bioconductor: RUVSeq | Projects | Ecosyste.ms: Papers

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

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago

10.1002/1873-3468.12684

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.1093/bioinformatics/btw777

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Cited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago

10.3390/genes12030352

Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data
Cited by: 10
Author(s): Vera-Khlara S. Oh, Robert W. Li
Software Mentions: 12
Published: over 3 years ago

10.3390/cancers11091248

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features
Cited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: about 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

10.1186/s12859-017-1770-1

CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Cited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: over 7 years ago

10.1186/s13041-020-00681-7

Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer’s disease
Cited by: 22
Author(s): Karissa Barthelson, Stephen Pederson, Morgan Newman, Michael Lardelli
Software Mentions: 9
Published: about 4 years ago

10.1038/s41598-020-66998-4

Comparison of differential accessibility analysis strategies for ATAC-seq data
Cited by: 26
Author(s): Paul Gontarz, Shuhua Fu, Xiaoyun Xing, Shaopeng Liu, Benpeng Miao, Viktoriia Bazylianska, Akhil Sharma, Pamela A. F. Madden, K. Lynn Cates, Andrew S. Yoo, Anna Moszczyńska, Ting Wang, Bo Zhang
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.58081

IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation
Cited by: 11
Author(s): Pan Li, Madeleine E. Lemieux, Tom Thomas, Julia M. Rogers, Colin H. Lipper, Winston Lee, C. Anderson Johnson, Lynette M. Sholl, Andrew P. South, Jarrod A. Marto, Guillaume Adelmant, Stephen C. Blacklow, Jon C. Aster
Software Mentions: 9
Published: about 4 years ago

10.15252/msb.20209667

Using single‐plant‐omics in the field to link maize genes to functions and phenotypes
Cited by: 17
Author(s): Daniel Felipe Cruz, Sam Meyer, Joke Ampe, Heike Sprenger, Dorota Herman, Tom Van Hautegem, Jolien De Block, Dirk Inzé, Hilde Nelissen, Steven Maere
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0224879

Long non-coding RNAs and latent HIV – A search for novel targets for latency reversal
Cited by: 17
Author(s): Wim Trypsteen, Cory H. White, Amey Mukim, Celsa A. Spina, Ward De Spiegelaere, Steve Lefever, Vicente Planelles, Alberto Bosque, Christopher H. Woelk, Linos Vandekerckhove, Nadejda Beliakova-Bethell
Software Mentions: 8
Published: almost 5 years ago

10.3389/fcvm.2018.00167

Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart
Cited by: 15
Author(s): Andrea Massaia, Patrícia Chaves, Sara Samari, Ricardo J. Miragaia, Kerstin B. Meyer, Sarah A. Teichmann, Michela Noseda
Software Mentions: 8
Published: almost 6 years ago

10.3390/cancers12010045

N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma
Cited by: 11
Author(s): Candace A. Frerich, Hailey N. Sedam, Huining Kang, Yoshitsugu Mitani, Adel K. El‐Naggar, Scott A. Ness
Software Mentions: 8
Published: almost 5 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

10.1002/1878-0261.12569

Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progression
Cited by: 34
Author(s): Bo Pang, Jiu Hua Xu, Jing Hu, Fenghua Guo, Linyun Wan, Mingjiang Cheng, Lin Pang
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0227760

A graph-based algorithm for RNA-seq data normalization
Cited by: 2
Author(s): Diem-Trang Tran, Aditya Bhaskara, Balagurunathan Kuberan, Matthew Might
Software Mentions: 7
Published: almost 5 years ago

10.1101/2021.05.27.21257952

Immune transcriptomes from hospitalized patients infected with the SARS-CoV-2 variants B.1.1.7 and B.1.1.7 carrying the E484K escape mutation
Cited by: 3
Author(s): Hye Kyung Lee, Ludwig Knabl, Manuel Wieser, Anna Mur, August Zabernigg, Jana Schumacher, Norbert Kaiser, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: over 3 years ago

10.1101/2020.09.01.20185884

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 0
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorothee von Laer, Lothar Hennighausen
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-021-83110-6

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 13
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Ludwig Knabl, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorotheé von Laer, Lothar Hennighausen
Software Mentions: 6
Published: over 3 years ago

10.1186/s13229-020-00402-w

Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm
Cited by: 23
Author(s): Hudson P. Santos, Arjun Bhattacharya, Robert M. Joseph, Lisa Smeester, Karl Kuban, Carmen J. Marsit, T. Michael O’Shea, Rebecca C. Fry
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.42374

A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
Cited by: 31
Author(s): Michelle C. Ward, Yoav Gilad
Software Mentions: 6
Published: over 5 years ago

10.3390/v12111303

Human Endogenous Retrovirus K Rec Forms a Regulatory Loop with MITF that Opposes the Progression of Melanoma to an Invasive Stage
Cited by: 16
Author(s): Manvendra Singh, Huiqiang Cai, Mario Bunse, Cédric Feschotte, Zsuzsanna Izsvák
Software Mentions: 6
Published: almost 4 years ago

10.7554/eLife.57345

Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes
Cited by: 37
Author(s): Michelle C. Ward, Nicholas E. Banovich, Abhishek Sarkar, Matthew Stephens, Yoav Gilad
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0235294

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury
Cited by: 22
Author(s): Elodie Ramond, Jan Paul Dudzic, Bruno Lemaître
Software Mentions: 6
Published: over 4 years ago

10.1101/2021.09.08.21263284

Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19
Cited by: 12
Author(s): Hye Kyung Lee, Ludwig Knabl, Ludwig Knabl, Sebastian Kapferer, Birgit Pateter, Mary Walter, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: about 3 years ago

10.3389/fcimb.2019.00392

Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution
Cited by: 13
Author(s): Regan J. Hayward, J. Wallis Marsh, Michael S. Humphrys, Wilhelmina M. Huston, Garry Myers
Software Mentions: 6
Published: almost 5 years ago

10.1186/s13059-020-1942-6

A framework for transcriptome-wide association studies in breast cancer in diverse study populations
Cited by: 60
Author(s): Arjun Bhattacharya, Montserrat García‐Closas, Andrew F. Olshan, Charles M. Perou, Melissa A. Troester, Michael I. Love
Software Mentions: 6
Published: over 4 years ago

10.1186/s12967-017-1201-0

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival
Cited by: 46
Author(s): Chinh Bkrong Nguyen, Lene Alsøe, Jessica M. Lindvall, Dag Sulheim, Even Fagermoen, Anette Winger, Mari Kaarbø, Hilde Nilsen, Vegard Bruun Wyller
Software Mentions: 6
Published: over 7 years ago

10.21203/rs.3.rs-69657/v1

Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community
Cited by: 0
Author(s): Hye Kyung Lee, Ludwig Knabl, Lisa Pipperger, André Volland, Priscilla A. Furth, Keunsoo Kang, Harold E. Smith, Romuald Bellmann, Christina Bernhard, Norbert Kaiser, Hannes Gänzer, Mathias Ströhle, Andreas Walser, Dorothee von Laer, Lothar Hennighausen
Software Mentions: 6
Published: about 4 years ago

10.21203/rs.3.rs-509143/v1

Impact of BNT162b First Vaccination on the Immune Transcriptome of Elderly Patients Infected with the B.1.351 SARS-CoV-2 Variant
Cited by: 3
Author(s): Ludwig Knabl, Hye Kyung Lee, Manuel Wieser, Anna Mur, August Zabernigg, Simon Rauch, Matthias Böck, Jana Schumacher, Norbert Kaiser, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: over 3 years ago

10.1101/2021.05.11.21256862

Impact of BNT162b first vaccination on the immune transcriptome of elderly patients infected with the B.1.351 SARS-CoV-2 variant
Cited by: 2
Author(s): Ludwig Knabl, Hye Kyung Lee, Manuel Wieser, Anna Mur, August Zabernigg, Simon Rauch, Matthias Böck, Jana Schumacher, Norbert Kaiser, Priscilla A. Furth, Lothar Hennighausen
Software Mentions: 6
Published: over 3 years ago

10.3389/fmolb.2021.716544

GeneTrail: A Framework for the Analysis of High-Throughput Profiles
Cited by: 1
Author(s): Nico Gerstner, Tim Kehl, Kerstin Lenhof, Lea Eckhart, Lara Schneider, Daniel Stöckel, Christina Backes, Eckart Meese, Andreas Keller, Hans‐Peter Lenhof
Software Mentions: 5
Published: about 3 years ago

10.1038/s42003-021-01656-7

Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumors
Cited by: 19
Author(s): Kelsey Yetsko, Jessica Farrell, Nicholas B. Blackburn, Liam Whitmore, Maximilian R Stammnitz, Jenny Whilde, Catherine B. Eastman, Devon Rollinson Ramia, Rachel Thomas, Aleksandar Krstić, Paul J. Linser, Simon Creer, Gary R. Carvalho, Mariana A. Devlin, Nina Nahvi, Ana C Leandro, Thomas W. deMaar, Brooke Burkhalter, Elizabeth P. Murchison, Christine E. Schnitzler, David J. Duffy
Software Mentions: 5
Published: almost 4 years ago

10.21203/rs.3.rs-119695/v1

Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors
Cited by: 5
Author(s): Hye Kyung Lee, Olive Jung, Lothar Hennighausen
Software Mentions: 5
Published: almost 4 years ago

10.1101/2021.01.15.426908

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Cited by: 2
Author(s): Jakub Jankowski, Hye Kyung Lee, Julia Wilflingseder, Lothar Hennighausen
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.42819

Shank3 modulates sleep and expression of circadian transcription factors
Cited by: 56
Author(s): Ashley M Ingiosi, Hannah Schoch, Taylor Wintler, Kristan G. Singletary, Dario Righelli, Leandro Gabriel Roser, E Medina, Davide Risso, Marcos G. Frank, Lucı́a Peixoto
Software Mentions: 5
Published: over 5 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

10.7717/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

10.1038/s42003-021-02167-1

JAK inhibitors dampen activation of interferon-stimulated transcription of ACE2 isoforms in human airway epithelial cells
Cited by: 15
Author(s): Hye Kyung Lee, Olive Jung, Lothar Hennighausen
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-019-5504-9

Streamlined computational pipeline for genetic background characterization of genetically engineered mice based on next generation sequencing data
Cited by: 5
Author(s): Carlos Farkas, Francisco Fuentes-Villalobos, Boris Rebolledo‐Jaramillo, Fernando Benavides, Ariel F. Castro, Roxana Pincheira
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.00684

Increase in DNA Damage by MYCN Knockdown Through Regulating Nucleosome Organization and Chromatin State in Neuroblastoma
Cited by: 3
Author(s): Xinjie Hu, Weisheng Zheng, Qianshu Zhu, Liang Gu, Yanhua Du, Zhe Han, Xiaobai Zhang, Daniel Carter, Belamy B. Cheung, Andong Qiu, Cizhong Jiang
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-020-01960-1

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons
Cited by: 35
Author(s): Peipei Li, Elizabeth Ensink, Sean Lang, Lee Marshall, Meghan Schilthuis, Jared Lamp, Irving E. Vega, Viviane Labrie
Software Mentions: 5
Published: over 4 years ago

10.1534/genetics.120.303460

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in <i>Drosophila pseudoobscura</i>
Cited by: 16
Author(s): Zachary L. Fuller, Spencer Koury, Christopher J. Leonard, Randee E. Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen W. Schaeffer, Nitin Phadnis
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.7107

Characterization of bidirectional gene pairs in The Cancer Genome Atlas (TCGA) dataset
Cited by: 8
Author(s): Juchuanli Tu, Xiaolu Li, Jianjun Wang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13024-018-0303-3

Inhibition of monocyte-like cell extravasation protects from neurodegeneration in DBA/2J glaucoma
Cited by: 44
Author(s): Pete A. Williams, Catherine E. Braine, Krishnakumar Kizhatil, Nicole E. Foxworth, Nicholas G. Tolman, Jeffrey M. Harder, R. Scott, Gregory L. Sousa, Alyssa Panitch, Gareth R. Howell, Simon W. M. John
Software Mentions: 4
Published: almost 6 years ago

10.1007/s12035-021-02296-y

The Coding and Small Non-coding Hippocampal Synaptic RNAome
Cited by: 9
Author(s): Robert Epple, Dennis M. Krüger, Tea Berulava, Gerrit Brehm, Momchil Ninov, Rezaul Islam, Sarah Köster, André Fischer
Software Mentions: 4
Published: over 3 years ago

10.3390/ijms22020736

Omics Analysis of Blood-Responsive Regulon in Bordetella pertussis Identifies a Novel Essential T3SS Substrate
Cited by: 2
Author(s): Jakub Držmíšek, Daniel Štipl, Denisa Petráčková, Branislav Večerek, Ana Dienstbier
Software Mentions: 4
Published: almost 4 years ago

10.3390/ani11082241

Transcriptomic Response under Heat Stress in Chickens Revealed the Regulation of Genes and Alteration of Metabolism to Maintain Homeostasis
Cited by: 8
Author(s): Hana Kim, Hye‐Ran Kim, Pil‐Nam Seong, D. K. Arora, Donghyun Shin, Woncheoul Park, Jong-Eun Park
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.13806

Bronchial airway gene expression signatures in mouse lung squamous cell carcinoma and their modulation by cancer chemopreventive agents
Cited by: 20
Author(s): Donghai Xiong, Jing Pan, Qi Zhang, Éva Szabó, Mark Steven Miller, Ronald A. Lubet, Ming You, Yian Wang
Software Mentions: 4
Published: almost 8 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.630988

Transcriptomic Profiling of Fibropapillomatosis in Green Sea Turtles (Chelonia mydas) From South Texas
Cited by: 9
Author(s): Nicholas B. Blackburn, Ana C Leandro, Nina Nahvi, Mariana A. Devlin, Marcelo Leandro, Ignacio Martinez Escobedo, Juan M. Peralta, Jeff George, Brian A. Stacy, Thomas W. deMaar, John Blangero, Megan Keniry, Joanne E. Curran
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2019.02096

Plasmacytoid DCs From Patients With Sjögren's Syndrome Are Transcriptionally Primed for Enhanced Pro-inflammatory Cytokine Production
Cited by: 37
Author(s): Maarten R Hillen, Aridaman Pandit, Sofie L M Blokland, Sarita A. Y. Hartgring, Cornelis P. J. Bekker, Eefje Hanna Martine van der Heijden, Nila Hendrika Servaas, Marzia Rossato, Aike A. Kruize, Joël A G van Roon, Timothy R D J Radstake
Software Mentions: 4
Published: about 5 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

10.3389/fmicb.2019.02195

Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces
Cited by: 5
Author(s): Yu-Wen Lai, Chi Nam Ignatius Pang, Leona T. Campbell, Wen Chen, Marc R. Wilkins, Dee Carter
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-42308-5

Gene Expression Profiles Associated with Brain Aging are Altered in Schizophrenia
Cited by: 12
Author(s): Sarven Sabunciyan
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008617

Inhibition of the oligosaccharyl transferase in Caenorhabditis elegans that compromises ER proteostasis suppresses p38-dependent protection against pathogenic bacteria
Cited by: 8
Author(s): Dae‐Eun Jeong, Yujin Lee, Seokjin Ham, Dong-Yeop Lee, Sujeong Kwon, Hae‐Eun H. Park, Sunyoung Hwang, Joo‐Yeon Yoo, Tae-Young Roh, Seung-Jae Lee
Software Mentions: 4
Published: over 4 years ago

10.1038/s41597-021-00836-8

LC-MS based plant metabolic profiles of thirteen grassland species grown in diverse neighbourhoods
Cited by: 10
Author(s): Sue Marr, Jos A. Hageman, Ron Wehrens, Nicole M. van Dam, Helge Bruelheide, Steffen Neumann
Software Mentions: 3
Published: over 3 years ago

10.1016/j.ccell.2018.08.015

The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation
Cited by: 75
Author(s): N Martinez-Soria, Lynsey McKenzie, Julia Draper, Anetta Ptasińska, Hasan Issa, Sandeep Potluri, Helen J. Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Dan Coleman, Sirintra Nakjang, Salam A. Assi, Victoria J. Forster, Mojgan Reza, Edward Law, Philip Berry, Dorothée Mueller, Cameron S. Osborne, Alex Elder, Simon Bomken, Deepali Pal, James M. Allan, Gareth J. Veal, Peter N. Cockerill, Christian Wichmann, Josef Vormoor, Georges Lacaud, Constanze Bonifer, Olaf Heidenreich
Software Mentions: 3
Published: about 6 years ago

10.3389/fimmu.2020.00974

Airway Epithelial Cell Immunity Is Delayed During Rhinovirus Infection in Asthma and COPD
Cited by: 51
Author(s): Punnam Chander Veerati, Niamh M. Troy, Andrew T Reid, Ngan Fung Li, Kristy S Nichol, Parwinder Kaur, Steven Maltby, Peter Wark, Darryl A. Knight, Anthony Bosco, Christopher Grainge, Nathan W. Bartlett
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.535673

Transcriptome and miRNome Analysis Provide New Insight Into Host Lipid Accumulation, Innate Immunity, and Viral Persistence in Hepatitis C Virus Infection in vitro
Cited by: 5
Author(s): Chong Li, Lungen Lu, Zhongtian Qi, Yaping Zhu, Fengtao Su, Ping Zhao
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.ppat.1006026

Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model
Cited by: 25
Author(s): Cory H. White, Bastiaan Moesker, Nadejda Beliakova-Bethell, Laura J. Martins, Celsa A. Spina, David M. Margolis, Douglas D. Richman, Vicente Planelles, Alberto Bosque, Christopher H. Woelk
Software Mentions: 3
Published: almost 8 years ago

10.1111/acel.12795

Differential aging-related changes in neurophysiology and gene expression in IB4-positive and IB4-negative nociceptive neurons
Cited by: 5
Author(s): Malgorzata A. Mis, Mark F. Rogers, Aaron R. Jeffries, Anna Wilbrey, Lubin Chen, Yang Yang, Sulayman D. Dib‐Hajj, Stephen G. Waxman, Edward B. Stevens, Andrew D. Randall
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-47389-w

Electrical stimulation shifts healing/scarring towards regeneration in a rat limb amputation model
Cited by: 30
Author(s): Karla Mychellyne Costa Oliveira, John H. Barker, Eugène Berezikov, Lukas Pindur, S Kynigopoulos, Maria Eischen-Loges, Zhongchao Han, Mit Balvantray Bhavsar, Dirk Henrich, Liudmila Leppik
Software Mentions: 3
Published: over 5 years ago

10.1128/mSystems.00017-20

Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078
Cited by: 19
Author(s): Tinghua Li, Yan Zhang, Ke Dong, C.J. Kuo, Chong Li, Yaping Zhu, Jinhong Qin, Qingtian Li, Yung‐Fu Chang, Xiaokui Guo, Yongzhang Zhu
Software Mentions: 3
Published: over 4 years ago

10.1016/j.jlr.2021.100056

Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells
Cited by: 6
Author(s): Stacey L. Borrego, Johannes F. Fahrmann, Jue Hou, Dawei Lin, Bruce J. Tromberg, Oliver Fiehn, Peter Kaiser
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.52473

Rejuvenating conventional dendritic cells and T follicular helper cell formation after vaccination
Cited by: 46
Author(s): Marisa Stebegg, Alexandre Bignon, Danika L. Hill, Alyssa Silva-Cayetano, Christel Krueger, Ine Vanderleyden, Silvia Innocentin, Louis Boon, Jiong Wang, Martin S. Zand, James Dooley, Jonathan Clark, Adrian Liston, Edward J Carr, Michelle A. Linterman
Software Mentions: 3
Published: over 4 years ago

10.7554/eLife.38904

Single cell functional genomics reveals the importance of mitochondria in cell-to-cell phenotypic variation
Cited by: 29
Author(s): Riddhiman Dhar, Alsu Missarova, Ben Lehner, Lucas B. Carey
Software Mentions: 3
Published: almost 6 years ago

10.3390/ijms21082818

Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions
Cited by: 14
Author(s): Siriluck Ponsuksili, Henry Reyer, Frieder Hadlich, Frank Weber, Nares Trakooljul, Michael Oster, Puntita Siengdee, Eduard Muráni, M. Rodehutscord, Amélia Camarinha‐Silva, Jörn Bennewitz, Klaus Wimmers
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21114003

Dexfenfluramine and Pergolide Cause Heart Valve Disease via Valve Metabolic Reprogramming and Ongoing Matrix Remodeling
Cited by: 1
Author(s): Cécile Oury, Patrick Maréchal, Nathalie Donis, Alexia Hulin, Alexandre Hego, Julien Tridetti, Mai-Linh Nguyen, Raluca Dulgheru, Marianne Fillet, Alain Nchimi, Patrizio Lancellotti
Software Mentions: 3
Published: over 4 years ago

10.1128/mSystems.00106-20

Characterizing the Mechanism of Action of an Ancient Antimicrobial, Manuka Honey, against Pseudomonas aeruginosa Using Modern Transcriptomics
Cited by: 28
Author(s): Daniel Bouzo, Nural N. Cokcetin, Liping Li, Giulia Ballerin, Amy L. Bottomley, James Lazenby, Cynthia B. Whitchurch, Ian T. Paulsen, Karl A. Hassan, Elizabeth J. Harry
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.20607

Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano
Cited by: 40
Author(s): Magda Grudniewska, Stijn Mouton, Daniil Simanov, Frank W. Beltman, Margriet Grelling, Katrien De Mulder, Wibowo Arindrarto, Philipp M. Weissert, Stefan van der Elst, Eugène Berezikov
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pgen.1005690

Compound Heterozygosity for Y Box Proteins Causes Sterility Due to Loss of Translational Repression
Cited by: 35
Author(s): Elizabeth M. Snyder, Ramani Soundararajan, Manju Sharma, Andrea Dearth, Benjamin Smith, Robert E. Braun
Software Mentions: 2
Published: almost 9 years ago

10.3390/v12070776

Tiotropium Is Predicted to Be a Promising Drug for COVID-19 Through Transcriptome-Based Comprehensive Molecular Pathway Analysis
Cited by: 17
Author(s): Keunsoo Kang, Hoo Hyun Kim, Yuni Choi
Software Mentions: 2
Published: over 4 years ago

10.1038/s41398-019-0579-2

A combined miRNA–piRNA signature to detect Alzheimer’s disease
Cited by: 69
Author(s): Gaurav Jain, Anne Stuendl, Pooja Rao, Tea Berulava, Tonatiuh Peña Centeno, Lalit Kaurani, Susanne Burkhardt, Ivana Delalle, Johannes Kornhuber, Michael Hüll, Wolfgang Maier, Oliver Peters, Hermann Esselmann, Claudia Schulte, Christian Deuschle, Matthis Synofzik, Jens Wiltfang, Brit Mollenhauer, Walter Maetzler, Anja Schneider, André Fischer
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-56981-z

Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures
Cited by: 16
Author(s): Dilara Ayyildiz, Giulia Antoniali, Chiara D’Ambrosio, Giovanna Mangiapane, Emiliano Dalla, Andrea Scaloni, Gianluca Tell, Silvano Piazza
Software Mentions: 2
Published: almost 5 years ago

10.1007/s11306-016-1015-8

Improved batch correction in untargeted MS-based metabolomics
Cited by: 158
Author(s): Ron Wehrens, Jos A. Hageman, Fred van Eeuwijk, Rik Kooke, Pádraic J. Flood, Erik Wijnker, Joost J. B. Keurentjes, Arjen Lommen, Henriëtte D. L. M. van Eekelen, Robert D. Hall, Roland Mumm, Ric C. H. de Vos
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-019-49836-0

Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei
Cited by: 27
Author(s): Luca Peruzza, M. S. Shekhar, Karthik Kumar, A. Swathi, K. Karthic, Chris Hauton, K.K. Vijayan
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-017-11635-w

Prenatal Glucocorticoid Exposure Modifies Endocrine Function and Behaviour for 3 Generations Following Maternal and Paternal Transmission
Cited by: 89
Author(s): Vasilis G. Moisiadis, Andrea Constantinof, Alisa Kostaki, Moshe Szyf, Stephen G. Matthews
Software Mentions: 2
Published: about 7 years ago

10.1016/j.celrep.2018.09.057

Defective Mitochondrial Cardiolipin Remodeling Dampens HIF-1α Expression in Hypoxia
Cited by: 40
Author(s): Arpita Chowdhury, Abhishek Aich, Gaurav Jain, Katharina Wozny, Christian Lüchtenborg, Milan J. M. Hartmann, Olaf Bernhard, Martina Balleiniger, Ezzaldin Ahmed Alfar, Anke Zieseniß, Karl Toischer, Kaomei Guan, Silvio O. Rizzoli, Britta Brügger, André Fischer, Dörthe M. Katschinski, Peter Rehling, Jan Dudek
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.58029

Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network
Cited by: 32
Author(s): Shreyasi Mukherjee, Praneet Chaturvedi, Scott A. Rankin, Margaret Fish, Marcin Wlizla, Kitt D. Paraiso, Melissa MacDonald, Marc E. Rothenberg, Matthew T. Weirauch, Ira L. Blitz, Ken Wy. Cho, Aaron M. Zorn
Software Mentions: 2
Published: about 4 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.0234427

Characterization of microRNA profiles in the mammary gland tissue of dairy goats at the late lactation, dry period and late gestation stages
Cited by: 19
Author(s): Rong Xuan, Tianle Chao, Aili Wang, Fuhong Zhang, Ping Sun, Shuang Liu, Maosen Guo, Guizhi Wang, Zhibin Ji, Jianmin Wang, Ming Cheng
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-15379-5

The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species
Cited by: 15
Author(s): Nicholas M. Negretti, Christopher R. Gourley, Gérémy Clair, Joshua N. Adkins, Michael E. Konkel
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-020-79008-4

The bivariate NRIP1/ZEB2 RNA marker permits non-invasive presymptomatic screening of pre-eclampsia
Cited by: 3
Author(s): Vera Manders, Allerdien Visser, Remco Keijser, Naomi Min, Ankie Poutsma, Joyce Mulders, Tarah van den Berkmortel, Marjolein Hortensius, Aldo Jongejan, Eva Pajkrt, Erik A. Sistermans, Daoud Sie, Myron G. Best, Tom Würdinger, Marjon A. de Boer, Gijs B. Afink, Cees B.M. Oudejans
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-020-06986-0

Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium
Cited by: 16
Author(s): Junhong Cao, Jin-Quan Huang, Xia Liu, Chao-Chen Huang, Zishou Zheng, Xiufang Zhang, Xiao‐Xia Shangguan, Ling-Jian Wang, Yugao Zhang, Jonathan F. Wendel, Corrinne E. Grover, Zhiwen Chen
Software Mentions: 1
Published: about 4 years ago

10.3390/biom11050621

Overcoming the Challenges of High Quality RNA Extraction from Core Needle Biopsy
Cited by: 6
Author(s): Hanne Locy, Rohann J.M. Correa, Dorien Autaers, Ann Schiettecatte, Jan Jonckheere, Wim Waelput, Louise Cras, Stefanie Brock, Stefaan Verhulst, Keith Kwan, Marian Vanhoeij, Kris Thielemans, Karine Breckpot
Software Mentions: 1
Published: over 3 years ago

10.1194/jlr.RA120001101

Generation and validation of a conditional knockout mouse model for the study of the Smith-Lemli-Opitz syndrome
Cited by: 1
Author(s): Babunageswararao Kanuri, Vincent Fong, Sithara Raju Ponny, Keri A. Tallman, Sriganesh Ramachandra Rao, Ned A. Porter, Steven J. Fliesler, Shailendra B. Patel
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.jlr.2021.100028

Generation and validation of a conditional knockout mouse model for desmosterolosis
Cited by: 3
Author(s): Babunageswararao Kanuri, Vincent Fong, Sithara Raju Ponny, Ranjuna Weerasekera, Kirthi Pulakanti, Kriya S. Patel, Roman Tyshynsky, Shailendra B. Patel
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-76278-w

Molecular insights into the mechanisms of susceptibility of Labeo rohita against oomycete Aphanomyces invadans
Cited by: 11
Author(s): Pravata Kumar Pradhan, Dev Kumar Verma, Luca Peruzza, Shubham Gupta, Syed Assim Haq, Sergei Shubin, K Morgan, Franziska Trusch, Vindhya Mohindra, Chris Hauton, Pieter van West, Neeraj Sood
Software Mentions: 1
Published: almost 4 years ago

Projects: bioconductor: RUVSeq

Papers Mentioning RUVSeq 91