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: pypi: HTSeq
https://packages.ecosyste.ms/registries/pypi.org/packages/HTSeq
A framework to process and analyze data from high-throughput sequencing (HTS) assays
79 versions
Latest release: over 1 year ago
3 dependent packages
21,995 downloads last month
Papers Mentioning HTSeq 3,071
10.15252/msb.20209539
Predictive features of gene expression variation reveal mechanistic link with differential expressionCited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago
10.1186/s12859-019-2879-1
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal componentsCited by: 146
Author(s): Fédérico Marini, Harald Binder
Software Mentions: 18
Published: over 5 years ago
10.3389/fimmu.2017.00445
Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell PopulationsCited by: 15
Author(s): Michael T. Zimmermann, Richard B. Kennedy, Diane E. Grill, Ann L. Oberg, Krista M. Goergen, Inna G. Ovsyannikova, Iana H. Haralambieva, Gregory A. Poland
Software Mentions: 16
Published: over 7 years ago
10.3389/fgene.2016.00163
Single-Cell Transcriptomics Bioinformatics and Computational ChallengesCited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: about 8 years ago
10.1136/jitc-2020-000705
SITC cancer immunotherapy resource document: a compass in the land of biomarker discoveryCited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: almost 4 years ago
10.1186/s12859-017-1994-0
PIVOT: platform for interactive analysis and visualization of transcriptomics dataCited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: almost 7 years ago
10.12688/f1000research.8987.2
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipelineCited by: 415
Author(s): Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth
Software Mentions: 15
Published: over 8 years ago
10.12688/f1000research.8900.2
DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomicsCited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: almost 8 years ago
10.1093/bioinformatics/btw777
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in RCited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago
10.1038/s41598-020-67753-5
Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samplesCited by: 13
Author(s): Shradha Mukherjee
Software Mentions: 14
Published: over 4 years ago
10.1186/s12864-016-3278-x
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics dataCited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: almost 8 years ago
10.1186/s12920-017-0274-1
Quantitative analysis of cryptic splicing associated with TDP-43 depletionCited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: over 7 years ago
10.12688/f1000research.19236.3
Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signaturesCited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: about 5 years ago
10.3389/fgene.2021.665888
A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single CellsCited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 3 years ago
10.1186/s13059-021-02493-x
Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafishCited 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: about 3 years ago
10.7554/eLife.63003
Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary diseaseCited 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
10.26508/lsa.202000770
In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancerCited 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: about 4 years ago
10.1371/journal.pone.0190152
RNA-Seq differential expression analysis: An extended review and a software toolCited by: 389
Author(s): Juliana Costa-Silva, Douglas Silva Domingues, Fabrício Martins Lopes
Software Mentions: 12
Published: almost 7 years ago
10.3390/ijms21010167
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory MechanismCited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: almost 5 years ago
10.3389/fcimb.2021.687607
Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis InfectionsCited 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: about 3 years ago
10.1186/s12864-017-3819-y
RNA sequencing and transcriptome arrays analyses show opposing results for alternative splicing in patient derived samplesCited by: 67
Author(s): Petr V. Nazarov, Arnaud Muller, Tony Kaoma, Nathalie Nicot, Cristina Máximo, Philippe Birembaut, Nhan L. Tran, Gunnar Dittmar, Laurent Vallar
Software Mentions: 11
Published: over 7 years ago
10.1016/j.celrep.2020.107908
Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse ModelsCited 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: over 4 years ago
10.1016/j.cels.2018.09.003
Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive PluripotencyCited 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: about 6 years ago
10.1016/j.csbj.2021.05.040
Robustness of differential gene expression analysis of RNA-seqCited 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: almost 4 years ago
10.3390/ijms20225621
APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved SurvivalCited by: 45
Author(s): Mariko Asaoka, Takashi Ishikawa, Kazuaki Takabe, Santosh K. Patnaik
Software Mentions: 11
Published: almost 5 years ago
10.1016/j.celrep.2019.05.026
ZIC3 Controls the Transition from Naive to Primed PluripotencyCited by: 41
Author(s): Shen Hsi Yang, Munazah Andrabi, Rebecca Biss, Syed Murtuza Baker, Mudassar Iqbal, Andrew D. Sharrocks
Software Mentions: 11
Published: over 5 years ago
10.7554/eLife.64846
NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1Cited 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: about 3 years ago
10.1186/s12864-021-07381-z
Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencingCited 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: almost 4 years ago
10.7717/peerj.1981
DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studiesCited by: 6
Author(s): Christophe D. Chabbert, Lars M. Steinmetz, Bernd Klaus
Software Mentions: 11
Published: over 8 years ago
10.1038/s41598-019-44765-4
Monozygotic twins and triplets discordant for amyotrophic lateral sclerosis display differential methylation and gene expressionCited by: 35
Author(s): Ingrid Tarr, Emma McCann, Beben Benyamin, Timothy J. Peters, Natalie A. Twine, Katharine Y. Zhang, Qiongyi Zhao, Zong Hong Zhang, Dominic B. Rowe, Garth A. Nicholson, Denis C. Bauer, Susan J. Clark, Ian P. Blair, Kelly L. Williams
Software Mentions: 11
Published: over 5 years ago
10.1186/s13073-016-0285-0
Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteinsCited 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: over 8 years ago
10.1371/journal.pone.0188873
A comprehensive analysis of breast cancer microbiota and host gene expressionCited 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: almost 7 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: about 4 years ago
10.1186/s13059-016-0927-y
Design and computational analysis of single-cell RNA-sequencing experimentsCited by: 409
Author(s): Rhonda Bacher, Christina Kendziorski
Software Mentions: 10
Published: over 8 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: over 3 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: over 7 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: over 4 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: almost 4 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: about 3 years ago
10.7554/eLife.18683
Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex developmentCited by: 185
Author(s): Felipe Mora‐Bermúdez, Farhath Badsha, Sabina Kanton, J. Gray Camp, Benjamin Vernot, Kathrin Köhler, Birger Voigt, Keisuke Okita, Tomislav Maričić, Zhisong He, Robert Lachmann, Svante Pääbo, Barbara Treutlein, Wieland B. Huttner
Software Mentions: 10
Published: about 8 years ago
10.1126/sciadv.abc3781
Extensive tissue-specific expression variation and novel regulators underlying circadian behaviorCited by: 21
Author(s): Maria Litovchenko, Antonio C. A. Meireles-Filho, Michael Frochaux, R. Bevers, Alessio Prunotto, Ane Martín Anduaga, Brian Hollis, Vincent Gardeux, Virginie Braman, Julie Russeil, Sebastián Kadener, Matteo Dal Peraro, Bart Deplancke
Software Mentions: 10
Published: almost 4 years ago
10.1186/s12864-015-2356-9
QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualizationCited by: 33
Author(s): Shanrong Zhao, Li Xi, Jie Quan, Hualin Simon Xi, Ying Zhang, David von Schack, Michael S. Vincent, Baohong Zhang
Software Mentions: 10
Published: almost 9 years ago
10.1186/s12859-020-03866-y
Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipelineCited by: 7
Author(s): Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen, Rafi Ahmad
Software Mentions: 10
Published: almost 4 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: over 5 years ago
10.15252/msb.20209522
Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and gliomaCited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: over 3 years ago
10.1186/s41065-021-00202-z
RNA-Seq based transcriptome analysis in oral lichen planusCited by: 5
Author(s): Haoyu Wang, Yiwen Deng, Siqi Peng, Yán Li, Hui Xu, Qingzhong Wang, Zhenhua Shen
Software Mentions: 10
Published: about 3 years ago
10.1038/s41598-017-06110-5
High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding lociCited by: 10
Author(s): Brian Gloss, Bethany Signal, Seth W. Cheetham, Franziska Gruhl, Dominik C. Kaczorowski, Andrew C. Perkins, Marcel E. Dinger
Software Mentions: 10
Published: over 7 years ago
10.26508/lsa.202000794
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK–driven lymphomagenesisCited 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: almost 4 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: about 5 years ago
10.1186/s12864-018-5166-z
RIVET: comprehensive graphic user interface for analysis and exploration of genome-wide translatomics dataCited by: 17
Author(s): Amanda Ernlund, Robert J. Schneider, Kelly V. Ruggles
Software Mentions: 9
Published: almost 6 years ago
10.3389/fnins.2020.00209
A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer’s DiseaseCited by: 6
Author(s): Sze Chung Yuen, Hongmei Zhu, Siu-wai Leung
Software Mentions: 9
Published: over 4 years ago
10.1186/1471-2164-16-S6-S3
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web applicationCited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: over 9 years ago
10.1371/journal.pbio.2004045
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebratesCited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: about 7 years ago
10.1371/journal.pbio.3001158
Disparate temperature-dependent virus–host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epitheliumCited 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 3 years ago
10.1016/j.celrep.2019.11.077
Integrated Epigenome, Exome, and Transcriptome Analyses Reveal Molecular Subtypes and Homeotic Transformation in Uterine FibroidsCited by: 42
Author(s): Jitu W. George, Huihui Fan, Benjamin K. Johnson, Tyler J. Carpenter, Kelly K. Foy, Anindita Chatterjee, Amanda L. Patterson, Julie Koeman, Marie Adams, Zachary Madaj, David Chesla, Erica E. Marsh, Timothy J. Triche, Hui Shen, Jose Teixeira
Software Mentions: 9
Published: almost 5 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: over 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
10.1186/s12867-018-0111-x
Coincidence cloning recovery of Brucella melitensis RNA from goat tissues: advancing the in vivo analysis of pathogen gene expression in brucellosisCited 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: over 6 years ago
10.7554/eLife.33105
Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasitesCited by: 152
Author(s): Adam J. Reid, Arthur M. Talman, Hayley M. Bennett, Ana Gomes, Mandy Sanders, Christopher J. R. Illingworth, Oliver Billker, Matthew Berriman, Mara Lawniczak
Software Mentions: 9
Published: over 6 years ago
10.1038/s41598-020-60336-4
Linagliptin and telmisartan induced effects on renal and urinary exosomal miRNA expression in rats with 5/6 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: over 4 years ago
10.1371/journal.pone.0240895
RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beefCited by: 9
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Chad Carr, Raluca G. Mateescu
Software Mentions: 9
Published: almost 4 years ago
10.1186/1471-2164-14-892
RNA-Seq optimization with eQTL gold standardsCited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: almost 11 years ago
10.1186/s12859-016-1323-z
variancePartition: interpreting drivers of variation in complex gene expression studiesCited by: 390
Author(s): Gabriel E. Hoffman, Eric E. Schadt
Software Mentions: 9
Published: almost 8 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 tissuesCited 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: over 3 years ago
10.1186/1471-2164-16-S7-S14
Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped readsCited by: 12
Author(s): Hung I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang, Yidong Chen
Software Mentions: 9
Published: over 9 years ago
10.1371/journal.pgen.1008671
PEA15 loss of function and defective cerebral development in the domestic catCited by: 3
Author(s): Emily C. Graff, J. Nicholas Cochran, Christopher B. Kaelin, Kenneth Day, Heather L. Gray‐Edwards, Rie Watanabe, Jey W. Koehler, Rebecca A. Falgoust, Jeremy W. Prokop, R Myers, Nancy R. Cox, Gregory S. Barsh, Douglas R. Martin
Software Mentions: 9
Published: almost 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: almost 4 years ago
10.15252/msb.20177862
Comprehensive innate immune profiling of chikungunya virus infection in pediatric casesCited by: 53
Author(s): Daniela Michlmayr, Theodore R. Pak, Adeeb Rahman, El ad David Amir, Eun Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G. Stewart, Guajira P. Thomas, Ángel Balmaseda, Li Wang, Jun Zhu, Mayte Suárez‐Fariñas, Steven M. Wolinsky, Andrew Kasarskis, Eva Harris
Software Mentions: 9
Published: over 6 years ago
10.1186/1471-2105-15-224
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencingCited by: 275
Author(s): Krishna R. Kalari, Asha Nair, Jaysheel Bhavsar, Daniel R. O’Brien, Jaime Davila, Matthew A. Bockol, Jinfu Nie, Xiaojia Tang, Saurabh Baheti, Jay B. Doughty, Sumit Middha, Hugues Sicotte, E. Aubrey Thompson, Yan W. Asmann, Jean-Pierre A. Kocher
Software Mentions: 8
Published: over 10 years ago
10.1186/s12859-017-1803-9
XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylationCited by: 11
Author(s): Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson‐Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodríguez, Yidong Chen
Software Mentions: 8
Published: about 7 years ago
10.3390/plants10081536
Variation in Gene Expression between Two Sorghum bicolor Lines Differing in Innate Immunity ResponseCited by: 2
Author(s): Yaya Cui, Dongqin Chen, Yuyong Jiang, Dong Xu, Peter Balint‐Kurti, Gary Stacey
Software Mentions: 8
Published: over 3 years ago
10.7717/peerj.9056
Transcriptional profiling to identify the key genes and pathways of pterygiumCited by: 11
Author(s): Yihui Chen, Haoyu Wang, Yaping Jiang, Xiaoyan Zhang, Qingzhong Wang
Software Mentions: 8
Published: over 4 years ago
10.1016/j.celrep.2019.10.018
Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B CellsCited by: 91
Author(s): Christopher Piper, Elizabeth C. Rosser, Kristīne Oļeiņika, Kiran Nistala, Thomas Krausgruber, André F. Rendeiro, Aggelos Banos, Ignat Drozdov, Matteo Villa, Scott Thomson, Georgina Xanthou, Christoph Bock, Brigitta Stockinger, Claudia Mauri
Software Mentions: 8
Published: about 5 years ago
10.1038/s41422-018-0053-3
Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysisCited by: 162
Author(s): Xiaoying Fan, Ji Dong, Shaobo Zhong, Wei Yuan, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao, Wei Wang, Jie Yan, Xiaoqun Wang, Jie Qiao, Fuchou Tang
Software Mentions: 8
Published: over 6 years ago
10.1016/j.patter.2021.100270
ACSNI: An unsupervised machine-learning tool for prediction of tissue-specific pathway components using gene expression profilesCited by: 1
Author(s): Chinedu Anthony Anene, Faraz Khan, Findlay Bewicke-Copley, Eleni Maniati, Jun Wang
Software Mentions: 8
Published: over 3 years ago
10.7554/eLife.64513
Chondrocytes in the resting zone of the growth plate are maintained in a Wnt-inhibitory environmentCited by: 25
Author(s): Shawn A Hallett, Yuki Matsushita, Wanida Ono, Naoko Sakagami, Koji Mizuhashi, Nicha Tokavanich, Mizuki Nagata, Annabelle Zhou, Takao Hanabusa, Henry M. Kronenberg, Noriaki Ono
Software Mentions: 8
Published: over 3 years ago
10.1016/j.isci.2021.102762
NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cellsCited by: 9
Author(s): Azzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber, Robin Allshire, Kamil R. Kranc, David Tollervey, Dónal O’Carroll
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0224879
Long non-coding RNAs and latent HIV – A search for novel targets for latency reversalCited by: 17
Author(s): Wim Trypsteen, Cory H. White, Amey Mukim, Celsa A. Spina, Ward De Spiegelaere, Steve Lefever, Vicente Planelles, Alberto Bosque, Christopher H. Woelk, Linos Vandekerckhove, Nadejda Beliakova-Bethell
Software Mentions: 8
Published: almost 5 years ago
10.1038/srep40655
Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiaeCited by: 66
Author(s): Elena Gómez-Díaz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Anna Cohuet, M. Jordan Rowley, Jean-Bosco Ouédraogo, Victor G. Corcés
Software Mentions: 8
Published: almost 8 years ago
10.1186/s12915-020-00863-8
Functional signatures of evolutionarily young CTCF binding sitesCited by: 7
Author(s): Dhoyazan Azazi, Jonathan M. Mudge, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: about 4 years ago
10.1371/journal.pone.0051609
Comparative Transcriptome Profiling of the Early Response to Magnaporthe oryzae in Durable Resistant vs Susceptible Rice (Oryza sativa L.) GenotypesCited by: 129
Author(s): Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Simona Urso, Laura Crispino, Pamela Abbruscato, Pietro Piffanelli, Elisabetta Lupotto, Luigi Cattivelli, Giampiero Valè
Software Mentions: 8
Published: almost 12 years ago
10.1038/s41598-017-06929-y
A systems approach to a spatio-temporal understanding of the drought stress response in maizeCited by: 64
Author(s): Zhenyan Miao, Zhaoxue Han, Ting Zhang, Siyuan Chen, Chuang Ma
Software Mentions: 8
Published: over 7 years ago
10.1093/gigascience/giz147
Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapaCited by: 16
Author(s): Miriam Payá‐Milans, Laura Poza‐Viejo, Patxi San Martín-Úriz, David Lara‐Astiaso, Mark D. Wilkinson, Pedro Crevillén
Software Mentions: 8
Published: almost 5 years ago
10.1016/j.heliyon.2019.e01558
Factor Analysis for Bicluster Acquisition (FABIA) revealed vincristine-sensitive transcript pattern of canine transmissible venereal tumorsCited by: 5
Author(s): Kaj Chokeshaiusaha, Denis Puthier, Cong Tu Nguyen, Pansawut Sudjaidee, Thanida Sananmuang
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pgen.1008515
Dynamic and regulated TAF gene expression during mouse embryonic germ cell developmentCited by: 15
Author(s): Megan A. Gura, Maria M. Mikedis, Kimberly A. Seymour, Dirk G. de Rooij, David C. Page, Richard N. Freiman
Software Mentions: 8
Published: almost 5 years ago
10.1016/j.gpb.2019.09.007
Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient BerberineCited by: 59
Author(s): Xizhan Xu, Zezheng Gao, Fuchao Yang, Yingying Yang, Liang Chen, Han Chieh Lin, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue Ma, Lian Shu, Xueyou Hu, Na Lyu, Yuanlong Pan, Baoli Zhu, Linhua Zhao, Xiaolin Tong, Jun Wang
Software Mentions: 8
Published: almost 4 years ago
10.15252/msb.20209667
Using single‐plant‐omics in the field to link maize genes to functions and phenotypesCited by: 17
Author(s): Daniel Felipe Cruz, Sam Meyer, Joke Ampe, Heike Sprenger, Dorota Herman, Tom Van Hautegem, Jolien De Block, Dirk Inzé, Hilde Nelissen, Steven Maere
Software Mentions: 8
Published: almost 4 years ago
10.3389/fpls.2018.00796
An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napusCited by: 23
Author(s): Hongge Li, Xi Cheng, Liping Zhang, Jihong Hu, Fugui Zhang, Biyun Chen, Kun Xu, Guizhen Gao, Hao Li, Lixia Li, Qian Huang, Zaiyun Li, Guiqin Yan, Xiaoming Wu
Software Mentions: 8
Published: over 6 years ago
10.18632/oncotarget.12122
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosisCited by: 37
Author(s): Jing Hu, Jiu Hua Xu, Lin Pang, Hongying Zhao, Feng Li, Yulan Deng, Ling Liu, Yujia Lan, Xinxin Zhang, Tingting Zhao, Chaohan Xu, Xu Chun, Yun Xiao, Xia Li
Software Mentions: 8
Published: about 8 years ago
10.1186/gb-2013-14-9-r95
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq dataCited by: 594
Author(s): Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E. Mason, Nicholas D. Socci, Doron Betel
Software Mentions: 8
Published: almost 12 years ago
10.1084/jem.20210615
Single cell analysis of <i>M. tuberculosis</i> phenotype and macrophage lineages in the infected lungCited by: 63
Author(s): Davide Pisu, Lu Huang, Vipin Narang, Monique E. Theriault, Gabrielle Lê-Bury, Bernett Lee, Agnes E Lakudzala, David Mzinza, David V. Mhango, Steven C Mitini-Nkhoma, Kondwani Jambo, Amit Singhal, Henry C. Mwandumba, David G. Russell
Software Mentions: 8
Published: over 3 years ago
10.1186/s13073-020-00812-8
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expressionCited by: 89
Author(s): Trine Line Hauge Okholm, Shashank Sathe, Samuel S. Park, Andreas Bjerregaard Kamstrup, Asta Mannstaedt Rasmussen, Archana Shankar, Zong Ming Chua, Niels Fristrup, Morten Muhlig Nielsen, Søren Vang, Lars Dyrskjøt, Stefan Aigner, Christian Kroun Damgaard, G Yeo, Jakob Skou Pedersen
Software Mentions: 8
Published: almost 4 years ago
10.18632/oncotarget.24506
Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access dataCited by: 13
Author(s): Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0153782
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis ToolsCited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: over 8 years ago
10.1371/journal.pone.0125000
From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics DataCited by: 6
Author(s): Jilong Li, Jie Hou, Sun Liang, Jordan Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, C. Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng
Software Mentions: 8
Published: over 9 years ago
10.1128/mSystems.00917-20
FADU: a Quantification Tool for Prokaryotic Transcriptomic AnalysesCited by: 7
Author(s): Matthew Chung, Ricky S. Adkins, John Mattick, Katie R. Bradwell, Amol Shetty, Lisa Sadzewicz, Luke J. Tallon, Claire M. Fraser, David A. Rasko, Anup Mahurkar, Julie C. Dunning Hotopp
Software Mentions: 8
Published: over 3 years ago
10.1038/tp.2015.169
Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brainCited by: 56
Author(s): Aslihan Dincer, David P. Gavin, Ke Xu, B Zhang, Joel T. Dudley, Eric E. Schadt, Schahram Akbarian
Software Mentions: 8
Published: almost 9 years ago
10.3389/fgene.2018.00588
DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq DataCited by: 10
Author(s): Zhihua Gao, Zhiyuan Zhao, Wenqiang Tang
Software Mentions: 8
Published: almost 6 years ago
10.1186/s13059-018-1435-z
RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellumCited by: 152
Author(s): Chunhui Ma, Mengqi Chang, Hongyi Lv, Zhiwei Zhang, Weilong Zhang, Xue He, Gaolang Wu, Shuaiyang Zhao, Yao Zhang, Di Wang, Xufei Teng, Chunying Liu, Qing Li, Arne Klungland, Yamei Niu, Shuhui Song, Wei‐Min Tong
Software Mentions: 8
Published: over 6 years ago
10.1038/s41598-017-14366-0
Erythropoietin Signaling Regulates Key Epigenetic and Transcription Networks in Fetal Neural Progenitor CellsCited by: 10
Author(s): Christina Sollinger, Jacquelyn Lillis, Jeffrey Malik, Michael Getman, Christoph Pröschel, Laurie A. Steiner
Software Mentions: 7
Published: about 7 years ago