bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.3390/microorganisms9010092

Grapevine Microbiota Reflect Diversity among Compartments and Complex Interactions within and among Root and Shoot Systems
Cited by: 23
Author(s): Joel F. Swift, Megan E. Hall, Zachary N. Harris, Misha T. Kwasniewski, Allison J. Miller
Software Mentions: 13
Published: over 3 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: about 4 years ago

10.3389/fgene.2019.00317

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis
Cited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: about 5 years ago

10.3389/fonc.2021.678694

A Novel Ferroptosis-Related Pathway for Regulating Immune Checkpoints in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Tianbo Xu, Xiaoping Zhang
Software Mentions: 13
Published: almost 3 years ago

10.1186/s13068-019-1584-7

A transcriptional response of Clostridium beijerinckii NRRL B-598 to a butanol shock
Cited by: 14
Author(s): Karel Sedlář, Jan Kolek, Markus Gruber, Katerina Jureckova, Barbora Branská, Gergely Csaba, Maryna Vasylkivska, Ralf Zimmer, Petra Patáková, Ivo Provazník
Software Mentions: 13
Published: over 4 years ago

10.1186/s12859-015-0794-7

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data
Cited by: 47
Author(s): Min Tang, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 13
Published: over 8 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: over 7 years ago

10.1186/s12859-021-04268-4

A comprehensive database for integrated analysis of omics data in autoimmune diseases
Cited by: 10
Author(s): Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troulé, Gonzalo Gómez‐López, Fátima Al‐Shahrour, Víctor González‐Rumayor, María Peña‐Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón‐Riquelme, Pedro Carmona-Sáez
Software Mentions: 13
Published: almost 3 years ago

10.3390/cancers13174311

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: over 2 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: over 2 years ago

10.3390/ijms22031075

A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients
Cited by: 7
Author(s): Luca Bedon, Michele Dal Bo, Monica Mossenta, Davide Busato, Giuseppe Toffoli, Maurizio Polano
Software Mentions: 13
Published: over 3 years ago

10.1186/s13073-020-00823-5

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
Cited by: 169
Author(s): Anna C. Aschenbrenner, Maria Mouktaroudi, Benjamin Krämer, Marie Oestreich, Nikolaos Antonakos, Melanie Nuesch-Germano, Konstantina Gkizeli, Lorenzo Bonaguro, Nico Reusch, Kevin Baßler, Maria Saridaki, Rainer Knoll, Tal Pecht, Theodore S. Kapellos, Sarandia Doulou, Charlotte Kröger, Miriam Herbert, Lisa Holsten, Arik Horne, Ioanna Gemünd, Nikoletta Rovina, Shobhit Agrawal, K. Dahm, Martina van Uelft, Anna Drews, Lena Lenkeit, Niklas Bruse, Jelle Gerretsen, Jannik Gierlich, Matthias Becker, Kristian Händler, Michael Kraut, Heidi Theis, Simachew Abebe Mengiste, Elena De Domenico, Jonas Schulte-Schrepping, Lea Seep, Jan Raabe, Christoph Hoffmeister, Michael ToVinh, Verena Keitel, Gereon J Rieke, Valentina Talevi, Dirk Skowasch, N. Ahmad Aziz, Peter Pickkers, Frank L. van de Veerdonk, Mihai G. Netea, Joachim L. Schultze, Matthijs Kox, Monique M.B. Breteler, Jacob Nattermann, Antonia Koutsoukou, Evangelos J. Giamarellos‐Bourboulis, Thomas Ulas
Software Mentions: 13
Published: over 3 years ago

10.1186/s12859-019-3029-5

CAGEfightR: analysis of 5′-end data using R/Bioconductor
Cited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: over 4 years ago

10.1186/s12864-020-07204-7

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout
Cited by: 5
Author(s): Pratima Chapagain, Donald M. Walker, Timothy D. Leeds, Beth M. Cleveland, Mohamed Salem
Software Mentions: 13
Published: over 3 years ago

10.1186/s12859-015-0763-1

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Cited by: 29
Author(s): Ivana Ihnatová, Eva Budínská
Software Mentions: 12
Published: over 8 years ago

10.1186/s13059-021-02493-x

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish
Cited by: 7
Author(s): Hyo Sik Jang, Yujie Chen, Jiaxin Ge, Alicia N Wilkening, Yiran Hou, Hyung Joo Lee, You Rim Choi, Rebecca F. Lowdon, Xiaoyun Xing, Daofeng Li, Charles Kaufman, Stephen L. Johnson, Ting Wang
Software Mentions: 12
Published: over 2 years ago

10.3390/jcm10184071

Diagnostic and Prognostic Potential of MiR-379/656 MicroRNA Cluster in Molecular Subtypes of Breast Cancer
Cited by: 2
Author(s): Megha Lal, Asgar Hussain Ansari, Anurag Agrawal, Arijit Mukhopadhyay
Software Mentions: 12
Published: over 2 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: about 3 years ago

10.1371/journal.pone.0190152

RNA-Seq differential expression analysis: An extended review and a software tool
Cited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: over 6 years ago

10.3390/cancers13081788

Analysis of Intra-Tumoral Macrophages and T Cells in Non-Small Cell Lung Cancer (NSCLC) Indicates a Role for Immune Checkpoint and CD200-CD200R Interactions
Cited by: 7
Author(s): Anders Tøndell, Yashwanth Subbannayya, Sissel Gyrid Freim Wahl, Arnar Flatberg, Sveinung Sørhaug, Magne Børset, Markus Haug
Software Mentions: 12
Published: about 3 years ago

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: over 5 years ago

10.7554/eLife.63003

Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease
Cited by: 17
Author(s): Gang Wu, Yin Yeng Lee, Evelyn M. Gulla, Andrew Potter, Joseph A. Kitzmiller, Marc D. Ruben, Nathan Salomonis, JA Whitsett, Lauren J. Francey, John B. Hogenesch, Smith Dl
Software Mentions: 12
Published: over 3 years ago

10.1128/mBio.02782-18

Fitness Cost of Aflatoxin Production in Aspergillus flavus When Competing with Soil Microbes Could Maintain Balancing Selection
Cited by: 21
Author(s): Milton T. Drott, Tracy Debenport, Steven A. Higgins, Daniel H. Buckley, Michael G. Milgroom
Software Mentions: 12
Published: about 5 years ago

10.3389/fcimb.2021.687607

Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections
Cited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: over 2 years ago

10.15252/embj.2020106388

Unraveling the features of somatic transposition in the <i>Drosophila</i> intestine
Cited by: 25
Author(s): Katarzyna Siudeja, Marius van den Beek, Nick Riddiford, Benjamin Boumard, Annabelle Wurmser, Marine Stefanutti, Sonia Lameiras, Allison J. Bardin
Software Mentions: 12
Published: about 3 years ago

10.7554/eLife.37551

Species and cell-type properties of classically defined human and rodent neurons and glia
Cited by: 55
Author(s): Xiao Xu, Elitsa I Stoyanova, Agata E. Lemiesz, Jie Xing, Deborah C. Mash, Nathaniel Heintz
Software Mentions: 12
Published: over 5 years ago

10.1186/s13059-018-1563-5

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: over 5 years ago

10.3389/fmolb.2021.681526

Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Min Zhang, Rongxin Dai, Qianqian Zhao, Lina Zhou, Yunfei An, Xuemei Tang, Xiaodong Zhao
Software Mentions: 12
Published: almost 3 years ago

10.12688/f1000research.27893.1

A guide to creating design matrices for gene expression experiments
Cited by: 18
Author(s): Charity W. Law, Kathleen Zeglinski, Xueyi Dong, Monther Alhamdoosh, Gordon K. Smyth, Matthew E. Ritchie
Software Mentions: 12
Published: over 3 years ago

10.1186/s12920-015-0121-1

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities
Cited by: 52
Author(s): Eduardo Castro-Nallar, Ying Shen, Robert J. Freishtat, Marcos Pérez‐Losada, Solaiappan Manimaran, Gang Lv, W. Evan Johnson, Keith A. Crandall
Software Mentions: 12
Published: almost 9 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: about 7 years ago

10.3389/fgene.2019.01200

Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease
Cited by: 22
Author(s): Anna Bogucka‐Kocka, Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki
Software Mentions: 12
Published: over 4 years ago

10.1186/s13059-019-1766-4

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
Cited by: 74
Author(s): Nelson Johansen, Gerald Quon
Software Mentions: 12
Published: almost 5 years ago

10.3390/ijms21010167

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
Cited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: over 4 years ago

10.12688/f1000research.24187.2

ExploreModelMatrix: Interactive exploration for improved understanding of design matrices and linear models in R
Cited by: 0
Author(s): Charlotte Soneson, Fédérico Marini, Florian Geier, Michael I. Love, Michael Stadler
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.17082.2

Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)
Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: about 5 years ago

10.26508/lsa.202000770

In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer
Cited by: 12
Author(s): Linda Rushworth, Victoria Harle, Peter Repiščák, William Clark, Robin Shaw, Holly Hall, Martin Bushell, Hing Y. Leung, Rachana Patel
Software Mentions: 12
Published: over 3 years ago

10.1038/s41396-018-0251-5

Terrestriality and bacterial transfer: a comparative study of gut microbiomes in sympatric Malagasy mammals
Cited by: 56
Author(s): Amanda C. Perofsky, Rebecca J. Lewis, Lauren Ancel Meyers
Software Mentions: 12
Published: almost 6 years ago

10.7717/peerj.10469

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis
Cited by: 5
Author(s): Daniel Dimitrov, Quan Gu
Software Mentions: 12
Published: over 3 years ago

10.3389/fgene.2021.667610

The Construction and Analysis of ceRNA Network and Immune Infiltration in Kidney Renal Clear Cell Carcinoma
Cited by: 10
Author(s): Lugang Deng, Peixi Wang, Zhi Qu, Nan Liu
Software Mentions: 12
Published: over 2 years ago

10.7717/peerj.5661

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
Cited by: 17
Author(s): Camila Duarte Ritter, Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher J. Barnes, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 12
Published: over 5 years ago

10.3390/genes12030352

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

10.15252/emmm.201809443

<scp>PDX</scp> models recapitulate the genetic and epigenetic landscape of pediatric T‐cell leukemia
Cited by: 35
Author(s): Paulina Richter-Pechańska, Joachim Kunz, Beat Bornhäuser, Caroline Von Knebel Doeberitz, Tobias Rausch, Büşra Erarslan-Uysal, Yassen Assenov, Viktoras Frismantas, Blerim Marovca, Sebastian M. Waszak, Martin Zimmermann, Julia Seemann, Margit Happich, Martin Stanulla, Martin Schrappe, Gunnar Cario, Gabriele Escherich, Kseniya Bakharevich, Renate Kirschner-Schwabe, Cornelia Eckert, Martina U. Muckenthaler, Jan O. Korbel, Jean‐Pierre Bourquin, Andreas E. Kulozik
Software Mentions: 12
Published: over 5 years ago

10.3389/fcell.2020.618552

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation
Cited by: 12
Author(s): Jenny Ostrop, Rosalie T. Zwiggelaar, Marianne Terndrup Pedersen, François Gerbe, Korbinian Bösl, Håvard T. Lindholm, Alberto Díez-Sánchez, Naveen Parmar, Silke Radetzki, Jens Peter von Kries, Philippe Jay, Kim B. Jensen, C.H. Arrowsmith, Menno J. Oudhoff
Software Mentions: 12
Published: over 3 years ago

10.3389/fmicb.2019.00697

Taxonomic and Functional Characterization of the Microbial Community During Spontaneous in vitro Fermentation of Riesling Must
Cited by: 28
Author(s): Kimmo Sirén, Sarah S.T. Mak, Chrats Melkonian, Christian Carøe, Jan H. Swiegers, Douwe Molenaar, Ulrich Fischer, M. Thomas P. Gilbert
Software Mentions: 12
Published: about 5 years ago

10.3389/fgene.2021.609174

METTL14 Acts as a Potential Regulator of Tumor Immune and Progression in Clear Cell Renal Cell Carcinoma
Cited by: 11
Author(s): Tianbo Xu, Su Gao, Hailong Ruan, Jingchong Liu, Yuenan Liu, Di Liu, Junwei Tong, Jian Shi, Hongmei Yang, Ke Chen, Xiaoping Zhang
Software Mentions: 11
Published: almost 3 years ago

10.7717/peerj.1981

DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies
Cited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: about 8 years ago

10.1371/journal.pone.0132783

Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities
Cited by: 388
Author(s): Mads Albertsen, Søren Michael Karst, Anja Ziegler, Rasmus Hansen Kirkegaard, Per Halkjær Nielsen
Software Mentions: 11
Published: almost 9 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: almost 3 years ago

10.1038/s41421-021-00314-w

Single-cell RNA-Seq reveals transcriptional heterogeneity and immune subtypes associated with disease activity in human myasthenia gravis
Cited by: 12
Author(s): Jin Wu, Qi Yang, Yuyao Peng, Chengkai Yan, Yi Li, Zhaohui Luo, Bo Xiao, Liqun Xu, Huan Yang
Software Mentions: 11
Published: over 2 years ago

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: almost 3 years ago

10.3390/cells10020322

Light-Dependent Translation Change of Arabidopsis psbA Correlates with RNA Structure Alterations at the Translation Initiation Region
Cited by: 7
Author(s): Piotr Gawroński, Christel Enroth, Peter Kindgren, Sebastian Marquardt, Stanisław Karpiński, Dario Leister, Poul Erik Jensen, Jeppe Vinther, Lars B. Scharff
Software Mentions: 11
Published: over 3 years ago

10.3389/fonc.2021.640150

Construction of Competitive Endogenous RNA Network and Verification of 3-Key LncRNA Signature Associated With Distant Metastasis and Poor Prognosis in Patients With Clear Cell Renal Cell Carcinoma
Cited by: 19
Author(s): Yang Su, Tianxiang Zhang, Jiapeng Tang, Li Zhang, Song Fan, Jun Zhou, Chaozhao Liang
Software Mentions: 11
Published: about 3 years ago

10.7554/eLife.51276

A genome-wide view of the de-differentiation of central nervous system endothelial cells in culture
Cited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: over 4 years ago

10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia
Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Software Mentions: 11
Published: almost 3 years ago

10.7717/peerj.1140

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls
Cited by: 190
Author(s): Eduardo Castro-Nallar, Matthew L. Bendall, Marcos Pérez‐Losada, Sarven Sabuncyan, Emily G. Severance, Faith Dickerson, Jennifer R. Schroeder, Robert H. Yolken, Keith A. Crandall
Software Mentions: 11
Published: over 8 years ago

10.1016/j.devcel.2018.11.009

From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo
Cited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: over 5 years ago

10.1186/s42523-020-00045-5

Influences of claywater and greenwater on the skin microbiome of cultured larval sablefish (Anoplopoma fimbria)
Cited by: 4
Author(s): Emily Dodd, Melissa L. Pierce, Jonathan S. F. Lee, Rachel Poretsky
Software Mentions: 11
Published: almost 4 years ago

10.1186/s12859-020-3360-x

ShinyOmics: collaborative exploration of omics-data
Cited by: 11
Author(s): Defne Surujon, Tim van Opijnen
Software Mentions: 11
Published: over 4 years ago

10.1016/j.celrep.2019.05.026

ZIC3 Controls the Transition from Naive to Primed Pluripotency
Cited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: almost 5 years ago

10.3390/jcm9041055

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn’s Disease Patients
Cited by: 12
Author(s): Andrew Y. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert D’Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
Software Mentions: 11
Published: about 4 years ago

10.1016/j.cels.2018.09.003

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Cited by: 56
Author(s): Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0188873

A comprehensive analysis of breast cancer microbiota and host gene expression
Cited by: 105
Author(s): Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio Jeraldo, Marina Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Jingwen Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard Weinshilboum, Judy C. Boughey, Jean Pierre A. Kocher, Heidi Nelson, Matthew P. Goetz, Krishna R. Kalari
Software Mentions: 11
Published: over 6 years ago

10.1080/21623945.2019.1697563

Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes
Cited by: 6
Author(s): Mahmoud Ahmed, Deok Ryong Kim
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0220961

Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data
Cited by: 4
Author(s): Amanda H. Pendegraft, Boyi Guo, Nengjun Yi
Software Mentions: 11
Published: over 4 years ago

10.1242/dev.177428

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures
Cited by: 182
Author(s): Sandra Ruiz García, Marie Deprez, Kévin Lebrigand, Amélie Cavard, Agnès Paquet, Marie-Jeanne Arguel, Virginie Magnone, Marin Truchi, Ignacio Caballero, Sylvie Leroy, Charles‐Hugo Marquette, Brice Marcet, Pascal Barbry, Laure‐Emmanuelle Zaragosi
Software Mentions: 11
Published: over 4 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: about 8 years ago

10.1186/s42523-020-00029-5

Microbiota characterization of Exaiptasia diaphana from the Great Barrier Reef
Cited by: 19
Author(s): Leon M. Hartman, Madeleine J. H. van Oppen, Linda L. Blackall
Software Mentions: 11
Published: about 4 years ago

10.1186/s42523-020-00066-0

Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary
Cited by: 16
Author(s): Rebecca J. Stevick, Anton F. Post, Marta Gómez-Chiarri
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-020-03846-2

ARPIR: automatic RNA-Seq pipelines with interactive report
Cited by: 10
Author(s): Giulio Spinozzi, Valentina Tini, Alessia Adorni, Brunangelo Falini, Maria Paola Martelli
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-016-1386-x

Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Cited by: 0
Author(s): Yuanzhe Bei, Pengyu Hong
Software Mentions: 11
Published: over 7 years ago

10.3390/ijms21218148

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-019-2968-1

Visualization methods for differential expression analysis
Cited by: 6
Author(s): Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham, Dianne Cook
Software Mentions: 11
Published: over 4 years ago

10.1016/j.celrep.2020.107908

Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models
Cited by: 174
Author(s): Ying-Wooi Wan, Rami Al‐Ouran, Carl Grant Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine S. Allison, Vivek Swarup, Cory C. Funk, Chris Gaiteri, Mariet Allen, Minghui Wang, Sarah M. Neuner, Catherine C. Kaczorowski, Vivek Philip, Gareth R. Howell, Heidi Martini‐Stoica, Hui Zheng, Hongkang Mei, Xiaoyan Zhong, Jungwoo Wren Kim, Valina L. Dawson, Ted M. Dawson, Ping‐Chieh Pao, Li‐Huei Tsai, Jean‐Vianney Haure‐Mirande, Michelle E. Ehrlich, Paramita Chakrabarty, Yona Levites, Xue Wang, Eric B. Dammer, Gyan Srivastava, Sumit Mukherjee, Solveig K. Sieberts, Larsson Omberg, Kristen K. Dang, James A. Eddy, Phil Snyder, Yooree Chae, Sandeep Amberkar, Wenbin Wei, Winston Hide, Christoph Preuß, Ayla Ergün, Philip J. Ebert, David Airey, Sara Mostafavi, Lei Yu, Hans‐Ulrich Klein, Gregory W. Carter, David A. Collier, Todd E. Golde, Aĺlan I. Levey, David A. Bennett, Karol Estrada, T. Matthew Townsend, Bin Zhang, Eric E. Schadt, Philip L. De Jager, Nathan D. Price, Nilüfer Ertekin-Taner, Zhandong Liu, Zhandong Liu, Lara M. Mangravite, Benjamin A. Logsdon
Software Mentions: 11
Published: almost 4 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: almost 4 years ago

10.3389/fgene.2021.625145

Identification of Tumor Microenvironment-Related Prognostic Biomarkers for Ovarian Serous Cancer 3-Year Mortality Using Targeted Maximum Likelihood Estimation: A TCGA Data Mining Study
Cited by: 2
Author(s): Lu Wang, Xiaoru Sun, Chuandi Jin, Yue Fan, Fuzhong Xue
Software Mentions: 11
Published: almost 3 years ago

10.1038/s41598-018-28356-3

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver
Cited by: 34
Author(s): Chris Duncan, Sara A. Grimm, Daniel L. Morgan, Pierre R. Bushel, Brian D. Bennett, John D. Roberts, Frederick L. Tyson, B. Alex Merrick, Paul A. Wade
Software Mentions: 11
Published: almost 6 years ago

10.1128/mSphere.00481-19

Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities
Cited by: 15
Author(s): Ryan B. Ghannam, Laura G. Schaerer, Timothy Butler, Stephen M. Techtmann
Software Mentions: 11
Published: about 4 years ago

10.3389/fmicb.2019.02291

Reduced Gut Microbiome Diversity and Metabolome Differences in Rhinoceros Species at Risk for Iron Overload Disorder
Cited by: 25
Author(s): Terri L. Roth, Alexandra D. Switzer, Miki Watanabe-Chailland, Elisabeth M. Bik, David A. Relman, Lindsey E. Romick-Rosendale, Nicholas J. Ollberding
Software Mentions: 11
Published: over 4 years ago

10.1186/s12864-021-07381-z

Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing
Cited by: 11
Author(s): Benjamin P. Kellman, Hratch Baghdassarian, Tiziano Pramparo, Isaac Shamie, Vahid H. Gazestani, Arjana Begzati, Shangzhong Li, Srinivasa Nalabolu, Sarah Murray, Linda Lopez, Karen Pierce, Eric Courchesne, Nathan E. Lewis
Software Mentions: 11
Published: over 3 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
Published: almost 5 years ago

10.1016/j.csbj.2015.08.004

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
Cited by: 73
Author(s): Daniel Spies, Constance Ciaudo
Software Mentions: 11
Published: over 9 years ago

10.1016/j.csbj.2021.05.040

Robustness of differential gene expression analysis of RNA-seq
Cited by: 31
Author(s): Alexey Stupnikov, Caitríona E. McInerney, Kienan I. Savage, Stuart McIntosh, Frank Emmert‐Streib, Richard D. Kennedy, Manuel Salto-Tellez, Kevin M. Prise, Darragh G. McArt
Software Mentions: 11
Published: over 3 years ago

10.1016/j.molcel.2019.03.024

Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression
Cited by: 187
Author(s): Nadezda A. Fursova, Neil P. Blackledge, Manabu Nakayama, Shinsuke Ito, Haruhiko Koseki, Anca M. Farcas, Hamish W King, Haruhiko Koseki, Robert J. Klose
Software Mentions: 11
Published: almost 5 years ago

10.1038/s41598-021-94324-z

Modest changes in Spi1 dosage reveal the potential for altered microglial function as seen in Alzheimer’s disease
Cited by: 17
Author(s): Ruth Jones, Robert Andrews, Peter Holmans, Matthew Hill, Philip R. Taylor
Software Mentions: 11
Published: almost 3 years ago

10.3389/fmicb.2020.619226

Terroir Is the Main Driver of the Epiphytic Bacterial and Fungal Communities of Mango Carposphere in Reunion Island
Cited by: 4
Author(s): Ahmed Taïbi, Ronan Rivallan, Véronique Broussolle, Dominique Pallet, Sylvie Lortal, Jean-Christophe Meile, Florentin Constancias
Software Mentions: 11
Published: over 3 years ago

10.1016/j.molcel.2019.12.001

PRC1 Catalytic Activity Is Central to Polycomb System Function
Cited by: 163
Author(s): Neil P. Blackledge, Nadezda A. Fursova, Jessica R. Kelley, Miles K. Huseyin, Angelika Feldmann, Robert J. Klose
Software Mentions: 11
Published: over 4 years ago

10.3389/fbioe.2020.00034

A Guide to Conquer the Biological Network Era Using Graph Theory
Cited by: 129
Author(s): Mikaela Koutrouli, Evangelos Karatzas, David Páez-Espino, Georgios A. Pavlopoulos
Software Mentions: 11
Published: over 4 years ago

10.1111/jcmm.16773

Peripheral blood transcriptome heterogeneity and prognostic potential in lung cancer revealed by RNA‐Seq
Cited by: 3
Author(s): Qi Zhang, Manchao Kuang, Haiyin An, Yajing Zhang, Kai Zhang, Feng Li, Lei Zhang, Shujun Cheng
Software Mentions: 11
Published: almost 3 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: almost 5 years ago

10.3389/fpls.2021.657796

Identification of Candidate Susceptibility Genes to Puccinia graminis f. sp. tritici in Wheat
Cited by: 8
Author(s): Eva C Henningsen, Vahid Omidvar, Rafael Della Coletta, Jean Michel Michno, Erin Gilbert, Feng Li, Marisa E. Miller, Chad L. Myers, Sean P. Gordon, John P. Vogel, Brian J. Steffenson, Shahryar F. Kianian, Cory D. Hirsch, Melania Figueroa
Software Mentions: 11
Published: about 3 years ago

10.7554/eLife.49921

Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices
Cited by: 21
Author(s): Claudia Racioppi, Keira A Wiechecki, Lionel Christiaen
Software Mentions: 11
Published: over 4 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: almost 3 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: almost 3 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 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 daedalea
Cited by: 47
Author(s): Katarina Damjanovic, Madeleine Jh van Oppen, Patricia Menéndez, Linda L. Blackall
Software Mentions: 10
Published: almost 5 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 3 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: almost 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 3 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: over 2 years ago

Projects: bioconductor: DESeq2

Papers Mentioning DESeq2 9,583