bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3389/fonc.2021.729103

Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade Glioma
Cited by: 17
Author(s): Shenbin Xu, Zefeng Wang, Juan Ye, Shuhao Mei, Jianmin Zhang
Software Mentions: 10
Published: about 5 years ago

10.3389/fimmu.2021.722860

Transcriptional Changes in Regulatory T Cells From Patients With Autoimmune Polyendocrine Syndrome Type 1 Suggest Functional Impairment of Lipid Metabolism and Gut Homing
Cited by: 1
Author(s): A Berger, Eirik Bratland, Thea Sjøgren, Marte Heimli, Torgeir Tyssedal, Øyvind Bruserud, Stefan Johansson, Eystein S. Husebye, Bergithe E. Oftedal, Anette Susanne Bøe Wolff
Software Mentions: 10
Published: about 5 years ago

10.1172/jci.insight.138970

Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation program
Cited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: over 5 years ago

10.1242/dev.193060

Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pcbi.1008947

Chromosomal neighbourhoods allow identification of organ specific changes in gene expression
Cited by: 1
Author(s): Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Élodie Renvoisé, Jukka Jernvall
Software Mentions: 10
Published: almost 5 years ago

10.1038/s41598-020-76881-x

Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysis
Cited by: 81
Author(s): Luis A. Corchete, Elizabeta A. Rojas, Diego Alonso-López, Javier De Las Rivas, Norma C. Gutiérrez, F.J. Burguillo
Software Mentions: 10
Published: almost 6 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: about 9 years ago

10.1186/s13059-021-02337-8

Best practices on the differential expression analysis of multi-species RNA-seq
Cited by: 36
Author(s): Matthew Chung, Vincent M. Bruno, David A. Rasko, Christina A. Cuomo, José F. Muñoz, Jonathan Livny, Amol Shetty, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 10
Published: over 5 years ago

10.1038/s41396-021-00940-y

Locally adapted gut microbiomes mediate host stress tolerance
Cited by: 28
Author(s): Shira Houwenhuyse, Robby Stoks, Shinjini Mukherjee, Ellen Decaestecker
Software Mentions: 10
Published: over 5 years ago

10.1186/s41065-021-00202-z

RNA-Seq based transcriptome analysis in oral lichen planus
Cited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: almost 5 years ago

10.1186/s13059-020-02245-3

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts
Cited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 10
Published: over 5 years ago

10.1007/s10456-020-09743-9

Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cells
Cited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: almost 6 years ago

10.1186/s12859-021-04211-7

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Cited by: 6
Author(s): Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti
Software Mentions: 10
Published: over 5 years ago

10.15252/msb.20188339

Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks
Cited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 7 years ago

10.1186/s12859-021-03967-2

tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R
Cited by: 7
Author(s): Charlie M. Carpenter, Daniel N. Frank, Kayla Williamson, Jaron Arbet, Brandie D. Wagner, Katerina Kechris, Miranda Kroehl
Software Mentions: 10
Published: over 5 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 9 years ago

10.18632/aging.203257

Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastoma
Cited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: about 5 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: about 8 years ago

10.15252/msb.20209923

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
Cited by: 122
Author(s): Dénes Türei, Alberto Valdeolivas, Lejla Gul, Nicolàs Palacio-Escat, Michal Klein, Olga Ivanova, Márton Ölbei, Attila Gábor, Fabian J. Theis, Dezső Módos, Tamás Korcsmáros, Julio Sáez-Rodríguez
Software Mentions: 10
Published: over 5 years ago

10.1186/s42523-019-0007-1

Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob mice
Cited by: 15
Author(s): Alireza Kashani, Asker Brejnrod, Chunyu Jin, Timo Kern, Andreas Nygaard Madsen, Louise Holm, Georg K. Gerber, Jens-Christian Holm, Torben Hansen, Birgitte Holst, Manimozhiyan Arumugam
Software Mentions: 10
Published: about 7 years ago

10.1186/s42523-020-00039-3

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata
Cited by: 20
Author(s): H. Pieter J. van Veelen, Joana Falcão Salles, Kevin D. Matson, Marco van der Velde, B. Irene Tieleman
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pone.0223909

Effects of MCHM on yeast metabolism
Cited by: 6
Author(s): Amaury Pupo, Kang‐Mo Ku, Jennifer E. G. Gallagher
Software Mentions: 10
Published: almost 7 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: over 9 years ago

10.1186/s40168-019-0756-9

Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cycling
Cited by: 174
Author(s): Jennifer E. Schmidt, Angela D. Kent, Vanessa Brisson, Amélie C. M. Gaudin
Software Mentions: 10
Published: almost 7 years ago

10.3390/ijms22179601

In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia
Cited by: 7
Author(s): Hande Öngün Yılmaz, Halil Ibrahim Toy, Stephan Marquardt, Gökhan Karakülah, Can Küçük, Panagiota I. Kontou, Stella Logotheti, Athanasia Pavlopoulou
Software Mentions: 10
Published: about 5 years ago

10.1186/s12859-021-04254-w

ORFik: a comprehensive R toolkit for the analysis of translation
Cited by: 13
Author(s): Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski, Eivind Valen
Software Mentions: 10
Published: about 5 years ago

10.3390/ijms22157974

Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice
Cited by: 4
Author(s): Yu Te Lin, Yong Shiou Lin, Wen Cheng, Jui-Chih Chang, Yi Chun Chao, Chin San Liu, An-Chi Wei
Software Mentions: 10
Published: about 5 years ago

10.3390/ijms20061510

Placenta Transcriptome Profiling in Intrauterine Growth Restriction (IUGR)
Cited by: 48
Author(s): Marta Majewska, Aleksandra Lipka, Łukasz Paukszto, J Jastrzebski, Karol Szeszko, Marek Gowkielewicz, Ewa Lepiarczyk, Marcin Jóźwik, Mariusz Majewski
Software Mentions: 10
Published: over 7 years ago

10.3390/ijms22083975

Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive Compounds
Cited by: 11
Author(s): Debosmita Sardar, Brittney Lozzi, Junsung Woo, Teng-Wei Huang, Caroline Cvetkovic, Chad J. Creighton, Robert Krencik, Benjamin Deneen
Software Mentions: 10
Published: over 5 years ago

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 6 years ago

10.1371/journal.pgen.1009376

Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: over 5 years ago

10.1093/biostatistics/kxz034

Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
Cited by: 10
Author(s): Britta Velten, Wolfgang Huber
Software Mentions: 10
Published: almost 7 years ago

10.1371/journal.pbio.2005396

Gut microbiome transition across a lifestyle gradient in Himalaya
Cited by: 109
Author(s): Aashish R. Jha, Emily Davenport, Yoshina Gautam, Dinesh Bhandari, Sarmila Tandukar, Katharine M. Ng, Gabriela K. Fragiadakis, Susan Holmes, Guru Prasad Gautam, Jeff D. Leach, Jeevan Bahadur Sherchand, Carlos D. Bustamante, Justin L. Sonnenburg
Software Mentions: 10
Published: almost 8 years ago

10.1038/s41416-020-0887-6

UGT2B17 modifies drug response in chronic lymphocytic leukaemia
Cited by: 12
Author(s): Éric P. Allain, Michèle Rouleau, Katrina Vanura, Sophie Tremblay, Joanie Vaillancourt, Vincent Bat, Patrick Caron, Lyne Villeneuve, Adrien Labriet, Véronique Turcotte, Trang Le, Medhat Shehata, Susanne Schnabl, Dita Demirtas, Rainer Hubmann, Charles Joly-Beauparlant, Arnaud Droit, Ulrich Jäger, Philipp B. Staber, Éric Lévesque, Chantal Guillemette
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pone.0251804

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs
Cited by: 4
Author(s): Adrián López-García, Rita Benítez, Yolanda Núñez, E. Gómez-Izquierdo, E. de Mercado, Juan García‐Casco, Óscar González-Recio, C. J. López‐Bote, Jordi Estellé, Cristina Óvilo
Software Mentions: 10
Published: over 5 years ago

10.1186/s13073-021-00919-6

Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery
Cited by: 14
Author(s): Rima Chakaroun, Lucas Massier, Anna Heintz‐Buschart, Nedal Said, Jörg Fallmann, Alyce Crane, Tatjana Schütz, Arne Dietrich, Matthias Blüher, Michael Stümvoll, Niculina Musat, Peter Kovacs
Software Mentions: 10
Published: about 5 years ago

10.3389/fonc.2021.747300

High Throughput Transcriptome Data Analysis and Computational Verification Reveal Immunotherapy Biomarkers of Compound Kushen Injection for Treating Triple-Negative Breast Cancer
Cited by: 2
Author(s): Xinkui Liu, Yang Wu, Yingying Zhang, Dechao Bu, Chao Wu, Shan Lu, Zhihong Huang, Yurong Song, Yi Zhao, Fengying Guo, Peizhi Ye, Changgeng Fu, Liangliang Shen, Jingyuan Zhang, Haojia Wang, Xianchun Duan, Jiarui Wu
Software Mentions: 10
Published: almost 5 years ago

10.3389/fgene.2018.00461

TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in Melanoma
Cited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: almost 8 years ago

10.1093/molbev/msaa218

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate<i>Cis</i>-Regulatory Alleles Underlying Rapid Craniofacial Divergence
Cited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: about 6 years ago

10.1371/journal.pgen.1008458

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Cited by: 23
Author(s): Jessica A. Lee, Siavash Riazi, Shahla Nemati, Jannell V. Bazurto, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
Software Mentions: 10
Published: almost 7 years ago

10.1534/g3.120.401309

CeMbio - The<i>Caenorhabditis elegans</i>Microbiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: about 6 years ago

10.1534/g3.120.401534

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts
Cited by: 3
Author(s): Matthew Chung, Preston J. Basting, Rayanna S. Patkus, Alexandra Grote, Ashley N. Luck, Elodie Ghedin, Barton E. Slatko, Michelle L. Michalski, Jeremy M. Foster, Casey M. Bergman, Julie C. Dunning Hotopp
Software Mentions: 10
Published: about 6 years ago

10.1186/s13073-020-0710-2

Interactions between the gut microbiome and host gene regulation in cystic fibrosis
Cited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: over 6 years ago

10.7554/eLife.36187

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells
Cited by: 167
Author(s): Mark F Sabbagh, Jacob S Heng, Chongyuan Luo, Rosa Castanon, Joseph R. Nery, Amir Rattner, Loyal A. Goff, Joseph R. Ecker, Jeremy Nathans
Software Mentions: 10
Published: about 8 years ago

10.7554/eLife.43257

Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures
Cited by: 65
Author(s): Yanshu Wang, Mark F Sabbagh, Xiaowu Gu, Amir Rattner, John Williams, Jeremy Nathans
Software Mentions: 10
Published: over 7 years ago

10.3389/fmicb.2019.01702

Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea
Cited by: 47
Author(s): Katarina Damjanovic, Madeleine Jh van Oppen, Patricia Menéndez, Linda L. Blackall
Software Mentions: 10
Published: about 7 years ago

10.1038/s41422-020-00451-z

Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma
Cited by: 38
Author(s): Xiaofei Wang, Ran Zhou, Yanzhen Xiong, Lingling Zhou, Xiang Yan, Manli Wang, Li Fan, Chuanxing Xie, Yiming Zhang, Zongyao Huang, Chaoqiong Ding, Ke Shi, Weida Li, Liu Yu, Cao Zeyi, Zhenning Zhang, Shengtao Zhou, Chong Chen, Yan Zhang, Lu Chen, Yuan Wang
Software Mentions: 10
Published: over 5 years ago

10.1038/s41598-020-79875-x

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models
Cited by: 23
Author(s): Marta Relvas, Alba Regueira-Iglesias, Carlos Balsa-Castro, Filomena Salazar, José Júlio Pacheco, Cristina Cabral, Corsina Velazco de Henriques, Inmaculada Tomás
Software Mentions: 10
Published: over 5 years ago

10.3389/fgene.2021.616686

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests
Cited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.ppat.1007945

Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype
Cited by: 28
Author(s): Bernd Hommel, Aude Sturny-Leclère, Stevenn Volant, Nathanaël Veluppillai, Magalie Duchateau, Chen-Hsin Albert Yu, Véronique Hourdel, Hugo Varet, Mariette Matondo, John R. Perfect, Arturo Casadevall, Françoise Dromer, Alexandre Alanio
Software Mentions: 10
Published: about 7 years ago

10.3389/fgene.2019.00279

Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data Analysis
Cited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: over 7 years ago

10.7717/peerj.8027

Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps
Cited by: 0
Author(s): Cédric Boué, Tonia DeBellis, Lisa Venier, Timothy T. Work, Steven W. Kembel
Software Mentions: 10
Published: over 6 years ago

10.1371/journal.pgen.1009531

Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes
Cited by: 12
Author(s): Anthony Aylward, Mei-Lin Okino, Paola Benaglio, Joshua Chiou, Elisha Beebe, José Padilla, Sharlene Diep, Kyle J. Gaulton
Software Mentions: 10
Published: over 5 years ago

10.3389/fmicb.2018.01095

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software
Cited by: 99
Author(s): Toby Wilkinson, Sharon Huws, Joan E. Edwards, Alison H. Kingston‐Smith, Karen Siu-Ting, Martin Hughes, Francesco Rubino, Maximillian Friedersdorff, Christopher J. Creevey
Software Mentions: 10
Published: over 8 years ago

10.3389/fgene.2021.584164

Four Novel Prognostic Genes Related to Prostate Cancer Identified Using Co-expression Structure Network Analysis
Cited by: 14
Author(s): Tao Feng, Dechao Wei, Qiankun Li, Xiaobing Yang, Yili Han, Yunping Luo, Yongguang Jiang
Software Mentions: 10
Published: over 5 years ago

10.1371/journal.pone.0186275

Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma
Cited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: almost 9 years ago

10.1186/s12867-018-0111-x

Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosis
Cited by: 4
Author(s): Paola M. Boggiatto, Daniel Fitzsimmons, Darrell O. Bayles, David P. Alt, Catherine E. Vrentas, Steven C. Olsen
Software Mentions: 9
Published: about 8 years ago

10.1016/j.celrep.2020.108308

Developmental Gene Expression Differences between Humans and Mammalian Models
Cited by: 34
Author(s): Margarida Cardoso-Moreira, Ioannis Sarropoulos, Britta Velten, Matthew Mort, David Neil Cooper, Wolfgang Huber, Henrik Kaessmann
Software Mentions: 9
Published: almost 6 years ago

10.12688/f1000research.7563.2

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
Cited by: 795
Author(s): Charlotte Soneson, Michael I. Love, Mark D. Robinson
Software Mentions: 9
Published: over 10 years ago

10.1016/j.mad.2021.111437

Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice
Cited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: over 5 years ago

10.1016/j.molcel.2018.08.004

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Cited by: 226
Author(s): Mateusz Mendel, Kuan-Ming Chen, David Homolka, Pascal Gos, Radha Raman Pandey, A.A. McCarthy, Ramesh S. Pillai
Software Mentions: 9
Published: about 8 years ago

10.7554/eLife.55862

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants
Cited by: 16
Author(s): Carlos Martínez-Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 9
Published: about 6 years ago

10.26508/lsa.202000794

Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesis
Cited by: 5
Author(s): Elisa Redl, Raheleh Sheibani-Tezerji, Crhistian de Jesus Cardona, Patricia Hamminger, Gerald Timelthaler, Melanie R. Hassler, Maša Zrimšek, Sabine Lagger, Thomas Dillinger, Lorena Hofbauer, Kristina Draganić, Andreas Tiefenbacher, Michael Kothmayer, C. Dietz, Bernard Ramsahoye, Lukas Kenner, Christoph Bock, Christian Seiser, Wilfried Ellmeier, Gabriele Schweikert, Gerda Egger
Software Mentions: 9
Published: over 5 years ago

10.3390/cancers12030653

Molecular-Clinical Correlation in Pediatric Medulloblastoma: A Cohort Series Study of 52 Cases in Taiwan
Cited by: 6
Author(s): Kuo Sheng Wu, Donald Ming Tak Ho, Shiann-Tarng Jou, Alice L. Yu, Huy Tran, Muh Lii Liang, Hsin Hung Chen, Yi Yen Lee, Yi Wei Chen, Shih Chieh Lin, Feng Chi Chang, Meng‐Li Tsai, Yen‐Lin Liu, Hsin Lun Lee, Kevin Hsieh, Wen Chang Huang, Shian Ying Sung, Che-Chang Chang, Chun A. Changou, Kung‐Hao Liang, Tsung Han Hsieh, Yun Ru Liu, Meng En Chao, Chonghua Wan, Shing Shung Chu, Er Chieh Cho, Tai-Tong Wong
Software Mentions: 9
Published: over 6 years ago

10.1186/s13059-021-02363-6

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Cited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Software Mentions: 9
Published: over 5 years ago

10.3389/fphys.2020.624677

Dynamic RNA Regulation in the Brain Underlies Physiological Plasticity in a Hibernating Mammal
Cited by: 8
Author(s): Rui Fu, Austin E. Gillen, Katharine R. Grabek, Kent Riemondy, L. Elaine Epperson, Carlos D. Bustamante, Jay R. Hesselberth, Sandra L. Martin
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.65905

Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia
Cited by: 28
Author(s): Sumiko Takao, Lauren Forbes, Masahiro Uni, Shu‐Yuan Cheng, Jose Mario Bello Pineda, Yusuke Tarumoto, Paolo Cifani, Gerard Minuesa, Celine Chen, Michael G. Kharas, Robert K. Bradley, Christopher R. Vakoc, Richard P. Koche, Alex Kentsis
Software Mentions: 9
Published: over 5 years ago

10.7554/eLife.69431

Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2
Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: over 5 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: almost 6 years ago

10.1186/s12974-018-1113-9

Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness
Cited by: 45
Author(s): David G. Ashbrook, Benjamin Hing, Lindsay T. Michalovicz, Kimberly A. Kelly, Julie V. Miller, Wilfred C. de Vega, Diane B. Miller, Gordon Broderick, James P. O’Callaghan, Patrick O. McGowan
Software Mentions: 9
Published: over 8 years ago

10.1038/s42003-021-01945-1

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression
Cited by: 5
Author(s): Andrea Cerase, Alexander N. Young, Nerea Ruiz, Andreas Buneß, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, Giuseppe Trigiante, Sarah Marzi, Philip Avner
Software Mentions: 9
Published: over 5 years ago

10.3389/fmicb.2020.00175

Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient Gradients
Cited by: 10
Author(s): Johanna Gutleben, Catarina Loureiro, Laura Adriana Ramírez Romero, Sudarshan A. Shetty, René H. Wijffels, Hauke Smidt, Detmer Sipkema
Software Mentions: 9
Published: over 6 years ago

10.7554/eLife.69040

Common virulence gene expression in adult first-time infected malaria patients and severe cases
Cited by: 15
Author(s): Jan Stephan Wichers, Gerry Tonkin‐Hill, Thorsten Thye, Ralf Krumkamp, Benno Kreuels, Jan Strauss, Heidrun von Thien, Jochen Scholz, Helle Hansson, Rasmus Weisel Jensen, Louise Turner, Freia-Raphaella Lorenz, Anna Schöllhorn, Iris Bruchhaus, Egbert Tannich, Rolf Fendel, Thomas D. Otto, Thomas Lavstsen, Tim‐Wolf Gilberger, Michael Duffy, Anna Bachmann
Software Mentions: 9
Published: over 5 years ago

10.3389/fmicb.2020.01536

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations
Cited by: 13
Author(s): Elias Broman, Xiaole Sun, Christian Stranne, Marco Salgado, Stefano Bonaglia, M. C. Geibel, Martin Jakobsson, Alf Norkko, Christoph Humborg, Francisco J. A. Nascimento
Software Mentions: 9
Published: about 6 years ago

10.1128/mBio.00399-21

Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
Cited by: 12
Author(s): Anna-Lisa E. Lawrence, Basel H. Abuaita, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Mary X. O’Riordan
Software Mentions: 9
Published: about 5 years ago

10.3389/fmicb.2018.01323

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish
Cited by: 37
Author(s): Dylan Dahan, Brooke A. Jude, Regina Lamendella, Felicia Keesing, Gabriel G. Perron
Software Mentions: 9
Published: about 8 years ago

10.1371/journal.pgen.1008671

PEA15 loss of function and defective cerebral development in the domestic cat
Cited by: 3
Author(s): Emily C. Graff, J. Nicholas Cochran, Christopher B. Kaelin, Kenneth Day, Heather L. Gray‐Edwards, Rie Watanabe, Jey W. Koehler, Rebecca A. Falgoust, Jeremy W. Prokop, R Myers, Nancy R. Cox, Gregory S. Barsh, Douglas R. Martin
Software Mentions: 9
Published: almost 6 years ago

10.12688/f1000research.7035.1

RNA-Seq workflow: gene-level exploratory analysis and differential expression
Cited by: 253
Author(s): Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber
Software Mentions: 9
Published: almost 11 years ago

10.3389/fmicb.2018.02452

Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter
Cited by: 52
Author(s): Umer Zeeshan Ijaz, Lojika Sivaloganathan, Aaron McKenna, Anne Richmond, Carmel Kelly, Mark Linton, Alexandros Ch. Stratakos, Ursula Lavery, Abdi Elmi, Brendan W. Wren, Nick Dorrell, Nicolae Corcionivoschi, Ozan Gundogdu
Software Mentions: 9
Published: almost 8 years ago

10.7554/eLife.42675

The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila
Cited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: over 7 years ago

10.1016/j.celrep.2020.108546

RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions
Cited by: 33
Author(s): Panagiotis Kotsantis, Sandra Segura-Bayona, Pol Margalef, Paulina Marzec, Phil Ruis, Graeme Hewitt, Roberto Bellelli, Harshil Patel, Robert Goldstone, Anna R. Poetsch, Simon J. Boulton
Software Mentions: 9
Published: almost 6 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: about 6 years ago

10.1038/s41598-020-59516-z

Variability in estimated gene expression among commonly used RNA-seq pipelines
Cited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: over 6 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 6 years ago

10.3390/jcm10194354

Application of an Exploratory Knowledge-Discovery Pipeline Based on Machine Learning to Multi-Scale OMICS Data to Characterise Myocardial Injury in a Cohort of Patients with Septic Shock: An Observational Study
Cited by: 3
Author(s): Bernardo Bollen Pinto, Vicent Ribas Ripoll, Paula Subías-Beltrán, Antoine Herpain, Cristina Barlassina, Eliandre de Oliveira, Roberta Pastorelli, Daniele Braga, Matteo Barcella, Laia Subirats, Julia Bauzá‐Martinez, Antonia Odena, Manuela Ferrario, Giuseppe Baselli, Federico Aletti, Karim Bendjelid
Software Mentions: 9
Published: almost 5 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: about 7 years ago

10.1371/journal.pone.0241529

Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation
Cited by: 5
Author(s): Anita Silver, Sean Perez, Melanie Gee, Bethany Xu, Shreeya Garg, Kipling Will, Amanjit Gill
Software Mentions: 9
Published: over 5 years ago

10.3389/fgene.2020.00817

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure
Cited by: 17
Author(s): Júber Herrera-Uribe, Haibo Li, Kristen A Byrne, Zahra F Bond, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 9
Published: about 6 years ago

10.3389/fonc.2020.573141

Significance of Tumor Mutation Burden in Immune Infiltration and Prognosis in Cutaneous Melanoma
Cited by: 57
Author(s): Kai Kang, Fucun Xie, Jianshan Mao, Yi Bai, Xiang Wang
Software Mentions: 9
Published: almost 6 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: over 7 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: almost 6 years ago

10.1186/s12943-021-01405-8

Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality
Cited by: 6
Author(s): Salvatore Benfatto, Özdemirhan Serçin, Francesca R. Dejure, Amir Abdollahi, Frank T. Zenke, Balca R. Mardin
Software Mentions: 9
Published: about 5 years ago

10.1186/s12864-015-1676-0

deGPS is a powerful tool for detecting differential expression in RNA-sequencing studies
Cited by: 14
Author(s): Chengcai Chu, Zhiming Fang, Xing Hua, Yaning Yang, Enguo Chen, Allen W. Cowley, Mingyu Liang, Pengyuan Liu, Yan Lu
Software Mentions: 9
Published: about 11 years ago

10.1186/s12890-021-01588-2

A novel ferroptosis-related genes model for prognosis prediction of lung adenocarcinoma
Cited by: 9
Author(s): Fēi Li, Dongcen Ge, Shulan Sun
Software Mentions: 9
Published: about 5 years ago

10.3390/cancers13102498

Comparative Transcriptomics of Immune Checkpoint Inhibitor Myocarditis Identifies Guanylate Binding Protein 5 and 6 Dysregulation
Cited by: 16
Author(s): Daniel Finke, Markus Heckmann, Janek Salatzki, Johannes Riffel, Esther Herpel, Lucie Heinzerling, Benjamin Meder, Mirko Völkers, Oliver Müller, Norbert Frey, Hugo A. Katus, Florian Leuschner, Ziya Kaya, Lorenz Lehmann
Software Mentions: 9
Published: over 5 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 5 years ago

10.3389/fnins.2020.00061

Regionally Distinct Astrocytes Display Unique Transcription Factor Profiles in the Adult Brain
Cited by: 35
Author(s): Brittney Lozzi, Teng-Wei Huang, Debosmita Sardar, Anna Yu-Szu Huang, Benjamin Deneen
Software Mentions: 9
Published: over 6 years ago

10.1186/1471-2164-16-S7-S14

Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads
Cited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: about 11 years ago

10.3389/fonc.2021.695006

Tumor-Infiltrating PD-1hiCD8+-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers
Cited by: 7
Author(s): Zhenyu Yang, Yulan Deng, Jinghui Cheng, Shiyou Wei, Hao Luo, Lunxu Liu
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: over 7 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

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Papers Mentioning DESeq2 9,583