bioconductor: EDASeq | Projects | Ecosyste.ms: Papers

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.15252/emmm.202012640

Mithramycin induces promoter reprogramming and differentiation of rhabdoid tumor
Cited by: 7
Author(s): Maggie H. Chassé, Benjamin K. Johnson, Elissa A. Boguslawski, Katie M. Sorensen, Jessica E Rosien, Min H. Kang, C. Patrick Reynolds, Lyong Heo, Zachary Madaj, Ian Beddows, Gabrielle E. Foxa, Susan M. Kitchen-Goosen, Bart O. Williams, Timothy J. Triche, Patrick J. Grohar
Software Mentions: 18
Published: almost 4 years ago

10.12688/f1000research.8923.2

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
Cited by: 105
Author(s): Tiago C. Silva, Antonio Colaprico, Catharina Olsen, Fulvio D’Angelo, Gianluca Bontempi, Michele Ceccarelli, Houtan Noushmehr
Software Mentions: 17
Published: almost 8 years ago

10.1186/s13059-014-0550-8

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Cited by: 49,504
Author(s): Michael I. Love, Wolfgang Huber, Simon Anders
Software Mentions: 16
Published: almost 10 years ago

10.3389/fgene.2021.559998

Gene Size Matters: An Analysis of Gene Length in the Human Genome
Cited by: 55
Author(s): Inês Lopes, Gulam Altab, Priyanka Raina, João Pedro de Magalhães
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-016-0884-1

Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
Cited by: 62
Author(s): Ludwig Geistlinger, Gergely Csaba, Ralf Zimmer
Software Mentions: 14
Published: almost 9 years ago

10.1186/s12864-017-4423-x

Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis
Cited by: 31
Author(s): Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Isabella Castiglioni
Software Mentions: 12
Published: almost 7 years ago

10.1186/1471-2164-14-892

RNA-Seq optimization with eQTL gold standards
Cited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: almost 11 years ago

10.3390/cancers12030690

Comparative Molecular Analysis of Cancer Behavior Cultured In Vitro, In Vivo, and Ex Vivo
Cited by: 17
Author(s): Nicholas R. Hum, Aimy Sebastian, Sean F. Gilmore, Wei He, Kelly A. Martin, Aubree Hinckley, Karen Dubbin, Monica L. Moya, Elizabeth K. Wheeler, Matthew A. Coleman, Gabriela G. Loots
Software Mentions: 7
Published: over 4 years ago

10.1186/s13148-015-0123-z

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases
Cited by: 32
Author(s): Daniel Nätt, I. Johansson, Tomas Faresjö, Johnny Ludvigsson, Annika Thorsell
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-020-3399-8

iSeqQC: a tool for expression-based quality control in RNA sequencing
Cited by: 15
Author(s): Gaurav Kumar, Adam Ertel, George J. Feldman, Joan Kupper, Paolo Fortina
Software Mentions: 6
Published: almost 5 years ago

10.1016/j.ccell.2017.07.004

Swarm Intelligence-Enhanced Detection of Non-Small-Cell Lung Cancer Using Tumor-Educated Platelets
Cited by: 212
Author(s): Myron G. Best, Nik Sol, Sjors G J G In ‘t Veld, Adrienne Vancura, Mirte Muller, Anna-Larissa N. Niemeijer, Aniko V. Fejes, Lee Ann Tjon Kon Fat, Anna Egberdina Huis In 't Veld, Cyra E. Leurs, Tessa Y. Le Large, Laura L. Meijer, Irsan Kooi, François Rustenburg, Pepijn Schellen, Heleen Verschueren, Edward P. Post, Laurine E. Wedekind, Jillian Wilhelmina Paulina Bracht, Michelle Esenkbrink, Leon J. Wils, Francesca Favaro, Jilian D. Schoonhoven, Jihane Tannous, Hanne Meijers-Heijboer, Geert Kazemier, Elisa Giovannetti, Jaap C. Reijneveld, Sander Idema, Joep Killestein, Michal Heger, Saskia C.A. de Jager, Rolf T. Urbanus, Imo E. Hoefer, Gérard Pasterkamp, Christine Mannhalter, José Gomez-Arroyo, Harm Jan Bogaard, David P. Noske, W. Peter Vandertop, Daan van den Broek, Bauke Ylstra, R. Jonas A. Nilsson, Jelle Wesseling, Niki Karachaliou, Rafael Rosell, Elizabeth Lee-Lewandrowski, Kent Lewandrowski, Bakhos A. Tannous, Adrianus J. de Langen, Egbert F. Smit, Michel M. van den Heuvel, Thomas Würdinger
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pcbi.1006794

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
Cited by: 7
Author(s): Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel Christiaen, David Gresham, Daniel Tranchina
Software Mentions: 5
Published: over 5 years ago

10.1186/s13619-021-00092-6

Coordination of EZH2 and SOX2 specifies human neural fate decision
Cited by: 3
Author(s): Yuan Zhao, Tianyu Wang, Yanqi Zhang, Liang Shi, Cong Zhang, Jingyuan Zhang, Jiao Yao, Qianyu Chen, Xiaofen Zhong, Yanxing Wei, Yongli Shan, Guangjin Pan
Software Mentions: 5
Published: about 3 years ago

10.3389/fpls.2020.597589

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves
Cited by: 3
Author(s): Sophie Moreau, Géraldine van Aubel, Rekin’s Janky, Pierre Van Cutsem
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-019-5511-x

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
Cited by: 35
Author(s): Kirti Shekhawat, Hugh-G. Patterton, Florian F. Bauer, Mathabatha Evodia Setati
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: over 3 years ago

10.3389/fgene.2021.589160

Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)
Cited by: 9
Author(s): Delphine Giraud, Oscar Lima, Mathieu Rousseau‐Gueutin, Armel Salmon, Malika L. Aïnouche
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.4619

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs
Cited by: 6
Author(s): Tianle Chao, Zhibin Ji, Lei Hou, Jin Wang, Chunlan Zhang, Guizhi Wang
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pbio.3000481

Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias
Cited by: 45
Author(s): Shir Mandelboum, Zohar Manber, Orna Elroy‐Stein, Ran Elkon
Software Mentions: 5
Published: about 5 years ago

10.1210/endocr/bqz044

Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male Mice
Cited by: 8
Author(s): Poonamjot Deol, Elena Kozlova, Matthew C. Valdez, Catherine Ho, Ei-Wen Yang, H.J. Richardson, Gwendolyn Michelle Gonzalez, Edward Truong, Jack Reid, Joseph M. Valdez, Jonathan Deans, Jose Martinez-Lomeli, Jane R. Evans, Tao Jiang, Frances M. Sladek, Margarita Curras‐Collazo
Software Mentions: 5
Published: almost 5 years ago

10.3390/ijms21238898

MicroRNA Profiling in Oesophageal Adenocarcinoma Cell Lines and Patient Serum Samples Reveals a Role for miR-451a in Radiation Resistance
Cited by: 8
Author(s): Frederike Butz, Ann-Kathrin Eichelmann, George C. Mayne, Tingting Wang, Isabell Bastian, Karen Chiam, Shashikanth Marri, Pamela J. Sykes, Bas P. L. Wijnhoven, Eelke Toxopeus, Michael Michael, Christos S. Karapetis, Richard Hummel, David I. Watson, Damian J. Hussey
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-019-2994-z

An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets
Cited by: 29
Author(s): Arezo Torang, Paraag Gupta, David J. Klinke
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-1704-0

A semi-supervised approach uncovers thousands of intragenic enhancers differentially activated in human cells
Cited by: 6
Author(s): Juan González-Vallinas, Amadís Pagès, Babita Singh, Eduardo Eyras
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-016-3065-8

Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex
Cited by: 35
Author(s): Jason R. Gerstner, John N. Koberstein, Adam Watson, Nikolai Zapero, Davide Risso, Terence P. Speed, Marcos G. Frank, Lucı́a Peixoto
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0069401

TCW: Transcriptome Computational Workbench
Cited by: 16
Author(s): Carol Soderlund, William M. Nelson, Mark R. Willer, David R. Gang
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.ppat.1006084

Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection
Cited by: 24
Author(s): Apollo Stacy, Nader Abraham, Peter Jorth, Marvin Whiteley
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-018-37813-y

Both anti-inflammatory and antiviral properties of novel drug candidate ABX464 are mediated by modulation of RNA splicing
Cited by: 41
Author(s): Audrey Vautrin, Laurent Manchon, Aude Garcel, Noëlie Campos, Laure Lapasset, Abdelhamid Mahdi Laaref, Roman Bruno, Marie Gislard, Emeric Dubois, Didier Scherrer, J Hartmut Ehrlich, Jamal Tazi
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms18050922

Transcriptomic Analysis of Calcium Remodeling in Colorectal Cancer
Cited by: 37
Author(s): Enrique Pérez-Riesgo, Lucía Gutiérrez, Daniel Ubierna, Alberto Acedo, Mary Pat Moyer, Lucı́a Núñez, Carlos Alonso
Software Mentions: 4
Published: over 7 years ago

10.1080/07853890.2020.1858234

Increased expression of hypoxia-induced factor 1α mRNA and its related genes in myeloid blood cells from critically ill COVID-19 patients
Cited by: 40
Author(s): Keiko Taniguchi‐Ponciano, Eduardo Vadillo, Héctor Mayani, César González-Bonilla, Javier Torres, Abraham Majluf, Guillermo Flores‐Padilla, Niels H. Wacher, Juan Carlos Galán, Eduardo Ferat‐Osorio, Francisco Blanco-Favéla, Constantino López-Macı́as, Aldo Ferreira‐Hermosillo, Claudia Ramírez‐Rentería, Eduardo Peña-Martínez, Gloria Silva-Román, Sandra Vela-Patiño, Carlos Mata-Lozano, Roberto Carvente-Garcia, Lourdes Basurto-Acevedo, Renata Saucedo, Patricia Piña‐Sánchez, Antonieta Chávez‐González, Daniel Marrero‐Rodríguez, Moisés Mercado
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41418-021-00771-6

MECOM permits pancreatic acinar cell dedifferentiation avoiding cell death under stress conditions
Cited by: 19
Author(s): Elyne Backx, Elke Wauters, Jonathan Baldan, Mathias Van Bulck, Ellis Michiels, Yves Heremans, Diedert Luc De Paep, Mineo Kurokawa, Susumu Goyama, Luc Bouwens, Patrick Jacquemin, Isabelle Houbracken, Ilse Rooman
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0098376

Oak Root Response to Ectomycorrhizal Symbiosis Establishment: RNA-Seq Derived Transcript Identification and Expression Profiling
Cited by: 45
Author(s): Mónica Sebastiana, Bruno Miguel Vieira, Teresa Lino-Neto, Filipa Monteiro, Andreia Figueiredo, Lisete Sousa, M. S. Pais, R. M. Tavares, Octávio S. Paulo
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.1684

Insight into the maintenance of odontogenic potential in mouse dental mesenchymal cells based on transcriptomic analysis
Cited by: 4
Author(s): Yunfei Zheng, Lingfei Jia, Pengfei Liu, Dandan Yang, Waner Hu, Shubin Chen, Yuming Zhao, Jinglei Cai, Duanqing Pei, Lihong Ge, Shicheng Wei
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-016-3433-4

Short bowel syndrome results in increased gene expression associated with proliferation, inflammation, bile acid synthesis and immune system activation: RNA sequencing a zebrafish SBS model
Cited by: 24
Author(s): Kathy Schall, Matthew E. Thornton, Mubina Isani, Kathleen A. Holoyda, Xiaogang Hou, Ching‐Ling Lien, Brendan H. Grubbs, Tracy C. Grikscheit
Software Mentions: 3
Published: almost 8 years ago

10.3389/fmicb.2018.01845

Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens
Cited by: 17
Author(s): Manuel Salvador, Montserrat Argandoña, Emilia Naranjo, Francine Piubeli, Joaquı́n J. Nieto, L.N. Csonka, Carmen Regla Vargas
Software Mentions: 3
Published: over 6 years ago

10.3389/fmolb.2020.618088

DNA Damage Induces Dynamic Associations of BRD4/P-TEFb With Chromatin and Modulates Gene Transcription in a BRD4-Dependent and -Independent Manner
Cited by: 5
Author(s): Yawei Song, Gongcheng Hu, Jinping Jia, Maojin Yao, Xiaoshan Wang, Wenliang Lu, Andrew P. Hutchins, Jiekai Chen, Keiko Ozato, Hongjie Yao
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12915-020-00886-1

The CBP KIX domain regulates long-term memory and circadian activity
Cited by: 18
Author(s): Snehajyoti Chatterjee, Christopher C. Angelakos, Ethan Bahl, Joshua D. Hawk, Marie E. Gaine, Shane G. Poplawski, Anne Schneider‐Anthony, Manish Kumar Yadav, Giulia S. Porcari, Jean‐Christophe Cassel, K. Peter Giese, Jacob J. Michaelson, Lisa C. Lyons, Anne‐Laurence Boutillier, Ted Abel
Software Mentions: 3
Published: about 4 years ago

10.1534/g3.116.034595

<i>Obp56h</i>Modulates Mating Behavior in<i>Drosophila melanogaster</i>
Cited by: 21
Author(s): John R. Shorter, Lauren M. Dembeck, Logan J. Everett, Tatiana V. Morozova, Gunjan H. Arya, Lavanya Turlapati, Genevieve E. St. Armour, Coby Schal, Trudy F. C. Mackay, Robert R. H. Anholt
Software Mentions: 3
Published: about 8 years ago

10.1186/1471-2105-12-480

GC-Content Normalization for RNA-Seq Data
Cited by: 656
Author(s): Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2105-15-S1-S7

Reducing bias in RNA sequencing data: a novel approach to compute counts
Cited by: 39
Author(s): Francesca Finotello, Enrico Lavezzo, Luca Bianco, Luisa Barzon, Paolo Emilio Mazzon, Paolo Fontana, Stefano Toppo, Barbara Di Camillo
Software Mentions: 3
Published: almost 11 years ago

10.1038/srep09100

Genomic analysis of LPS-stimulated myeloid cells identifies a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses
Cited by: 41
Author(s): Andrew Paul Hutchins, Yoshiko Takahashi, Diego Miranda‐Saavedra
Software Mentions: 3
Published: over 9 years ago

10.1038/srep20837

Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model
Cited by: 15
Author(s): Els Willems, Carlos Guerrero-Bosagna, Eddy Decuypere, Steven Janssens, Johan Buyse, Nadine Buys, Per Jensen, Nadia Everaert
Software Mentions: 3
Published: almost 9 years ago

10.3390/ijms19051399

High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients
Cited by: 14
Author(s): Sara De Iudicibus, Marianna Lucafò, Nicola Vitulo, Stefano Martelossi, Rosanna Zimbello, Fabio De Pascale, Claudio Forcato, Samuele Naviglio, Alessia Di Silvestre, Marco Gerdol, Gabriele Stocco, Giorgio Valle, Alessandro Ventura, Matteo Bramuzzo, Giuliana Decorti
Software Mentions: 3
Published: over 6 years ago

10.1038/s41396-018-0331-6

The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen
Cited by: 105
Author(s): César Nicolás, Tomas Martin-Bertelsen, Dimitrios Floudas, Johan Bentzer, Mark M. Smits, Tomas Johansson, Carl Troein, Per Persson, Anders Tunlid
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers12092713

Hormonal Receptor Status Determines Prognostic Significance of FGFR2 in Invasive Breast Carcinoma
Cited by: 9
Author(s): Marcin Braun, Dominika Piasecka, Bartłomiej Tomasik, Kamil Mieczkowski, Konrad Stawiski, Aleksandra Zielińska, Janusz Kopczyński, Dariusz Nejc, Radzisław Kordek, Rafał Sądej, Hanna Romańska
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0176185

A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data
Cited by: 50
Author(s): Xiaohong Li, Guy Brock, Eric C. Rouchka, Nigel G. F. Cooper, Dongfeng Wu, Timothy E. O’Toole, Ryan Gill, Abdallah M. Eteleeb, Liz O’Brien, N. Shesh
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0194803

Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro-inflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation
Cited by: 32
Author(s): Jungnam Lee, Ivan Arisi, Ermanno Puxeddu, Lazarus K. Mramba, Massimo Amicosante, Carmen M. Swaisgood, Marco Pallante, Mark Brantly, C. Magnus Sköld, Cesare Saltini
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0206312

Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing
Cited by: 53
Author(s): Farnoosh Abbas‐Aghababazadeh, Qian Li, Brooke L. Fridley
Software Mentions: 2
Published: about 6 years ago

10.1080/2162402X.2016.1186314

Novel non-canonical role of STAT1 in Natural Killer cell cytotoxicity
Cited by: 12
Author(s): Eva Maria Putz, Andrea Majoros, Dagmar Gotthardt, Michaela Prchal-Murphy, Eva Zebedin-Brandl, Daniela Fux, Andreas Schlattl, Robert D. Schreiber, Sebastian Carotta, Mathias Müller, Christopher Gerner, Thomas Decker, Veronika Sexl
Software Mentions: 2
Published: over 8 years ago

10.3389/fonc.2020.01089

Integrated Transcriptome Analysis of Human Visceral Adipocytes Unravels Dysregulated microRNA-Long Non-coding RNA-mRNA Networks in Obesity and Colorectal Cancer
Cited by: 14
Author(s): Sabrina Tait, Antonella Baldassarre, Andrea Masotti, Enrica Calura, Paolo Martini, Rosaria Varı́, Beatrice Scazzocchio, Sandra Gessani, Manuela Del Cornò
Software Mentions: 2
Published: over 4 years ago

10.1038/srep46577

High-Throughput Sequencing and Co-Expression Network Analysis of lncRNAs and mRNAs in Early Brain Injury Following Experimental Subarachnoid Haemorrhage
Cited by: 37
Author(s): Jianhua Peng, Yue Wu, Xingui Tian, Jinwei Pang, Kuai Li, Fang Cao, Xinghu Qin, Jian Zhong, LI Xin-shen, Yong Li, Xiaochuan Sun, Ligang Chen, Yong Jiang
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers13092082

PRKCA Overexpression Is Frequent in Young Oral Tongue Squamous Cell Carcinoma Patients and Is Associated with Poor Prognosis
Cited by: 7
Author(s): Thomas Parzefall, Julia Schnoell, Laura Monschein, Elisabeth Foki, David T. Liu, Alexandra Frohne, Stefan Grasl, Johannes Pammer, Trevor Lucas, Lorenz Kadletz, Markus Brunner
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-68040-z

Klf9 is a key feedforward regulator of the transcriptomic response to glucocorticoid receptor activity
Cited by: 20
Author(s): Ian M. Gans, Ellen I. Hartig, Shusen Zhu, Andrea R. Tilden, Lucie N. Hutchins, Nathaniel J. Maki, Joel H. Graber, James A. Coffman
Software Mentions: 2
Published: over 4 years ago

10.3389/fnagi.2014.00075

Deciphering the Molecular Profile of Plaques, Memory Decline and Neuron Loss in Two Mouse Models for Alzheimerâ€™s Disease by Deep Sequencing
Cited by: 71
Author(s): Yvonne Bouter, Tim Kacprowski, Robert Weißmann, Katharina Dietrich, Henning Borgers, Andreas Brauß, Christian Sperling, Oliver Wirths, Mario Albrecht, Lars Riff Jensen, Andreas W. Kuß, Thomas A. Bayer
Software Mentions: 2
Published: over 10 years ago

10.1074/mcp.M115.054122

Glycomic Characterization of Induced Pluripotent Stem Cells Derived from a Patient Suffering from Phosphomannomutase 2 Congenital Disorder of Glycosylation (PMM2-CDG)
Cited by: 40
Author(s): Christina T. Thiesler, Samanta Cajic, Dirk Hoffmann, Christian Thiel, Laura van Diepen, René Hennig, Malte Sgodda, Robert Weiβmann, Udo Reichl, Doris Steinemann, Ulf Diekmann, Nicolas Huber, Astrid Oberbeck, Tobias Cantz, Andreas W. Kuß, Christian Körner, Axel Schambach, Erdmann Rapp, Falk F. R. Buettner
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms20082036

Role of Dusp6 Phosphatase as a Tumor Suppressor in Non-Small Cell Lung Cancer
Cited by: 18
Author(s): Verónica Moncho-Amor, Laura Pintado‐Berninches, Inmaculada Ibáñez de Cáceres, Ester Martín-Villar, Miguel Quintanilla, Probir Chakravarty, María Cortés-Sempere, Beatriz Fernández-Varas, Carlos Rodriguez-Antolín, Javier de Castro, Leandro Sastre, Rosario Perona
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1003255

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data
Cited by: 31
Author(s): Joshua G. Schraiber, Yulia Mostovoy, Tiffany Y. Hsu, Rachel B. Brem
Software Mentions: 1
Published: about 11 years ago

10.1038/s41598-018-26969-2

Molecular signature of progenitor cells isolated from young and adult human hearts
Cited by: 9
Author(s): Ann‐Sophie Walravens, Maarten Vanhaverbeke, Lara Ottaviani, Hilde Gillijns, Sander Trenson, Nina Vanden Driessche, Aernout Luttun, Bart Meyns, Paul Herijgers, Filip Rega, Ruth Heying, Maurilio Sampaolesi, Stefan Janssens
Software Mentions: 1
Published: over 6 years ago

10.3389/fimmu.2021.656433

Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses
Cited by: 9
Author(s): Yingying Cao, Xi Xu, Simo Kitanovski, Lina Song, Jun Wang, Pei Hao, Daniel Hoffmann
Software Mentions: 1
Published: over 3 years ago

10.1186/s13578-021-00604-6

Lipidomics profiling of goose granulosa cell model of stearoyl-CoA desaturase function identifies a pattern of lipid droplets associated with follicle development
Cited by: 8
Author(s): Xi Yuan, Shiyan Hu, Liang Li, Chunchun Han, Hehe Liu, Hua He, Lu Xia, Jiwei Hu, Bo Hu, Mingxia Ran, Yali Liu, Jiwen Wang
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: EDASeq

Papers Mentioning EDASeq 61