bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

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 4 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 4 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 4 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 4 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 4 years ago

10.1016/j.devcel.2018.01.022

Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus
Cited by: 40
Author(s): George E. Gentsch, Thomas Spruce, Rita S. Monteiro, Nick Owens, Stephen R. Martin, James C. Smith
Software Mentions: 10
Published: over 7 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: 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 8 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 4 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: over 7 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 4 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 6 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: almost 6 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: about 5 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 6 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 8 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 5 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 4 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 5 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 4 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: about 5 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: almost 4 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: about 5 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: about 4 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: over 4 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 6 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 7 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: almost 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: about 4 years ago

10.1186/s12575-018-0067-8

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results
Cited by: 23
Author(s): Shitao Zhao, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
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 5 years ago

10.3389/fnmol.2017.00045

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation
Cited by: 4
Author(s): Sanjeev V. Namjoshi, Kimberly F. Raab‐Graham
Software Mentions: 10
Published: over 8 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 6 years ago

10.3390/microorganisms9081723

Fecal Supernatant from Adult with Autism Spectrum Disorder Alters Digestive Functions, Intestinal Epithelial Barrier, and Enteric Nervous System
Cited 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 4 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: over 5 years ago

10.3390/ijms21051754

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data
Cited by: 10
Author(s): Enrico Gaffo, Michele Bortolomeazzi, Andrea Bisognin, Piero Di Battista, Federica Lovisa, Lara Mussolin, Stefania Bortoluzzi
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 4 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: about 4 years ago

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: almost 4 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: about 4 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 4 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: almost 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 oryzae
Cited by: 46
Author(s): Wei Zhang, Jun Huang, David E. Cook
Software Mentions: 10
Published: over 4 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: almost 7 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 4 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 4 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: over 6 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 6 years ago

10.3390/cancers13133175

Transcript-Level Dysregulation of BCL2 Family Genes in Acute Myeloblastic Leukemia
Cited by: 7
Author(s): Luiza Handschuh, Paweł Wojciechowski, Maciej Kaźmierczak, K Lewandowski
Software Mentions: 10
Published: about 4 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 4 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: about 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 6 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: about 4 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: about 6 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 4 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 7 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: about 4 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 4 years ago

10.1186/s13059-020-1935-5

Opportunities and challenges in long-read sequencing data analysis
Cited by: 1,295
Author(s): Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 9
Published: over 5 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: about 6 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: almost 7 years ago

10.1111/1462-2920.14870

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys
Cited 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 5 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 4 years ago

10.20900/immunometab20210022

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited 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: about 4 years ago

10.1186/s13059-020-02165-2

iMOKA: k-mer based software to analyze large collections of sequencing data
Cited by: 6
Author(s): Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron, William Ritchie
Software Mentions: 9
Published: almost 5 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 7 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 7 years ago

10.1038/s41598-018-38339-z

Spatial distribution of prokaryotic communities in hypersaline soils
Cited by: 26
Author(s): Blanca Vera-Gargallo, Taniya Roy Chowdhury, Joseph Brown, Sarah Fansler, Ana Durán‐Viseras, Cristina Sánchez‐Porro, Vanessa Bailey, Janet Jansson, António Ventosa
Software Mentions: 9
Published: over 6 years ago

10.1038/s41437-018-0059-0

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Cited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: over 7 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 4 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: almost 5 years ago

10.1007/s00040-018-0624-9

The gut microbiome is associated with behavioural task in honey bees
Cited 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 7 years ago

10.3389/fncel.2021.648570

Single-Cell Multiomic Approaches Reveal Diverse Labeling of the Nervous System by Common Cre-Drivers
Cited by: 5
Author(s): Rachel A. Keuls, Ronald J. Parchem
Software Mentions: 9
Published: over 4 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: about 4 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: about 4 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: over 4 years ago

10.1186/s13059-018-1414-4

QAPA: a new method for the systematic analysis of alternative polyadenylation from RNA-seq data
Cited by: 140
Author(s): Kevin C.H. Ha, Benjamin J. Blencowe, Quaid Morris
Software Mentions: 9
Published: over 7 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 5 years ago

10.1371/journal.pbio.3001158

Disparate temperature-dependent virus–host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium
Cited by: 66
Author(s): Philip V’kovski, Mitra Gultom, Jenna N. Kelly, Silvio Steiner, Julie Russeil, Bastien Mangeat, Elisa Cora, Joern Pezoldt, Melle Holwerda, Annika Kratzel, Laura Laloli, Manon Wider, Jasmine Portmann, Thao Thi Phuong Tran, Nadine Ebert, Hanspeter Stalder, Rune Hartmann, Vincent Gardeux, Daniel Alpern, Bart Deplancke, Volker Thiel, Ronald Dijkman
Software Mentions: 9
Published: over 4 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 7 years ago

10.1038/s41598-021-92648-4

Transmitting silks of maize have a complex and dynamic microbiome
Cited by: 5
Author(s): Eman M. Khalaf, Anuja Shrestha, Jeffrey Rinne, Michael D. J. Lynch, Charles Shearer, Victor Limay-Rios, L. M. Reid, Manish N. Raizada
Software Mentions: 9
Published: about 4 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 Ripening
Cited 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 5 years ago

10.15252/msb.20209819

Phosphoproteomics identifies microglial Siglec‐F inflammatory response during neurodegeneration
Cited by: 17
Author(s): Nader Morshed, William T. Ralvenius, Alexi Nott, L. Ashley Watson, Felicia H. Rodriguez, Leyla Anne Akay, Brian A. Joughin, Ping‐Chieh Pao, Jay Penney, Lauren M. LaRocque, Diego Mastroeni, Li Huei Tsai, Forest M. White
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 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 5 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 6 years ago

10.1002/ece3.7437

Mixing tree species associated with arbuscular or ectotrophic mycorrhizae reveals dual mycorrhization and interactive effects on the fungal partners
Cited by: 14
Author(s): Heike Heklau, Nicole Schindler, François Buscot, Nico Eisenhauer, Olga Ferlian, Luis Daniel Prada-Salcedo, Helge Bruelheide
Software Mentions: 9
Published: over 4 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 4 years ago

10.1002/ece3.6221

Effects of captivity, diet, and relocation on the gut bacterial communities of white‐footed mice
Cited by: 18
Author(s): Pauline van Leeuwen, Nadia Mykytczuk, Gabriela F. Mastromonaco, Albrecht I. Schulte‐Hostedde
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 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 5 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 10 years ago

10.15252/embj.2020104983

Interactions between lineage‐associated transcription factors govern haematopoietic progenitor states
Cited 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: almost 5 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 5 years ago

10.1242/dev.158501

Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast
Cited by: 143
Author(s): Giuliano Giuseppe Stirparo, Thorsten Boroviak, Ge Guo, Jennifer Nichols, Austin Smith, Paul Bertone
Software Mentions: 9
Published: over 7 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 4 years ago

10.1177/2515841419835460

RNA-sequencing in ophthalmology research: considerations for experimental design and analysis
Cited by: 6
Author(s): Nicholas Owen, Mariya Moosajee
Software Mentions: 9
Published: over 6 years ago

10.7150/thno.53092

Network- and systems-based re-engineering of dendritic cells with non-coding RNAs for cancer immunotherapy
Cited 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 4 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: almost 7 years ago

10.1186/s12859-017-1936-x

Software for rapid time dependent ChIP-sequencing analysis (TDCA)
Cited by: 1
Author(s): Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David J. Vocadlo
Software Mentions: 9
Published: over 7 years ago

10.18632/aging.203379

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues
Cited by: 8
Author(s): Margarida Ferreira, Stephany Francisco, Ana Raquel Soares, Ana Nobre, Miguel Pinheiro, Andreia Reis, Sonya Neto, Ana João Rodrigues, Nuno Sousa, Gabriela Moura, Manuel A. S. Santos
Software Mentions: 9
Published: almost 4 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583