Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: DESeq2
https://packages.ecosyste.ms/registries/bioconductor.org/packages/DESeq2
Differential gene expression analysis based on the negative binomial distribution
2 versions
Latest release: 7 months ago
132 dependent packages
2,500,059 downloads total
Papers Mentioning DESeq2 9,583
10.3390/microorganisms9081723
Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous SystemCited by: 7
Author(s): Jacques Gonzalès, Justine Marchix, Laetitia Aymeric, Catherine Le Berre‐Scoul, Johanna Zoppi, Philippe Bordron, Marie Burel, Laetitia Davidovic, J. L. Richard, Alexandru Gaman, Florian Lejuste, Julie Z. Brouillet, Françoise Le Vacon, Samuel Chaffron, Marion Leboyer, Hélène Boudin, Michel Neunlist
Software Mentions: 10
Published: almost 3 years ago
10.1371/journal.pgen.1009531
Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetesCited 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: about 3 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 populationsCited 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: over 4 years ago
10.1093/biostatistics/kxz034
Adaptive penalization in high-dimensional regression and classification with external covariates using variational BayesCited by: 10
Author(s): Britta Velten, Wolfgang Huber
Software Mentions: 10
Published: over 4 years ago
10.1371/journal.pgen.1009376
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzaeCited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: over 3 years ago
10.1186/s12859-021-04254-w
ORFik: a comprehensive R toolkit for the analysis of translationCited by: 13
Author(s): Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski, Eivind Valen
Software Mentions: 10
Published: almost 3 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 modelsCited 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 3 years ago
10.1186/s12575-018-0067-8
Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression ResultsCited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 10
Published: about 6 years ago
10.3389/fnmol.2017.00045
Screening the Molecular Framework Underlying Local Dendritic mRNA TranslationCited by: 4
Author(s): Sanjeev V. Namjoshi, Kimberly F. Raab‐Graham
Software Mentions: 10
Published: about 7 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 predictionCited by: 24
Author(s): Carlos Guzmán, Iván D’Orso
Software Mentions: 10
Published: almost 7 years ago
10.1186/s12859-021-03967-2
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in RCited 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 3 years ago
10.1371/journal.pbio.2005396
Gut microbiome transition across a lifestyle gradient in HimalayaCited 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: over 5 years ago
10.1186/s12859-017-1539-6
Model based heritability scores for high-throughput sequencing dataCited 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: about 7 years ago
10.18632/aging.203257
Characterization of ferroptosis signature to evaluate the predict prognosis and immunotherapy in glioblastomaCited by: 14
Author(s): Xiaopeng Zhu, Yuxiang Zhou, Yangqian Ou, Zebo Cheng, Deqing Han, Zhou Chu, Sian Pan
Software Mentions: 10
Published: almost 3 years ago
10.1186/s13059-021-02337-8
Best practices on the differential expression analysis of multi-species RNA-seqCited 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: about 3 years ago
10.1172/jci.insight.138970
Hypoxia acts as an environmental cue for the human tissue-resident memory T cell differentiation programCited by: 21
Author(s): Farah Hasan, Yulun Chiu, Rebecca Shaw, Junmei Wang, Cassian Yee
Software Mentions: 10
Published: almost 3 years ago
10.1186/s13059-020-02245-3
High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative startsCited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 10
Published: over 3 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 gliomaCited 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 3 years ago
10.1186/s42523-019-0007-1
Impaired glucose metabolism and altered gut microbiome despite calorie restriction of ob/ob miceCited 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: over 4 years ago
10.1186/s42523-020-00039-3
Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttataCited 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: almost 4 years ago
10.1371/journal.ppat.1007945
Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotypeCited 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: almost 5 years ago
10.1186/s12859-017-1498-y
Evaluation of logistic regression models and effect of covariates for case–control study in RNA-Seq analysisCited 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 7 years ago
10.1007/s10456-020-09743-9
Epigenetic regulation of the lineage specificity of primary human dermal lymphatic and blood vascular endothelial cellsCited by: 16
Author(s): Carlotta Tacconi, Yuliang He, Luca Ducoli, Michael Detmar
Software Mentions: 10
Published: over 3 years ago
10.1186/s13059-018-1466-5
Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing dataCited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: almost 6 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 sarcomaCited by: 38
Author(s): Kirsten M. Johnson, Cenny Taslim, Ranajeet S. Saund, Stephen L. Lessnick
Software Mentions: 10
Published: over 6 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 CancerCited 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: over 2 years ago
10.1371/journal.pone.0251804
Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigsCited 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: about 3 years ago
10.1186/s12859-020-03549-8
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq dataCited by: 12
Author(s): Pirunthan Perampalam, Frederick A. Dick
Software Mentions: 10
Published: almost 4 years ago
10.1371/journal.pone.0223909
Effects of MCHM on yeast metabolismCited by: 6
Author(s): Amaury Pupo, Kang‐Mo Ku, Jennifer E. G. Gallagher
Software Mentions: 10
Published: over 4 years ago
10.15252/msb.20209923
Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysisCited 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: about 3 years ago
10.1186/s12859-021-04211-7
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysisCited 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: almost 3 years ago
10.3389/fonc.2021.729103
Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade GliomaCited by: 17
Author(s): Shenbin Xu, Zefeng Wang, Juan Ye, Shuhao Mei, Jianmin Zhang
Software Mentions: 10
Published: over 2 years ago
10.1038/s41416-020-0887-6
UGT2B17 modifies drug response in chronic lymphocytic leukaemiaCited 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: about 4 years ago
10.1093/molbev/msaa218
Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate<i>Cis</i>-Regulatory Alleles Underlying Rapid Craniofacial DivergenceCited by: 16
Author(s): Joseph A. McGirr, Christopher H. Martin
Software Mentions: 10
Published: over 3 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: 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 HomingCited 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: over 2 years ago
10.15252/msb.20188339
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networksCited 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: about 5 years ago
10.1371/journal.pcbi.1008947
Chromosomal neighbourhoods allow identification of organ specific changes in gene expressionCited by: 1
Author(s): Rishi Das Roy, Outi Hallikas, Mona M. Christensen, Élodie Renvoisé, Jukka Jernvall
Software Mentions: 10
Published: over 2 years ago
10.1038/s41396-021-00940-y
Locally adapted gut microbiomes mediate host stress toleranceCited by: 28
Author(s): Shira Houwenhuyse, Robby Stoks, Shinjini Mukherjee, Ellen Decaestecker
Software Mentions: 10
Published: about 3 years ago
10.1186/s13073-020-0710-2
Interactions between the gut microbiome and host gene regulation in cystic fibrosisCited by: 65
Author(s): Gargi Dayama, Sambhawa Priya, David Niccum, Alexander Khoruts, Ran Blekhman
Software Mentions: 10
Published: over 4 years ago
10.3389/fgene.2021.616686
Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score TestsCited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: over 3 years ago
10.1186/s40168-019-0756-9
Agricultural management and plant selection interactively affect rhizosphere microbial community structure and nitrogen cyclingCited by: 174
Author(s): Jennifer E. Schmidt, Angela D. Kent, Vanessa Brisson, Amélie C. M. Gaudin
Software Mentions: 10
Published: over 4 years ago
10.3390/ijms22157974
Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic MiceCited 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: almost 3 years ago
10.3389/fgene.2018.00461
TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in MelanomaCited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: over 5 years ago
10.1038/s41598-020-76881-x
Systematic comparison and assessment of RNA-seq procedures for gene expression quantitative analysisCited 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: over 3 years ago
10.3389/fmicb.2018.01095
CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference SoftwareCited 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: almost 6 years ago
10.1186/s13073-021-00919-6
Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgeryCited 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: almost 3 years ago
10.3389/fgene.2019.00279
Integrative Differential Expression Analysis for Multiple EXperiments (IDEAMEX): A Web Server Tool for Integrated RNA-Seq Data AnalysisCited by: 46
Author(s): Verónica Jiménez-Jacinto, Alejandro Sánchez-Flores, Leticia Vega‐Alvarado
Software Mentions: 10
Published: about 5 years ago
10.1534/g3.120.401309
CeMbio - The<i>Caenorhabditis elegans</i>Microbiome ResourceCited 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: over 3 years ago
10.7717/peerj.9624
Genome‐wide identification of CpG island methylator phenotype related gene signature as a novel prognostic biomarker of gastric cancerCited by: 12
Author(s): Zhi Zeng, Daxing Xie, Jianping Gong
Software Mentions: 10
Published: almost 4 years ago
10.3390/ijms22083975
Mapping Astrocyte Transcriptional Signatures in Response to Neuroactive CompoundsCited 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: about 3 years ago
10.3389/fgene.2021.584164
Four Novel Prognostic Genes Related to Prostate Cancer Identified Using Co-expression Structure Network AnalysisCited by: 14
Author(s): Tao Feng, Dechao Wei, Qiankun Li, Xiaobing Yang, Yili Han, Yunping Luo, Yongguang Jiang
Software Mentions: 10
Published: about 3 years ago
10.3390/ijms22179601
In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid LeukemiaCited 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: over 2 years ago
10.7554/eLife.36187
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cellsCited 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: over 5 years ago
10.1534/g3.120.401534
A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different HostsCited 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: over 3 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 daedaleaCited by: 47
Author(s): Katarina Damjanovic, Madeleine Jh van Oppen, Patricia Menéndez, Linda L. Blackall
Software Mentions: 10
Published: almost 5 years ago
10.7554/eLife.65905
Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemiaCited 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 3 years ago
10.1038/s41421-021-00274-1
Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: almost 3 years ago
10.7554/eLife.42675
The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in DrosophilaCited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: about 5 years ago
10.1128/mSystems.00493-20
Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific ResponsesCited by: 3
Author(s): John L. Chodkowski, Ashley Shade
Software Mentions: 9
Published: over 3 years ago
10.1128/mSystems.00474-21
Metabolic Differentiation of Co-occurring Accumulibacter Clades Revealed through Genome-Resolved MetatranscriptomicsCited by: 12
Author(s): Elizabeth A. McDaniel, Francisco Moya-Flores, Natalie K. Beach, Pamela Y. Camejo, Ben O. Oyserman, Matthew Kizaric, Eng Hoe Khor, Daniel R. Noguera, Katherine D. McMahon
Software Mentions: 9
Published: over 2 years ago
10.1002/ece3.6221
Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed miceCited by: 18
Author(s): Pauline van Leeuwen, Nadia Mykytczuk, Gabriela F. Mastromonaco, Albrecht I. Schulte‐Hostedde
Software Mentions: 9
Published: about 4 years ago
10.3390/ijms22063200
Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells SpecimensCited by: 4
Author(s): Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Przemysław Kołodziej, Jolanta Szymańska, Bartosz J. Płachno, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki, Anna Bogucka‐Kocka
Software Mentions: 9
Published: about 3 years ago
10.3389/fgene.2020.00817
Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC ExposureCited 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: over 3 years ago
10.1128/mSystems.00897-19
Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream FermentersCited by: 26
Author(s): Zachary Liechty, Christian Santos‐Medellín, Joseph Edwards, Bao‐Anh Thi Nguyen, David Mikhail, Shane Eason, Gregory C. Phillips, Venkatesan Sundaresan
Software Mentions: 9
Published: over 4 years ago
10.1126/sciadv.abc8492
Persistent epigenetic reprogramming of sweet taste by dietCited by: 29
Author(s): Anoumid Vaziri, Morteza Khabiri, Brendan T. Genaw, Christina E. May, Peter L. Freddolino, Monica Dus
Software Mentions: 9
Published: over 3 years ago
10.1186/s40168-019-0745-z
Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantationCited by: 57
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 9
Published: over 4 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 pathwaysCited 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: about 3 years ago
10.15698/mic2021.08.757
Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genesCited by: 13
Author(s): Maria Paula Rueda‐Mejia, Lukas Nägeli, Stefanie Lutz, Richard D. Hayes, Adithi R. Varadarajan, Igor V. Grigoriev, Christian H. Ahrens, Florian M. Freimoser
Software Mentions: 9
Published: almost 3 years ago
10.1002/ece3.7437
Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partnersCited by: 14
Author(s): Heike Heklau, Nicole Schindler, François Buscot, Nico Eisenhauer, Olga Ferlian, Luis Daniel Prada-Salcedo, Helge Bruelheide
Software Mentions: 9
Published: about 3 years ago
10.1111/1462-2920.14870
Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida KeysCited by: 23
Author(s): Laura Weber, Patricia González‐Díaz, Maickel Armenteros, Víctor Manuel Ferrer, Fernando Bretos, Erich Bartels, Alyson E. Santoro, Amy Apprill
Software Mentions: 9
Published: over 4 years ago
10.3389/fmicb.2020.01536
Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane ConcentrationsCited 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: almost 4 years ago
10.3389/fmicb.2018.01323
Exposure to Arsenic Alters the Microbiome of Larval ZebrafishCited by: 37
Author(s): Dylan Dahan, Brooke A. Jude, Regina Lamendella, Felicia Keesing, Gabriel G. Perron
Software Mentions: 9
Published: almost 6 years ago
10.1038/s41396-019-0458-0
Virome heterogeneity and connectivity in waterfowl and shorebird communitiesCited by: 53
Author(s): Michelle Wille, Mǎng Shī, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
Software Mentions: 9
Published: almost 5 years ago
10.1264/jsme2.ME18109
Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural FieldsCited by: 33
Author(s): Turgut Yiğit Akyol, Rieko Niwa, Hideki Hirakawa, Hayato Maruyama, Takumi Sato, Takae Suzuki, Ayako Fukunaga, Takashi Sato, Shigenobu Yoshida, Keitaro Tawaraya, Masanori Saitô, Tatsuhiro Ezawa, Shusei Sato
Software Mentions: 9
Published: over 5 years ago
10.3389/fmicb.2020.00175
Cultivation of Bacteria From Aplysina aerophoba: Effects of Oxygen and Nutrient GradientsCited 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: about 4 years ago
10.7554/eLife.55862
Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire antsCited by: 16
Author(s): Carlos Martínez-Ruiz, Rodrigo Pracana, Eckart Stolle, Carolina Ivon Paris, Richard A. Nichols, Yannick Wurm
Software Mentions: 9
Published: almost 4 years ago
10.7150/thno.53092
Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapyCited by: 7
Author(s): Xin Lai, Florian S. Dreyer, Martina Cantone, Martin Eberhardt, Kerstin F. Gerer, Tanushree Jaitly, Steffen Uebe, Christopher Lischer, Arif B. Ekici, Jürgen Wittmann, Hans‐Martin Jäck, Niels Schaft, Jan Dörrie, Julio Vera
Software Mentions: 9
Published: over 3 years ago
10.3389/fmicb.2019.01793
The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult LifeCited by: 22
Author(s): Wentao Yang, Carola Petersen, Barbara Pees, Johannes Zimmermann, Silvio Waschina, Philipp Dirksen, Philip Rosenstiel, Andreas Tholey, Matthias Leippe, Katja Dierking, Christoph Kaleta, Hinrich Schulenburg
Software Mentions: 9
Published: almost 5 years ago
10.15252/embj.2020104983
Interactions between lineage‐associated transcription factors govern haematopoietic progenitor statesCited by: 17
Author(s): Iwo Kuciński, Nicola K. Wilson, Rebecca Hannah, Sarah Kinston, Pierre Cauchy, Aurelie Lenaerts, Rudolf Grosschedl, Berthold Göttgens
Software Mentions: 9
Published: over 3 years ago
10.3390/cancers13102498
Comparative Transcriptomics of Immune Checkpoint Inhibitor Myocarditis Identifies Guanylate Binding Protein 5 and 6 DysregulationCited 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: about 3 years ago
10.1038/s41437-018-0059-0
Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coralCited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: over 6 years ago
10.3389/fmicb.2020.01398
Microbiome Shifts Associated With the Introduction of Wild Atlantic Horseshoe Crabs (Limulus polyphemus) Into a Touch-Tank ExhibitCited by: 9
Author(s): Ariel D. Friel, Sean A. Neiswenter, Cale O. Seymour, Lauren Rose Bali, Ginger McNamara, Fabian Leija, Jack Jewell, Brian P. Hedlund
Software Mentions: 9
Published: almost 4 years ago
10.3389/fmicb.2018.02711
Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere CommunitiesCited by: 45
Author(s): Ricardo Schöps, Kezia Goldmann, Katharina Herz, Guillaume Lentendu, Ingo Schöning, Helge Bruelheide, Tesfaye Wubet, François Buscot
Software Mentions: 9
Published: over 5 years ago
10.3389/fncel.2021.648570
Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-DriversCited by: 5
Author(s): Rachel A. Keuls, Ronald J. Parchem
Software Mentions: 9
Published: about 3 years ago
10.3389/fpls.2020.01269
Analysis of Metabolites and Gene Expression Changes Relative to Apricot (Prunus armeniaca L.) Fruit Quality During Development and RipeningCited by: 27
Author(s): Beatriz Ester García-Gómez, David Ruiz, J. Salazar, M. Rubio, Pedro J. Martínez-García, Pedro Martínez‐Gómez
Software Mentions: 9
Published: almost 4 years ago
10.1177/2515841419835460
RNA-sequencing in ophthalmology research: considerations for experimental design and analysisCited by: 6
Author(s): Nicholas Owen, Mariya Moosajee
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 Aim2Cited 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: almost 3 years ago
10.1038/s41598-020-59516-z
Variability in estimated gene expression among commonly used RNA-seq pipelinesCited by: 37
Author(s): Sonali Arora, Siobhan S. Pattwell, Eric C. Holland, Hamid Bolouri
Software Mentions: 9
Published: over 4 years ago
10.1007/s00040-018-0624-9
The gut microbiome is associated with behavioural task in honey beesCited by: 75
Author(s): Julia C. Jones, Carmelo Fruciano, J. H. Marchant, Falk Hildebrand, Kristoffer Forslund, Peer Bork, Philipp Engel, William O. Hughes
Software Mentions: 9
Published: about 6 years ago
10.3390/ijms22031399
DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell TranscriptomicsCited by: 5
Author(s): Salim Ghannoum, Waldir Leoncio Netto, Damiano Fantini, Benjamin Ragan-Kelley, Amirabbas Parizadeh, Emma Jonasson, Anders Ståhlberg, Hesso Farhan, Alvaro Köhn‐Luque
Software Mentions: 9
Published: over 3 years ago
10.7554/eLife.58178
16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural developmentCited 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: over 3 years ago
10.20900/immunometab20210022
Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro ModelsCited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: almost 3 years ago
10.1038/s41598-020-66998-4
Comparison of differential accessibility analysis strategies for ATAC-seq dataCited 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: almost 4 years ago
10.7554/eLife.58081
IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiationCited 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: over 3 years ago
10.3389/fmicb.2020.587972
DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol SoilCited by: 11
Author(s): Julian Yu, Michael J. Pavia, Lauren M. Deem, Susan E. Crow, Jonathan Deenik, C. Ryan Penton
Software Mentions: 9
Published: over 3 years ago
10.1242/dev.158501
Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblastCited by: 143
Author(s): Giuliano Giuseppe Stirparo, Thorsten Boroviak, Ge Guo, Jennifer Nichols, Austin Smith, Paul Bertone
Software Mentions: 9
Published: over 6 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 miceCited by: 6
Author(s): Matías Fuentealba, Daniel K. Fabian, Handan Melike Dönertaş, Janet Thornton, Linda Partridge
Software Mentions: 9
Published: about 3 years ago
10.3390/ijms21134763
The Differential Effect of Carbon Dots on Gene Expression and DNA Methylation of Human Embryonic Lung Fibroblasts as a Function of Surface Charge and DoseCited by: 15
Author(s): Michal Šíma, Kristýna Vrbová, Táňa Závodná, K. Hoňková, Irena Chvojková, Antonín Ambrož, Jǐŕı Kléma, Andrea Rössnerová, Kateřina Poláková, Tomáš Malina, Jan Belza, Jan Topinka, Pavel Rőssner
Software Mentions: 9
Published: almost 4 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 nephrectomyCited 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: about 4 years ago