pypi: cufflinks | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009538

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
Cited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: over 3 years ago

10.1371/journal.pcbi.1003000

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
Cited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: over 11 years ago

10.3389/fgene.2021.652189

Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance
Cited by: 11
Author(s): Chirag Gupta, Venkategowda Ramegowda, Supratim Basu, Andy Pereira
Software Mentions: 13
Published: over 3 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: almost 8 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: almost 4 years ago

10.1016/j.dib.2020.105195

Dataset of depressive posts in Russian language collected from social media
Cited by: 12
Author(s): Sergazy Narynov, Daniyar Mukhtarkhanuly, Batyrkhan Omarov
Software Mentions: 10
Published: over 4 years ago

10.1111/1755-0998.13219

Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China
Cited by: 103
Author(s): Lei Zhang, Bo Liu, Wengang Zheng, Conghui Liu, Dandan Zhang, Shengyuan Zhao, Zaiyuan Li, Pengjun Xu, Kenneth Wilson, Amy Withers, Christopher M. Jones, Judith A. Smith, Gilson Chipabika, Donald L. Kachigamba, Kiwoong Nam, Emmanuelle d’Alençon, Bei Liu, Xinyue Liang, Minghui Jin, Chao Wu, Swapan Chakrabarty, Xinming Yang, Yuying Jiang, Jie Liu, Xiaolin Liu, Weipeng Quan, Guirong Wang, Wei Fan, Wanqiang Qian, Kongming Wu, Yutao Xiao
Software Mentions: 10
Published: over 4 years ago

10.1186/1471-2164-13-462

NG6: Integrated next generation sequencing storage and processing environment
Cited by: 54
Author(s): Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas, Christophe Klopp
Software Mentions: 10
Published: almost 13 years ago

10.1186/s40478-018-0548-7

Proteomic analysis of Medulloblastoma reveals functional biology with translational potential
Cited by: 35
Author(s): Samuel Rivero-Hinojosa, Ling San Lau, Mojca Stampar, Jerome A. Staal, Huizhen Zhang, Heather Gordish‐Dressman, Paul A. Northcott, Stefan M. Pfister, Michael D. Taylor, Kristy J. Brown, Brian R. Rood
Software Mentions: 10
Published: over 6 years ago

10.1186/s12859-016-1323-z

variancePartition: interpreting drivers of variation in complex gene expression studies
Cited by: 390
Author(s): Gabriel E. Hoffman, Eric E. Schadt
Software Mentions: 9
Published: about 8 years ago

10.3390/insects12070577

Transcriptome Analyses Provide Insights into the Aggressive Behavior toward Conspecific and Heterospecific in Thitarodes xiaojinensis (Lepidoptera: Hepialidae)
Cited by: 1
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Richou Han
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pbio.2004045

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
Cited 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

10.12688/f1000research.7563.2

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

10.3390/cancers12051122

The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer
Cited by: 11
Author(s): M. Friedrich, Karolin Wiedemann, Kristin Reiche, Sven-Holger Puppel, Gabriele Pfeifer, Ivonne Zipfel, Stefanie Petrou Binder, Ulrike Köhl, G Müller, Kurt Engeland, Achim Aigner, S. Füssel, M. Fröhner, Claudia Peitzsch, Anna Dubrovska, Michael Rade, Sabina Christ, S Schreiber, Jörg Hackermüller, Jörg Lehmann, Marieta Toma, Michael H. Muders, Ulrich Sommer, Gustavo Baretton, Manfred P. Wirth, Friedemann Horn
Software Mentions: 9
Published: over 4 years ago

10.1038/sdata.2019.34

Global transcriptome analysis of pig induced pluripotent stem cells derived from six and four reprogramming factors
Cited by: 11
Author(s): T. Fukuda, Keiko Doi, Kenichiro Donai, Kazumasa Takahashi, Hisato Kobayashi, Takashi Hirano, Katsuhiko Nishimori, Hiroshi Yasue
Software Mentions: 8
Published: almost 6 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 expression
Cited 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: about 4 years ago

10.1186/s13059-015-0862-3

Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage
Cited by: 107
Author(s): Charlotte Soneson, Katarina L. Matthes, Małgorzata Nowicka, Charity W. Law, Mark D. Robinson
Software Mentions: 8
Published: almost 9 years ago

10.1371/journal.pbio.2002054

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells
Cited by: 76
Author(s): Colin R. Lickwar, J. Gray Camp, Matthew Weiser, Jordan L. Cocchiaro, David M. Kingsley, Terrence S. Furey, Shehzad Z. Sheikh, John F. Rawls
Software Mentions: 8
Published: over 7 years ago

10.1128/mSystems.00917-20

FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
Cited 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: almost 4 years ago

10.1186/1471-2105-12-452

eXframe: reusable framework for storage, analysis and visualization of genomics experiments
Cited by: 5
Author(s): Amit Sinha, Emily Merrill, Scott A. Armstrong, Tim W. Clark, Sudeshna Das
Software Mentions: 7
Published: about 13 years ago

10.7554/eLife.13503

A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types
Cited by: 50
Author(s): Yasuyuki Shima, Ken Sugino, Chris M. Hempel, Masami Shima, Praveen Taneja, James B. Bullis, Sonam Mehta, Carlos Lois, Sacha B. Nelson
Software Mentions: 7
Published: almost 9 years ago

10.1186/s13059-017-1286-z

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Cited by: 68
Author(s): Matthias Heinig, Michiel E. Adriaens, Sebastian Schäfer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, András Varró, Nanette H. Bishopric, Alfred L. George, Cristobal dos Remedios, Aida Moreno‐Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J.R. Barton, Stuart A. Cook, Yigal M. Pinto, Connie R. Bezzina, Norbert Hübner
Software Mentions: 7
Published: over 7 years ago

10.1093/molbev/msz154

Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites
Cited by: 51
Author(s): Roy N. Platt, Marina McDew-White, Winka Le Clec’h, Frédéric D. Chevalier, Fiona Allan, Aidan M. Emery, Amadou Garba, Amina Amadou Hamidou, M. Shaali, Joanne P. Webster, David Rollinson, Bonnie L. Webster, Timothy J. Anderson
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-017-1197-z

H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity
Cited by: 66
Author(s): Yue Zhou, Francisco J. Romero–Campero, Ángeles Gómez-Zambrano, Franziska Turck, Myriam Calonje
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-018-24863-5

Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction
Cited by: 15
Author(s): Zhong Liu, Haiyuan Mu, Bingqiang Wen, Wei Zhang, Qingqing Wei, Ge Gao, Jianyong Han, Suying Cao
Software Mentions: 7
Published: over 6 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: about 11 years ago

10.1038/s41598-017-10853-6

The Schistosoma mansoni genome encodes thousands of long non-coding RNAs predicted to be functional at different parasite life-cycle stages
Cited by: 39
Author(s): Elton J. R. Vasconcelos, Luis DaSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo Sena Amaral, Sérgio Verjovski-Almeida
Software Mentions: 7
Published: over 7 years ago

10.1186/1471-2164-14-204

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome
Cited by: 63
Author(s): Yvan Wenger, Brigitte Galliot
Software Mentions: 7
Published: almost 12 years ago

10.1093/bib/bbz126

Systematic evaluation of differential splicing tools for RNA-seq studies
Cited by: 99
Author(s): Arfa Mehmood, Asta Laiho, Mikko S Venäläinen, Aidan McGlinchey, Ning Wang, Laura L. Elo
Software Mentions: 7
Published: about 5 years ago

10.7717/peerj.644

Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
Cited by: 73
Author(s): Olga Golosova, Ross Henderson, Yuriy Vaskin, Andrei Gabrielian, German Grekhov, Vijayaraj Nagarajan, Andrew J. Oler, Mariam Quiñones, Darrell E. Hurt, Mikhail Fursov, Yentram Huyen
Software Mentions: 7
Published: about 10 years ago

10.1093/conphys/coz018

Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight
Cited by: 8
Author(s): Marisa L. Trego, Andrew Whitehead, Nicholas M. Kellar, Morgane Lauf, Rebecca L. Lewison
Software Mentions: 6
Published: almost 6 years ago

10.1016/j.cub.2018.09.026

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis
Cited by: 35
Author(s): Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E. M. Furlong
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0029685

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Cited by: 104
Author(s): Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 6
Published: almost 13 years ago

10.7554/eLife.01256

Chromatin signature of widespread monoallelic expression
Cited by: 74
Author(s): Anwesha Nag, Virginia Savova, Ho Lim Fung, Alexander Miron, Guo Cheng Yuan, Kun Zhang, Alexander A. Gimelbrant
Software Mentions: 6
Published: almost 11 years ago

10.1186/1471-2105-14-370

Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
Cited by: 36
Author(s): Hubert Rehrauer, Lennart Opitz, Ge Tan, Lina Sieverling, Ralph Schlapbach
Software Mentions: 6
Published: about 11 years ago

10.1534/g3.113.006742

The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector
Cited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: over 11 years ago

10.1186/s13059-017-1284-1

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Cited by: 75
Author(s): N. Davidson, Anthony D. K. Hawkins, Alicia Oshlack
Software Mentions: 6
Published: over 7 years ago

10.18632/oncotarget.22942

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells
Cited by: 33
Author(s): Yan Wang, Zhong Sheng Sun, Moshe Szyf
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pgen.1005465

YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
Cited by: 272
Author(s): Christoph Stein, Anaïs F. Bardet, Guglielmo Roma, Sebastian Bergling, Ieuan Clay, Alexandra Ruchti, Claudia Agarinis, Tobias Schmelzle, Tewis Bouwmeester, Dirk Schübeler, Andreas Bauer
Software Mentions: 6
Published: over 9 years ago

10.1186/1471-2105-15-S3-A7

Oqtans: a multifunctional workbench for RNA-seq data analysis
Cited by: 0
Author(s): Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Kaushik Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pone.0053822

Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Cited by: 31
Author(s): Helena Storvall, Daniel Ramsköld, Rickard Sandberg
Software Mentions: 6
Published: almost 12 years ago

10.3389/fonc.2019.00221

Non-coding and Coding Transcriptional Profiles Are Significantly Altered in Pediatric Retinoblastoma Tumors
Cited by: 25
Author(s): Swetha Rajasekaran, Lakshmi Dhevi N. Selvan, Kathleen Dotts, Ranjith Kumar, Pukhraj Rishi, Vikas Khetan, Madhoolika Bisht, Karthikeyan Sivaraman, Subrmanian Krishnakumar, Debashis Sahoo, Moray J. Campbell, Sailaja Elchuri, Wayne Miles
Software Mentions: 6
Published: over 5 years ago

10.7554/eLife.16797

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians
Cited by: 46
Author(s): Jordi Solana, Manuel Irimia, Salah Ayoub, Marta Rodriguez Orejuela, Vera Zywitza, Marvin Jens, Javier Tapial, Debashish Ray, Quaid Morris, Timothy R. Hughes, Benjamin J. Blencowe, Nikolaus Rajewsky
Software Mentions: 6
Published: over 8 years ago

10.3389/fcell.2021.690167

Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs
Cited by: 0
Author(s): Miao Wang, Dong Chen, Huoqing Zheng, Luping Zhao, Xiao‐Feng Xue, Fengyun Yu, Yu Zhang, Chao Cheng, Qingsheng Niu, Shuai Wang, Yi Zhang, Liming Wu
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1007631

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic
Cited by: 16
Author(s): Peter A. Combs, Hunter B. Fraser
Software Mentions: 5
Published: about 6 years ago

10.1038/sdata.2016.51

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
Cited by: 40
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, J. J. Arranz
Software Mentions: 5
Published: over 8 years ago

10.1038/s41421-017-0003-0

ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
Cited by: 46
Author(s): Si Wang, Boqiang Hu, Zicheng Ding, Yujiao Dang, Jun Wu, Di Li, Xiaoling Liu, Bailong Xiao, Weiqi Zhang, Rui Ren, Jinghui Lei, Huifang Hu, Chang Chen, Piu Chan, Dong Liu, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-017-1304-1

Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis
Cited by: 16
Author(s): Maria Ninova, Sam Griffiths-Jones, Matthew Ronshaugen
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pone.0184471

Genome-wide miRNA response to anacardic acid in breast cancer cells
Cited by: 14
Author(s): David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine Waigel, Carolyn M. Klinge
Software Mentions: 5
Published: over 7 years ago

10.1111/pbi.13236

Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton ( Gossypium hirsutum )
Cited by: 42
Author(s): Syed Shan-e-Ali Zaidi, Rubab Zahra Naqvi, Muhammad Asif, Susan R. Strickler, Sara Shakir, Muhammad Shafiq, Ayesha Khan, Imran Amin, Bharat Mishra, M. Shahid Mukhtar, Brian E. Scheffler, Jodi A. Scheffler, Lukas A. Mueller, Shahid Mansoor
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-017-1302-3

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Cited by: 127
Author(s): Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey, James Whelan
Software Mentions: 5
Published: over 7 years ago

10.1093/molbev/msab122

Role of Sex-Concordant Gene Expression in the Coevolution of Exaggerated Male and Female Genitalia in a Beetle Group
Cited by: 4
Author(s): Shota Nomura, Tomochika Fujisawa, Teiji Sota
Software Mentions: 5
Published: over 3 years ago

10.1186/s12983-015-0109-x

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex
Cited by: 33
Author(s): Andrey Rozenberg, Mrutyunjaya Parida, Florian Leese, Linda C. Weiss, Ralph Tollrian, J. Robert Manak
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0075578

Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach
Cited by: 7
Author(s): Lucía Spangenberg, Alejandro Correa, Bruno Dallagiovanna, Hugo Naya
Software Mentions: 5
Published: about 11 years ago

10.18632/oncotarget.21031

Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window
Cited by: 22
Author(s): Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yi Xiong, Xiao Li, Aihua Wang, Peng Lin, Yaping Jin
Software Mentions: 5
Published: over 7 years ago

10.3390/ijms20092202

Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds
Cited by: 22
Author(s): Songnan Yang, Long Miao, Jianbo He, Kai Zhang, Yan Li, Junyi Gai
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.02024

MOF-associated complexes ensure stem cell identity and Xist repression
Cited by: 73
Author(s): Tomasz Chelmicki, Friederike Dündar, Matthew James Turley, Tasneem Khanam, Tuğçe Aktaş, Fidel Ramírez, Anne-Valérie Gendrel, Patrick R. Wright, Pavankumar Videm, Rolf Backofen, Edith Heard, Thomas Manke, Asifa Akhtar
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0185376

Cellular heterogeneity contributes to subtype-specific expression of ZEB1 in human glioblastoma
Cited by: 10
Author(s): Philipp Euskirchen, Josefine Radke, Marc Soeren Schmidt, Eva Schulze Heuling, Eric Kadikowski, Meron Maricos, Felix Knab, Ulrike Grittner, Norman Zerbe, Marcus Czabanka, Christoph Dieterich, Hrvoje Miletić, Sverre Mørk, Arend Koch, Matthias Endres, Christoph Harms
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-020-70131-w

Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy
Cited by: 6
Author(s): Paolo Montaldo, Aubrey J. Cunnington, Vânia Oliveira, Ravi Swamy, Prathik Bandya, Stuti Pant, Peter J Lally, Phoebe Ivain, Josephine Mendoza, Gaurav Atreja, Padmesh Vadakepat, Mythili Baburaj, Monica Sebastian, Indiramma Yasashwi, Chinnathambi Kamalarathnam, Rema Chandramohan, Mangalabharathi Sundaram, Kumutha Kumaraswami, Shobha Kumar, Naveen Benakappa, Swati Manerkar, Jayashree Mondhkar, Vinayagam Prakash, Mohammed Sajjid, Arasar Seeralar, Ismat Jahan, Sadeka Choudhury Moni, Mohammod Shahidullah, Radhika Sujatha, M Chandrasekaran, Siddarth Ramji, Seetha Shankaran, Myrsini Kaforou, Jethro Herberg, Sudhin Thayyil
Software Mentions: 5
Published: over 4 years ago

10.3389/fonc.2021.745166

A Co-Expression Network Reveals the Potential Regulatory Mechanism of lncRNAs in Relapsed Hepatocellular Carcinoma
Cited by: 6
Author(s): Yuan Fang, Yang Yang, Xiaoli Zhang, Na Li, Bo Yuan, Li Jin, Sheng Bao, Mengge Li, Dan Zhao, Lingrui Li, Zhong Zeng, Hanfei Huang
Software Mentions: 5
Published: over 3 years ago

10.1002/1878-0261.12754

Nonsense‐mediated decay factor SMG7 sensitizes cells to TNFα‐induced apoptosis via CYLD tumor suppressor and the noncoding oncogene Pvt1
Cited by: 8
Author(s): Limeng Yang, Vanessa A N Kraft, Susanne Pfeiffer, Juliane Merl-Pham, Xuanwen Bao, Yu An, Stefanie M. Hauck, Joel Schick
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-017-14451-4

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment
Cited by: 13
Author(s): Qingbin Zhang, Li Chen, Shiman Cui, Yan Li, Qi Zhao, Weimin Cao, Shixiang Lai, Sanjun Yin, Zhixiang Zuo
Software Mentions: 5
Published: about 7 years ago

10.1186/s13072-016-0070-8

Changes of 5-hydroxymethylcytosine distribution during myeloid and lymphoid differentiation of CD34+ cells
Cited by: 18
Author(s): Xavier Tekpli, Alfonso Urbanucci, Adnan Hashim, Cathrine Broberg Vågbø, Robert Lyle, Marianne Kristiansen Kringen, Anne Cathrine Staff, Ingunn Dybedal, Ian G. Mills, Arne Klungland, Judith Staerk
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-15-910

Transcriptomic portrait of human Mesenchymal Stromal/Stem cells isolated from bone marrow and placenta
Cited by: 50
Author(s): Beatriz Rosón-Burgo, Fermín Sánchez‐Guijo, Consuelo del Cañizo, Javier De Las Rivas
Software Mentions: 4
Published: about 10 years ago

10.12688/f1000research.15604.1

Androgen-dependent alternative mRNA isoform expression in prostate cancer cells
Cited by: 14
Author(s): Jennifer Munkley, Teresa Maia, Jesús Ibarluzea, Karen E. Livermore, Daniel Vodák, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa‐Morais, David Elliott
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1007785

Genetic variants influence on the placenta regulatory landscape
Cited by: 48
Author(s): Fabien Delahaye, Catherine Do, Yu Kong, Remi Ashkar, Martha Salas, Benjamin Tycko, Ronald J. Wapner, Francine Hughes
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-017-3566-0

Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development
Cited by: 51
Author(s): Steven Ge
Software Mentions: 4
Published: almost 8 years ago

10.1093/database/bav047

GraP: platform for functional genomics analysis of Gossypium raimondii
Cited by: 12
Author(s): Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Software Mentions: 4
Published: almost 10 years ago

10.1038/srep38439

RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery
Cited by: 40
Author(s): Siim Sõber, Kristiina Rull, Mario Reiman, Piret Ilisson, Pirkko Mattila, Maris Laan
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-016-3345-3

TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq
Cited by: 6
Author(s): Cole M. McQueen, Canaan Whitfield-Cargile, Kranti Konganti, Glenn P. Blodgett, Scott V. Dindot, Noah D. Cohen
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2164-15-218

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Cited by: 60
Author(s): José F. Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A. Botella, Iraida Amaya
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-019-5752-8

New insights from Opisthorchis felineus genome: update on genomics of the epidemiologically important liver flukes
Cited by: 25
Author(s): Nikita I. Ershov, В. А. Мордвинов, Egor Prokhortchouk, Maria Y. Pakharukova, Konstantin Gunbin, Kirill Ustyantsev, Mikhail A. Genaev, А. Г. Блинов, Alexander Mazur, Eugenia Boulygina, Svetlana Tsygankova, Ekaterina Khrameeva, Nikolay Chekanov, Guangyi Fan, An Xiao, He Zhang, Xun Xu, Huanming Yang, Victor Solovyev, Simon Ming‐Yuen Lee, Xin Liu, D. A. Afonnikov, K. G. Skryabin
Software Mentions: 4
Published: over 5 years ago

10.3390/cells10030692

CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Cited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1003997

Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
Cited by: 110
Author(s): Zeynep Kalender Atak, Valentina Gianfelici, Gert Hulselmans, Kim De Keersmaecker, Arun George Devasia, Ellen Geerdens, Nele Mentens, Sabina Chiaretti, Kaat Durinck, Anne Uyttebroeck, Peter Vandenberghe, Iwona Włodarska, Jacqueline Cloos, Robin Foà, Franki Speleman, Jan Cools, Stein Aerts
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pgen.1006589

Robust stratification of breast cancer subtypes using differential patterns of transcript isoform expression
Cited by: 52
Author(s): Thomas Stricker, Christopher D. Brown, Chaitanya Bandlamudi, Megan E. McNerney, Ralf Kittler, Vanessa Montoya, April Peterson, Robert L. Grossman, Kevin P. White
Software Mentions: 4
Published: almost 8 years ago

10.1002/cne.24994

Identification of regenerative processes in neonatal spinal cord injury in the opossum ( <scp> Monodelphis domestica </scp> ): A transcriptomic study
Cited by: 6
Author(s): Benjamin Wheaton, Johnny A. Sena, Anitha Sundararajan, Pooja Umale, Faye Schilkey, Robert D. Miller
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.ppat.1008401

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis
Cited by: 35
Author(s): Jérémie Bazin, Kadarkaraisamy Mariappan, Yunhe Jiang, Thomas Blein, Ronny Völz, Martín Crespi, Heribert Hirt
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1005619

Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection
Cited by: 18
Author(s): Musa A. Hassan, Kirk D. C. Jensen, Vincent Butty, Kenneth H. Hu, Erwan Boedec, Pjotr Prins, Jeroen P. J. Saeij
Software Mentions: 4
Published: about 9 years ago

10.3390/insects11010004

Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis
Cited by: 7
Author(s): Zhongchen Rao, Li Cao, Hua Wu, Xuehong Qiu, Guiqing Liu, Richou Han
Software Mentions: 4
Published: about 5 years ago

10.1038/srep23050

Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies
Cited by: 39
Author(s): Yuvraj Indoliya, Poonam Tiwari, Abhisekh Singh Chauhan, Ridhi Goel, Manju Shri, Sumit K. Bag, Debasis Chakrabarty
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-017-12401-8

Similarity-Based Segmentation of Multi-Dimensional Signals
Cited by: 14
Author(s): Rainer Machné, Douglas B. Murray, Peter F. Stadler
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: about 7 years ago

10.1186/s12896-015-0207-z

A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
Cited by: 22
Author(s): Kevin Lambirth, Adam M. Whaley, Ivory C. Blakley, Jessica A. Schlueter, Kenneth L. Bost, Ann E. Loraine, Kenneth J. Piller
Software Mentions: 4
Published: about 9 years ago

10.1002/cam4.2581

Clinical candidate and genistein analogue AXP107‐11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein‐coupled estrogen receptor signaling
Cited by: 11
Author(s): Fahmi Mesmar, Bingbing Dai, Ahmed Atef Ibrahim, Linnea Hases, Mohammed Hakim Jafferali, Jithesh J. Augustine, Sebastian DiLorenzo, Ya’an Kang, Yang Zhao, Jing Wang, Michael Kim, Chin Yo Lin, Anders Berkenstam, Jason B. Fleming, Cecilia Williams
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-07305-3

Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome
Cited by: 12
Author(s): Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng, Jie Wen
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0244593

Comparative RNA-Seq analysis unfolds a complex regulatory network imparting yellow mosaic disease resistance in mungbean [Vigna radiata (L.) R. Wilczek]
Cited by: 24
Author(s): Uttarayan Dasgupta, Gyan P. Mishra, Harsh Kumar Dikshit, Dwijesh Chandra Mishra, Tejas C. Bosamia, Anirban Roy, Jyotika Bhati, Priti, Muraleedhar S. Aski, Ranjeet Kumar, Amit Kumar Singh, Atul Kumar, S. K. Sinha, Sundeep Chaurasia, Shelly Praveen, Ramakrishnan M. Nair
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-018-2279-y

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
Cited by: 8
Author(s): Yasunobu Okamura, Kengo Kinoshita
Software Mentions: 4
Published: over 6 years ago

10.1186/s13062-015-0071-8

Experiences with workflows for automating data-intensive bioinformatics
Cited by: 51
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimerà, Aleksi Kallio, Eija Korpelainen, Maciej M. Kańduła, Milko Krachunov, David P. Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy, Dimitar Vassilev
Software Mentions: 4
Published: over 9 years ago

10.3390/genes8020068

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
Cited by: 34
Author(s): Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
Software Mentions: 4
Published: almost 8 years ago

10.3390/plants10040669

Integrative Analysis of Gene Expression and miRNAs Reveal Biological Pathways Associated with Bud Paradormancy and Endodormancy in Grapevine
Cited by: 4
Author(s): Shuchi Smita, Michael Robben, Anup Deuja, Monica Accerbi, Pamela J. Green, Senthil Subramanian, Anne Fennell
Software Mentions: 4
Published: over 3 years ago

10.3389/fphys.2018.00825

Transcriptomics and Fitness Data Reveal Adaptive Plasticity of Thermal Tolerance in Oysters Inhabiting Different Tidal Zones
Cited by: 28
Author(s): Ao Li, Wei Wang, Kai Song, Guofan Zhang
Software Mentions: 4
Published: over 6 years ago

10.3389/fpls.2016.01924

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Setting in Triploid Loquat (Eriobotrya japonica)
Cited by: 25
Author(s): Shuang Jiang, Luo Jun, Fanjie Xu, Xueying Zhang
Software Mentions: 4
Published: about 8 years ago

10.1186/s12870-016-0926-x

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq
Cited by: 9
Author(s): Nikolay A. Shmakov, Gennady V. Vasiliev, Natalya V. Shatskaya, А. В. Дорошков, Е. И. Гордеева, D. A. Afonnikov, Е. К. Хлесткина
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0132450

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)
Cited by: 11
Author(s): Dinesh Kumar Sahu, Soumya Prasad Panda, Prem Kumar Meher, Paramananda Das, P. Routray, Jitendra Kumar Sundaray, P. Jayasankar, Samiran Nandi
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-019-3244-0

DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data
Cited by: 6
Author(s): Henggang Cui, Hailin Hu, Jianyang Zeng, Ting Chen
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2019.00917

Nuclear Lamin B1 Interactions With Chromatin During the Circadian Cycle Are Uncoupled From Periodic Gene Expression
Cited by: 19
Author(s): Annaël Brunet, Frida Forsberg, Qiong Fan, Thomas Sæther, Philippe Collas
Software Mentions: 4
Published: about 5 years ago

10.1186/1471-2164-14-S1-S9

Improved moderation for gene-wise variance estimation in RNA-Seq via the exploitation of external information
Cited by: 2
Author(s): Ellis Patrick, Michael Buckley, David M. Lin, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 12 years ago

10.3389/fmicb.2018.00593

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases
Cited by: 51
Author(s): Edoardo Piombo, Noa Sela, Michael Wisniewski, Maria Hoffmann, M. L. Gullino, Marc W. Allard, E.J. Levin, D. Spadaro, Samir Droby
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5570-z

Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica
Cited by: 18
Author(s): Sarah Naiyer, Devinder Kaur, Jamaluddin Ahamad, Sanjai Singh, Yatendra Pratap Singh, Vivek Thakur, Alok Bhattacharya, Sudha Bhattacharya
Software Mentions: 4
Published: almost 6 years ago

Projects: pypi: cufflinks

Papers Mentioning cufflinks 415