bioconductor: apeglm | Projects | Ecosyste.ms: Papers

10.1186/s12859-020-03549-8

BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data
Cited by: 12
Author(s): Pirunthan Perampalam, Frederick A. Dick
Software Mentions: 10
Published: over 4 years ago

Interleukin-1 promotes autoimmune neuroinflammation by suppressing endothelial heme oxygenase-1 at the blood–brain barrier
Cited by: 44
Author(s): Judith Hauptmann, Lisa Johann, Fédérico Marini, Maja Kitic, E. Colombo, Ilgiz A. Mufazalov, Martin W. Krueger, Khalad Karram, Sonja Moos, Florian Wanke, Florian C. Kurschus, Matthias Klein, Sílvia Cardoso, Johannes Strauß, Subhashini Bolisetty, Fred Lühder, Markus Schwaninger, Harald Binder, Ingo Bechman, Tobias Bopp, Anupam Agarwal, Miguel P. Soares, Tommy Regen, Ari Waisman
Software Mentions: 9
Published: over 4 years ago

10.3389/fonc.2020.593760

Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue
Cited by: 4
Author(s): Rihards Saksis, Ivars Silamiķelis, Pola Laksa, Kaspars Megnis, Raitis Pečulis, Ilona Mandrika, Olesja Rogoza, Ramona Petrovska, Inga Balcere, Ilze Konrāde, Liva Steina, Jānis Stukēns, Austra Breikša, Jurijs Nazarovs, Jeļizaveta Sokolovska, Valdis Pīrāgs, Jānis Kloviņš, Vita Rovīte
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.20916.2

Fast effect size shrinkage software for beta-binomial models of allelic imbalance
Cited by: 11
Author(s): Joshua P. Zitovsky, Michael I. Love
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12915-020-00863-8

Functional signatures of evolutionarily young CTCF binding sites
Cited by: 7
Author(s): Dhoyazan Azazi, Jonathan M. Mudge, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: about 4 years ago

10.26508/lsa.202000897

Tissue-selective alternate promoters guide NLRP6 expression
Cited by: 1
Author(s): Nathan A. Bracey, Jaye M. Platnich, Arthur Lau, Hyunsoo Chung, M. Eric Hyndman, Justin A. MacDonald, Justin Chun, Paul L. Beck, Stephen E. Girardin, Paul M. Gordon, Daniel A. Muruve
Software Mentions: 7
Published: almost 4 years ago

10.3389/fcell.2021.624053

“All-In-One” Genetic Tool Assessing Endometrial Receptivity for Personalized Screening of Female Sex Steroid Hormones
Cited by: 7
Author(s): Pavel Deryabin, А. П. Домнина, Inga V. Gorelova, M. V. Rulev, М. А. Petrosyan, Nikolay Nikolsky, Aleksandra Borodkina
Software Mentions: 7
Published: over 3 years ago

10.3389/fonc.2020.614487

Distinguishable Prognostic miRNA Signatures of Head and Neck Squamous Cell Cancer With or Without HPV Infection
Cited by: 10
Author(s): Xinmei Luo, Min Zheng, Mingxin Cao, Weilong Zhang, Mengyuan Huang, Li Dai, Yaling Tang, Xin‐hua Liang
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-020-70967-2

Transcriptomics uncovers substantial variability associated with alterations in manufacturing processes of macrophage cell therapy products
Cited by: 14
Author(s): Olga L. Gurvich, Katja A. Puttonen, Aubrey Bailey, Anssi Kailaanmäki, Vita Skirdenko, Minna Sivonen, Sanna Pietikäinen, Nigel R. Parker, Seppo Ylä‐Herttuala, Tuija Kekarainen
Software Mentions: 7
Published: about 4 years ago

10.7554/eLife.52511

ERK3/MAPK6 controls IL-8 production and chemotaxis
Cited by: 23
Author(s): Katarzyna Bogucka, Malvika Pompaiah, Fédérico Marini, Harald Binder, Gregory S. Harms, Manuel Kaulich, Matthias Klein, Christian Michel, Markus P. Radsak, Sebastian Rosigkeit, Peter Grimminger, Hansjörg Schild, Krishnaraj Rajalingam
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2021.630389

Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells
Cited by: 6
Author(s): Zsuzsanna Ortutay, Anna Grönholm, Melina Laitinen, Melinda Keresztes-Andrei, Ismaïl Hermelo, Marko Pesu
Software Mentions: 6
Published: over 3 years ago

10.1126/sciadv.abe8978

Astrocytes and neurons share region-specific transcriptional signatures that confer regional identity to neuronal reprogramming
Cited by: 56
Author(s): Álvaro Herrero-Navarro, Lorenzo Puche-Aroca, Verónica Moreno‐Juan, Alejandro Sempere-Ferràndez, Ana Espinosa, Rafael Susín, Laia Torres-Masjoan, Eduardo Leyva-Díaz, Marisa Karow, María Figueres-Oñate, Laura López‐Mascaraque, José P. López‐Atalaya, Benedikt Berninger, Guillermina López‐Bendito
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-81103-z

Cysteine: an overlooked energy and carbon source
Cited by: 19
Author(s): Luise Göbbels, Anja Poehlein, Albert Dumnitch, Richard Egelkamp, Cathrin Kröger, Johanna Haerdter, Thomas Hackl, Artur Feld, H. Weller, Rolf Daniel, Wolfgang R. Streit, Marie Charlotte Schoelmerich
Software Mentions: 6
Published: almost 4 years ago

10.3389/fonc.2020.01383

Prognostic Molecular Signatures for Metastatic Potential in Clinically Low-Risk Stage I and II Clear Cell Renal Cell Carcinomas
Cited by: 2
Author(s): Andrew Shih, Neal Murphy, Zachary Kozel, Paras Shah, Oksana Yaskiv, Houman Khalili, Anthony Liew, Louis R. Kavoussi, Simon Hall, Manish Vira, Xinhua Zhu, Annette T. Lee
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.ppat.1009290

Shiga toxin remodels the intestinal epithelial transcriptional response to Enterohemorrhagic Escherichia coli
Cited by: 8
Author(s): Alyson R. Warr, Carole J. Kuehl, Matthew K. Waldor
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.molcel.2019.11.021

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression
Cited by: 208
Author(s): Simone Tamburri, Elisa Lavarone, Daniel Fernández-Pérez, E. J. Conway, Marika Zanotti, Daria Manganaro, Diego Pasini
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.52611

Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides
Cited by: 108
Author(s): Jamie R Wangen, Rachel Green
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41389-020-0224-1

Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor
Cited by: 24
Author(s): Jenna M. Gedminas, Maggie H. Chassé, Mitchell McBrairty, Ian Beddows, Susan M. Kitchen-Goosen, Patrick J. Grohar
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1009121

A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome
Cited by: 20
Author(s): Benjamin L. S. Furman, Caroline M S Cauret, Martin Knytl, Xuhong Song, Tharindu Premachandra, Caleb Ofori‐Boateng, Danielle C. Jordan, Marko E. Horb, Ben Evans
Software Mentions: 5
Published: almost 4 years ago

10.3389/fcimb.2021.641261

Common Dysregulation of Innate Immunity Pathways in Human Primary Astrocytes Infected With Chikungunya, Mayaro, Oropouche, and Zika Viruses
Cited by: 5
Author(s): Victor Emmanuel Viana Geddes, Otávio J. B. Brustolini, Liliane Tavares de Faria Cavalcante, Filipe Romero Rebello Moreira, Fernando Luz de Castro, Ana P. Guimarães, Alexandra Lehmkuhl Gerber, C. Figueiredo, Luan Pereira Diniz, Eurico de Arruda Neto, Amílcar Tanuri, Renan Pedra de Souza, Iranaia Assunção‐Miranda, Soniza Vieira Alves-Leon, Luciana Romão, Jorge Paes Barreto Marcondes de Souza, Ana Tereza Ribeiro de Vasconcelos, Renato Santana Aguiar
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-019-1674-7

Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list
Cited by: 38
Author(s): Paul F. Harrison, Andrew Pattison, David Powell, Traude H. Beilharz
Software Mentions: 5
Published: over 5 years ago

10.1080/15476286.2020.1729594

LncRNAs in molluscan and mammalian stages of parasitic schistosomes are developmentally-regulated and coordinately expressed with protein-coding genes
Cited by: 13
Author(s): Hyung Chul Kim, Ahmad M. Khalil, Emmitt R. Jolly
Software Mentions: 4
Published: over 4 years ago

10.1016/j.molcel.2021.06.020

BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation
Cited by: 38
Author(s): E. J. Conway, Federico Rossi, Daniel Fernández-Pérez, Eleonora Ponzo, Karin Johanna Ferrari, Marika Zanotti, Daria Manganaro, Simona Rodighiero, Simone Tamburri, Diego Pasini
Software Mentions: 4
Published: about 3 years ago

10.1186/s13048-021-00802-3

Small RNA sequencing reveals distinct nuclear microRNAs in pig granulosa cells during ovarian follicle growth
Cited by: 7
Author(s): Derek Toms, Bo Pan, Yinshan Bai, Julang Li
Software Mentions: 4
Published: over 3 years ago

10.1038/s41419-020-02884-1

NLRP7 plays a functional role in regulating BMP4 signaling during differentiation of patient-derived trophoblasts
Cited by: 18
Author(s): Aybuke Alici-Garipcan, Burcu Özçimen, Ilke Süder, Volkan Ülker, Tamer T. Önder, Nesrin Özören
Software Mentions: 4
Published: about 4 years ago

10.1128/mSphere.00009-21

Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality
Cited by: 16
Author(s): Scott Black Pollara, Jamie W. Becker, Brook L. Nunn, Rene Boiteau, Daniel J. Repeta, Miranda C. Mudge, Grayton Downing, Davis Chase, Elizabeth L. Harvey, Kristen E. Whalen
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2021.599805

Innate Lymphoid Cells Activation and Transcriptomic Changes in Response to Human Dengue Infection
Cited by: 6
Author(s): Tiraput Poonpanichakul, Wilawan Chan-in, Anunya Opasawatchai, Fabien Loison, Oranart Matangkasombut, Varodom Charoensawan, Ponpan Matangkasombut, Denfree Thailand
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-021-02366-w

Multiomic analysis of Schistosoma mansoni reveals unique expression profiles in cercarial heads and tails
Cited by: 1
Author(s): James R Hagerty, Hyung Chul Kim, Emmitt R. Jolly
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1008398

Genomic dissection of an extended phenotype: Oak galling by a cynipid gall wasp
Cited by: 40
Author(s): Jack Hearn, Mark Blaxter, Karsten Schönrogge, J. L. Nieves‐Aldrey, Juli Pujadé-Villar, Elisabeth Huguet, Jean‐Michel Drezen, Joseph D. Shorthouse, Graham N. Stone
Software Mentions: 3
Published: about 5 years ago

10.1002/ctm2.22

Erythrocyte microRNAs show biomarker potential and implicate multiple sclerosis susceptibility genes
Cited by: 5
Author(s): Kira Groen, Vicki E. Maltby, Rodney J. Scott, Lotti Tajouri, Jeannette Lechner‐Scott
Software Mentions: 3
Published: over 4 years ago

10.15252/emmm.202013610

Modeling genetic epileptic encephalopathies using brain organoids
Cited by: 18
Author(s): Daniel J. Steinberg, Srinivasarao Repudi, Afifa Saleem, I. M. Kustanovich, Sergey Viukov, Baraa Abudiab, Ehud Banne, Muhammad Mahajnah, Jacob Hanna, Shani Stern, Peter L. Carlen, Rami I. Aqeilan
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms21124404

Platelet-Released Growth Factors and Platelet-Rich Fibrin Induce Expression of Factors Involved in Extracellular Matrix Organization in Human Keratinocytes
Cited by: 11
Author(s): Andreas Bayer, Bernard Wijaya, Lena Möbus, Franziska Rademacher, Meno Rodewald, Mersedeh Tohidnezhad, Thomas Pufe, D. Drücke, Regine Gläser, Jürgen Harder
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2021.707217

Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients
Cited by: 9
Author(s): Miranda Houtman, Espen Hesselberg, Lars Rönnblom, Lars Klareskog, Vivianne Malmström, Leonid Padyukov
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2019.02728

The Glycerol Phosphatase Gpp2: A Link to Osmotic Stress, Sulfur Assimilation and Virulence in Cryptococcus neoformans
Cited by: 4
Author(s): Kevin Felipe Cruz Martho, Otávio J. B. Brustolini, Ana Tereza Ribeiro de Vasconcelos, Marcelo A. Vallim, Renata C. Pascon
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms21176322

The Lysine Specific Demethylase-1 Negatively Regulates the COL9A1 Gene in Human Articular Chondrocytes
Cited by: 6
Author(s): Anne-Laure Durand, Alexandre Dufour, E. Aubert-Foucher, Christine Oger-Desfeux, Marielle Pasdeloup, Sébastien Lustig, Elvire Servien, Gualter Vaz, Emeline Perrier‐Groult, Frédéric Mallein-Gerin, J. Lafont
Software Mentions: 3
Published: about 4 years ago

10.1210/clinem/dgz306

Arterial Wall Inflammation and Increased Hematopoietic Activity in Patients With Primary Aldosteronism
Cited by: 24
Author(s): Charlotte D C C van der Heijden, E. Smeets, Erik H.J.G. Aarntzen, Marlies P. Noz, Houshang Monajemi, Simone Kersten, Charlotte Kaffa, Alexander Hoischen, Jaap Deinum, Leo A. B. Joosten, Mihai G. Netea, Niels P. Riksen
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-96110-3

SARS-CoV-2 infection initiates interleukin-17-enriched transcriptional response in different cells from multiple organs
Cited by: 37
Author(s): Zobaer Hasan, Syful Islam, Kenichi Matsumoto, Taro Kawai
Software Mentions: 3
Published: about 3 years ago

10.18632/oncotarget.27546

Entinostat augments NK cell functions via epigenetic upregulation of IFIT1-STING-STAT4 pathway
Cited by: 20
Author(s): John M Idso, Shunhua Lao, Nathan J. Schloemer, Jeffrey Knipstein, Robert T. Burns, Monica S. Thakar, Subramaniam Malarkannan
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-48433-5

The regulation of the sulfur amino acid biosynthetic pathway in Cryptococcus neoformans: the relationship of Cys3, Calcineurin, and Gpp2 phosphatases
Cited by: 18
Author(s): Amanda Teixeira de Melo, Kevin Felipe Cruz Martho, Thiago Nunes Roberto, Erika Sayuri Nishiduka, Joel Machado, Otávio J. B. Brustolini, Alexandre Keiji Tashima, Ana Tereza Ribeiro de Vasconcelos, Marcelo A. Vallim, Renata C. Pascon
Software Mentions: 2
Published: about 5 years ago

10.1186/s12920-020-0666-5

Blood signatures for second stage human African trypanosomiasis: a transcriptomic approach
Cited by: 5
Author(s): Julius Mulindwa, Enock Matovu, John Enyaru, Christine Clayton
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41375-021-01172-x

Selective elimination of immunosuppressive T cells in patients with multiple myeloma
Cited by: 21
Author(s): Mohamed H.S. Awwad, Abdelrahman Mahmoud, Heiko Bruns, Hakim Echchannaoui, Katharina Kriegsmann, Raphael Lutz, Marc S. Raab, Uta Bertsch, Markus Munder, Anna Jauch, Katja Weisel, Bettina Maier, Niels Weinhold, Hans Salwender, Volker Eckstein, Mathias Hänel, Roland Fenk, Jan Dürig, Benedikt Brors, Axel Benner, Carsten Müller‐Tidow, Hartmut Goldschmidt, Michael Hundemer
Software Mentions: 2
Published: over 3 years ago

Projects: bioconductor: apeglm

Papers Mentioning apeglm 41