, Louise F. Roddam, Marc R. Wilkins
Software Mentions: 4
Published: over 7 years ago

10.1093/function/zqaa004

The Mechanism of High-Output Cardiac Hypertrophy Arising From Potassium Channel Gain-of-Function in Cantú Syndrome
Cited by: 17
Author(s): Conor McClenaghan, Yan Huang, Scot J. Matkovich, Attila Kovács, Carla J. Weinheimer, Ronald A. Perez, Thomas J. Broekelmann, Theresa Harter, Jin-Moo Lee, Marı́a S. Remedi, Colin G. Nichols
Software Mentions: 4
Published: almost 5 years ago

10.1534/g3.118.200726

Nuclear Transcriptomes of the Seven Neuronal Cell Types That Constitute the<i>Drosophila</i>Mushroom Bodies
Cited by: 43
Author(s): Min-Yi Shih, Fred P. Davis, Gilbert L. Henry, Josh Dubnau
Software Mentions: 4
Published: almost 6 years ago

10.1002/1878-0261.12478

Identification of tumor suppressor miRNAs by integrative miRNA and mRNA sequencing of matched tumor–normal samples in lung adenocarcinoma
Cited by: 38
Author(s): Namhee Yu, Seunghui Yong, Hong Kwan Kim, Yoon La Choi, Yeonjoo Jung, Doyeon Kim, Jihae Seo, Ye Eun Lee, Daehyun Baek, Jinseon Lee, Seungjae Lee, Jong Eun Lee, Jaesang Kim, Young Tae Kim, Sanghyuk Lee
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ijpara.2018.01.004

Transcriptomic profiling of nematode parasites surviving vaccine exposure
Cited by: 19
Author(s): Guillaume Sallé, Roz Laing, James A. Cotton, Kirsty Maitland, Axel Martinelli, Nancy Holroyd, Alan S. Tracey, Matthew Berriman, William D. Smith, G. F. J. Newlands, Eve Hanks, Eileen Devaney, Collette Britton
Software Mentions: 4
Published: over 6 years ago

10.1186/s13045-014-0089-x

Splicing factor 3b subunit 1 (Sf3b1) haploinsufficient mice display features of low risk Myelodysplastic syndromes with ring sideroblasts
Cited by: 20
Author(s): Valeria Visconte, Ali Tabarroki, Li Zhang, Yvonne Parker, Edy Hasrouni, R. Mahfouz, Kyoichi Isono, Haruhiko Koseki, Mikkael A. Sekeres, Yogen Saunthararajah, John Barnard, Daniel J. Lindner, Heesun J. Rogers, Ramon V. Tiu
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-016-2646-x

A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species
Cited by: 25
Author(s): Montserrat Torres-Oliva, Isabel Almudí, Alistair P. McGregor, Nico Posnien
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-020-58711-2

Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
Cited by: 5
Author(s): Takatoshi Hikida, Shuhei Yao, Tom Macpherson, Ayumi Fukakusa, Maki Morita, Haruhide Kimura, Keisuke Hirai, Tatsuya Ando, Hiroyoshi Toyoshiba, Akira Sawa
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-39615-2

Multiple molecular defense strategies in Brachypodium distachyon surmount Hessian fly (Mayetiola destructor) larvae-induced susceptibility for plant survival
Cited by: 9
Author(s): Subhashree Subramanyam, Jill A. Nemacheck, Andrea M. Hargarten, Nagesh Sardesai, Brandon J. Schemerhorn, Christie E. Williams
Software Mentions: 4
Published: over 5 years ago

10.1186/1755-8794-7-57

Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model
Cited by: 79
Author(s): Lisette J. A. Kogelman, Susanna Cirera, Daria V. Zhernakova, Merete Fredholm, Lude Franke, Haja N. Kadarmideen
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.ppat.1008851

Enteroaggregative E. coli Adherence to Human Heparan Sulfate Proteoglycans Drives Segment and Host Specific Responses to Infection
Cited by: 22
Author(s): Anubama Rajan, Matthew J. Robertson, Hannah E. Carter, Nina M. Poole, Justin R. Clark, Sabrina I. Green, Zachary K. Criss, Boyang Zhao, Umesh C. Karandikar, Yikun Xing, Mar Margalef-Català, Nikhil Jain, Reid Wilson, Fan Bai, Joseph M. Hyser, Joseph F. Petrosino, Noah F. Shroyer, Sarah E. Blutt, Cristian Coarfa, Xuezheng Song, B. V. Venkataram Prasad, Manuel R. Amieva, Jane Grande-Allen, Mary K. Estes, Pablo C. Okhuysen, Anthony W. Maresso
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-019-3107-8

Topology Consistency of Disease-specific Differential Co-regulatory Networks
Cited by: 4
Author(s): Maryam Nazarieh, Hema Sekhar Reddy Rajula, Volkhard Helms
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pcbi.1007309

miRWoods: Enhanced precursor detection and stacked random forests for the sensitive detection of microRNAs
Cited by: 8
Author(s): Jimmy D. Bell, Maureen K. Larson, Michelle Anne Kutzler, Massimo Bionaz, Christiane V. Löhr, David A. Hendrix
Software Mentions: 3
Published: about 5 years ago

10.3389/fimmu.2020.582358

Transcriptional Memory-Like Imprints and Enhanced Functional Activity in γδ T Cells Following Resolution of Malaria Infection
Cited by: 7
Author(s): Rasika Kumarasingha, Lisa J Ioannidis, Waruni Abeysekera, Stephanie I Studniberg, Dinidu S Wijesurendra, Ramin Mazhari, Daniel P. Poole, Ivo Müeller, Louis Schofield, Diana S. Hansen, Emily M. Eriksson
Software Mentions: 3
Published: about 4 years ago

10.3390/ijms22179120

Identifying the Main Functional Pathways Associated with Cognitive Resilience to Alzheimer’s Disease
Cited by: 11
Author(s): Marta Pérez-González, Sara Badesso, Elena Lorenzo, Elizabeth Guruceaga, Alberto Pérez-Mediavilla, Ana Garcı́a-Osta, Mar Cuadrado‐Tejedor
Software Mentions: 3
Published: about 3 years ago