cran: STAR | Projects | Ecosyste.ms: Papers

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: over 10 years ago

10.1016/j.celrep.2020.107694

A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging
Cited by: 24
Author(s): Qi Zhou, Qianfen Wan, Yuxi Jiang, Jin Liu, Qiang Li, Li Sun
Software Mentions: 7
Published: over 6 years ago

10.1016/j.ccell.2019.08.008

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer
Cited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: about 7 years ago

10.1016/j.ccell.2020.08.016

Metabolic Imaging Detects Resistance to PI3Kα Inhibition Mediated by Persistent FOXM1 Expression in ER+ Breast Cancer
Cited by: 35
Author(s): Susana Ros, Alan J. Wright, Paula D’Santos, De‐En Hu, Robin Hesketh, Yaniv Lubling, Dimitra Georgopoulou, Giulia Lerda, Dominique‐Laurent Couturier, Pedram Razavi, Rapahel Pelossof, Ankita Batra, Elizabeth Mannion, David Y. Lewis, Alistair Martin, Richard D. Baird, Mafalda Oliveira, Leonora W. de Boo, Sabine C. Linn, Maurizio Scaltriti, Oscar M. Rueda, Alejandra Bruna, Carlos Caldas, Kevin M. Brindle
Software Mentions: 7
Published: about 6 years ago

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: almost 9 years ago

10.3389/fgene.2019.00309

Targeted, High-Resolution RNA Sequencing of Non-coding Genomic Regions Associated With Neuropsychiatric Functions
Cited by: 26
Author(s): Simon A. Hardwick, Samuel D. Bassett, Dominik C. Kaczorowski, James Blackburn, Kirston Barton, Nenad Bartoniček, Shaun Carswell, Hagen Tilgner, Clement T. Loy, Glenda M. Halliday, Tim R. Mercer, Martin A. Smith, John S. Mattick
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.66788

An NKX2-1/ERK/WNT feedback loop modulates gastric identity and response to targeted therapy in lung adenocarcinoma
Cited by: 11
Author(s): Rediet Zewdu, Elnaz Mirzaei Mehrabad, Kelley Ingram, Pengshu Fang, Katherine L Gillis, Soledad A. Camolotto, Grace Orstad, Alex Jones, Michelle C. Mendoza, Benjamin T. Spike, Eric L. Snyder
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1007784

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways
Cited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.51529

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Cited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: almost 7 years ago

10.7554/eLife.56523

DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors
Cited by: 25
Author(s): Maria M. Mikedis, Yuting Fan, Peter K. Nicholls, Toshihiko Endo, Emily Jackson, Sarah A. Cobb, Dirk G. de Rooij, David C. Page
Software Mentions: 7
Published: over 6 years ago

10.3389/fgene.2019.00400

NormExpression: An R Package to Normalize Gene Expression Data Using Evaluated Methods
Cited by: 10
Author(s): Zhenfeng Wu, Weixiang Liu, Xiufeng Jin, Haishuo Ji, Hua Wang, Gustavo Glusman, Max Robinson, Lin Liu, Jishou Ruan, Shan Gao
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.34031

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Cited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: over 8 years ago

10.1371/journal.pgen.1008482

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival
Cited by: 12
Author(s): Rodrigo Guarischi-Sousa, Jhonatas Sirino Monteiro, Lilian Costa Alecrim, Jussara S. Michaloski, Laura Beatriz da Silva Cardeal, Elisa Napolitano Ferreira, Dirce Maria Carraro, Diana Noronha Nunes, Emmanuel Dias-Neto, Jüri Reimand, Paul C. Boutros, João Carlos Setúbal, Ricardo J. Giordano
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12859-016-1274-4

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
Cited by: 95
Author(s): Qian Qin, Shenglin Mei, Qiu Liang Wu, Hanfei Sun, Lewyn Li, Len Taing, Sujun Chen, Fugen Li, Tao Liu, Chongzhi Zang, Xu Han, Yiwen Chen, Clifford A. Meyer, Yong Zhang, Myles Brown, Henry W. Long, X. Shirley Liu
Software Mentions: 7
Published: about 10 years ago

10.3389/fgene.2020.00396

Single-Cell Transcriptomic Analysis Reveals Mitochondrial Dynamics in Oocytes of Patients With Polycystic Ovary Syndrome
Cited by: 34
Author(s): Lingbin Qi, Boxuan Liu, Xian Chen, Qiwei Liu, Wanqiong Li, Bo Lv, Xiaoyu Xu, Lu Wang, Qiao Zeng, Jinfeng Xue, Zhigang Xue
Software Mentions: 7
Published: over 6 years ago

10.1038/s41388-021-01876-5

The FLI portion of EWS/FLI contributes a transcriptional regulatory function that is distinct and separable from its DNA-binding function in Ewing sarcoma
Cited by: 12
Author(s): Megann A. Boone, Cenny Taslim, Julie Crow, Julia Selich‐Anderson, Andrea K. Byrum, Iftekhar A. Showpnil, Benjamin D. Sunkel, Meng Wang, Benjamin Z. Stanton, Emily R. Theisen, Stephen L. Lessnick
Software Mentions: 7
Published: over 5 years ago

10.1002/jev2.12127

Inflammasome‐induced extracellular vesicles harbour distinct RNA signatures and alter bystander macrophage responses
Cited by: 26
Author(s): Christina F. Budden, Linden J. Gearing, Romina Kaiser, Lena Standke, Paul J. Hertzog, Eicke Latz
Software Mentions: 7
Published: about 5 years ago

10.1186/1471-2105-16-S9-S2

Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis
Cited by: 17
Author(s): Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Calogero, Francesca Zolezzi
Software Mentions: 7
Published: over 11 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: over 9 years ago

10.3390/jof7090700

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi
Cited by: 3
Author(s): Grace N. Ijoma, Sylvie M Heri, Tonderayi Matambo, Memory Tekere
Software Mentions: 7
Published: about 5 years ago

10.1186/s10194-021-01285-9

Identification of disease- and headache-specific mediators and pathways in migraine using blood transcriptomic and metabolomic analysis
Cited by: 13
Author(s): Tímea Aczél, Tamás Körtési, József Kun, Péter Urbán, Witold Bauer, Róbert Herczeg, Robert Farkaš, K Kovács, Barna Vásárhelyi, Gellért Balázs Karvaly, Attila Gyenesei, Bernadett Tuka, János Tajti, László Vécsei, Kata Bölcskei, Zsuzsanna Helyes
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.29312

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis
Cited by: 35
Author(s): Isabelle Bergiers, Tallulah Andrews, Özge Vargel Bölükbaşı, Andreas Buneß, Ewa Janosz, Natalia López-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin, Paul Collier, Bianka Baying, Vladimı́r Beneš, Martin Hemberg, Christophe Lancrin
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-021-07489-2

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
Cited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: over 5 years ago

10.12688/f1000research.17145.2

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors
Cited by: 35
Author(s): Ashis Saha, Alexis Battle
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pgen.1009422

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest
Cited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: over 5 years ago

10.1093/bfgp/ely003

The impact of single-cell RNA sequencing on understanding the functional organization of the immune system
Cited by: 15
Author(s): Péter Végh, Muzlifah Haniffa
Software Mentions: 7
Published: over 8 years ago

10.12688/f1000research.17916.1

Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
Cited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: over 7 years ago

10.3390/ijms22094917

The Cellular Composition of Bovine Coccygeal Intervertebral Discs: A Comprehensive Single-Cell RNAseq Analysis
Cited by: 24
Author(s): Martina Caliò, Benjamin Gantenbein, Marcel Egli, Lucy Poveda, Fabian Ille
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2021.664424

Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues
Cited by: 5
Author(s): Eliah Overbey, Theros T Ng, Pietro Catini, Lisa Griggs, Paul A. Stewart, Suzana Tkalčić, R. David Hawkins, Yvonne Drechsler
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1006402

Gene co-expression network connectivity is an important determinant of selective constraint
Cited by: 96
Author(s): Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K. Ingvarsson, Nathaniel R. Street, Torgeir R. Hvidsten
Software Mentions: 7
Published: over 9 years ago

10.1002/bit.27209

Comparative genome‐scale analysis of Pichia pastoris variants informs selection of an optimal base strain
Cited by: 31
Author(s): Joseph Brady, Charles A. Whittaker, Melody C. Tan, D. Lee Kristensen, Duanduan Ma, Neil C. Dalvie, Kerry R. Love, J. Christopher Love
Software Mentions: 7
Published: almost 7 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in Drosophila heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: about 10 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Cited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: about 6 years ago

10.1111/1751-7915.13634

Soil microbiota influences clubroot disease by modulating Plasmodiophora brassicae and Brassica napus transcriptomes
Cited by: 19
Author(s): Stéphanie Daval, Kévin Gazengel, Arnaud Belcour, Juliette Linglin, Anne‐Yvonne Guillerm‐Erckelboudt, Alain Sarniguet, Maria Manzanares-Dauleux, Lionel Lebreton, Christophe Mougel
Software Mentions: 7
Published: over 6 years ago

10.1186/s13293-020-00312-9

Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Cited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: over 6 years ago

10.1186/s40478-020-01020-6

Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis
Cited by: 7
Author(s): Sharon Melamed, Roy Avraham, Deborah E. Rothbard, Noam Erez, Tomer Israely, Ziv Klausner, Anthony H. Futerman, Nir Paran, Einat B. Vitner
Software Mentions: 7
Published: about 6 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: almost 7 years ago

10.1093/gigascience/giy093

Leveraging multiple transcriptome assembly methods for improved gene structure annotation
Cited by: 110
Author(s): Luca Venturini, Shabhonam Caim, Gemy Kaithakottil, Daniel Mapleson, David Swarbreck
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-019-6349-y

Molecular evolution and expression of opsin genes in Hydra vulgaris
Cited by: 16
Author(s): Aide Macias-Muñoz, Rabi Murad, A Mortazavi
Software Mentions: 7
Published: almost 7 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 10 years ago

10.1038/s41598-021-84693-w

Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells
Cited by: 12
Author(s): Shang Liu, Biaofeng Zhou, Liang Wu, Yan Sun, Jie Chen, Shiping Liu
Software Mentions: 7
Published: over 5 years ago

10.1186/1471-2105-16-S13-S7

Enhancing cancer clonality analysis with integrative genomics
Cited by: 6
Author(s): Erich A. Peterson, Michael Bauer, Shweta S. Chavan, Cody Ashby, Niels Weinhold, Christoph Heuck, Gareth J. Morgan, Donald J. Johann
Software Mentions: 7
Published: almost 11 years ago

10.7554/eLife.51413

Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation
Cited by: 190
Author(s): Ankit Jambusaria, Zhigang Hong, Lianghui Zhang, Shubhi Srivastava, Arundhati Jana, Péter T. Tóth, Yang Dai, Asrar B. Malik, Jalees Rehman
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pgen.1008506

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging
Cited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: almost 7 years ago

10.1038/s41598-019-44491-x

The LL-100 panel: 100 cell lines for blood cancer studies
Cited by: 67
Author(s): Hilmar Quentmeier, Claudia Pommerenke, Wilhelm G. Dirks, Sonja Eberth, Max Koeppel, Roderick A.F. MacLeod, Stefan Nagel, Klaus G. Steube, Cord C. Uphoff, Hans G. Drexler
Software Mentions: 7
Published: over 7 years ago

10.3390/brainsci10020109

Chronic Chemogenetic Stimulation of the Nucleus Accumbens Produces Lasting Reductions in Binge Drinking and Ameliorates Alcohol-Related Morphological and Transcriptional Changes
Cited by: 27
Author(s): Dar'ya Pozhidayeva, Sean P. Farris, Calla M Goeke, Evan Firsick, Kayla G. Townsley, Marina Guizzetti, Angela R. Ozburn
Software Mentions: 7
Published: over 6 years ago

10.1038/s41598-018-26592-1

Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan
Cited by: 13
Author(s): Radek Šindelka, Pavel Abaffy, Yanyan Qu, Silvie Tománková, Monika Šídová, Ravindra Naraine, Michal Kolář, Elizabeth H. Peuchen, Liangliang Sun, Norman J. Dovic̀hi, Mikael Kubista
Software Mentions: 7
Published: over 8 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: over 5 years ago

10.1038/s42003-020-01318-0

Lung gene expression signatures suggest pathogenic links and molecular markers for pulmonary tuberculosis, adenocarcinoma and sarcoidosis
Cited by: 15
Author(s): Qiyao Chai, Zhe Lü, Zhidong Liu, Yanzhao Zhong, Fuzhen Zhang, Changgen Qiu, Bingxi Li, Jing Wang, Lingqiang Zhang, Yu Pang, Cui Hua Liu
Software Mentions: 7
Published: about 6 years ago

10.1002/edm2.191

Sex and oestrogen receptor β have modest effects on gene expression in the mouse brain posterior cortex
Cited by: 1
Author(s): Jasmine A. Fels, Gabriella Casalena, Giovanni Manfredi
Software Mentions: 7
Published: about 6 years ago

10.1186/s12864-018-4835-2

Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA)
Cited by: 15
Author(s): Julien Richard Albert, Takao Koike, Hamid Younesy, Iain Thompson, Aaron B. Bogutz, Mehdi Karimi, Matthew C. Lorincz
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-021-07744-6

The effect of methanol fixation on single-cell RNA sequencing data
Cited by: 19
Author(s): Xinlei Wang, Yu Liu, Angela Ruohao Wu
Software Mentions: 7
Published: over 5 years ago

10.1038/s42003-021-01897-6

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer
Cited by: 9
Author(s): Giorgia Maroni, Mahmoud A. Bassal, Indira Krishnan, Chee Wai Fhu, Virginia Savova, Rapolas Žilionis, Valerie A. Maymi, Nicole Pandell, Eva Csizmadia, Junyan Zhang, Barbara Storti, Julio Castaño, Riccardo Panella, Jia Li, Corinne E. Gustafson, Sam Fox, Rachel Levy, Claire Meyerovitz, Peter J. Tramontozzi, Kimberly Vermilya, Assunta De Rienzo, Stefania Crucitta, Daniela S. Bassères, Marla Weetall, Art Branstrom, Alessandra Giorgetti, Raffaele Ciampi, Marzia Del Re, Romano Danesi, Ranieri Bizzarri, Henry Yang, Olivier Kocher, Allon M. Klein, Robert S. Welner, Raphael Bueno, Maria Cristina Magli, John G. Clohessy, Azhar Ali, Daniel G. Tenen, Elena Levantini
Software Mentions: 7
Published: over 5 years ago

10.1038/s41418-021-00751-w

Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomas
Cited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: over 5 years ago

10.1038/sdata.2017.149

Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus
Cited by: 12
Author(s): Pirita Paajanen, Jan Strauss, Cock van Oosterhout, Mark McMullan, Matt Clark, Thomas Möck
Software Mentions: 7
Published: about 9 years ago

10.1186/1472-6807-13-2

Designing and benchmarking the MULTICOM protein structure prediction system
Cited by: 25
Author(s): Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng
Software Mentions: 7
Published: over 13 years ago

10.1038/sdata.2018.21

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich’s ataxia patients
Cited by: 22
Author(s): Marta Seco-Cervera, Daymé González-Rodríguez, José Santiago Ibáñez-Cabellos, Lorena Peiró-Chova, Federico V. Pallardó, José Luis García-Giménez
Software Mentions: 7
Published: over 8 years ago

10.1002/cti2.1173

Systematic analysis of the transcriptome in small‐cell carcinoma of the oesophagus reveals its immune microenvironment
Cited by: 2
Author(s): Qi Zhao, Yan‐Xing Chen, Qi‐Nian Wu, Chao Zhang, Min Liu, Yingnan Wang, Yan Feng, Jiajia Hu, Jianhua Fu, Hong Yang, Jingjing Qi, Zixian Wang, Yong Lu, Hui Sheng, Zexian Liu, Zhixiang Zuo, Jian Zheng, Jing‐Ping Yun, Jin‐Xin Bei, Wei‐Hua Jia, Dong Lin, Rui‐Hua Xu, Feng Wang
Software Mentions: 7
Published: almost 7 years ago

10.1186/s12864-021-07735-7

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola
Cited by: 11
Author(s): Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz‐Ferrer, Carolina Escobar, Tim De Meyer, Tina Kyndt
Software Mentions: 7
Published: over 5 years ago

10.1038/sdata.2016.90

Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice
Cited by: 5
Author(s): Tonatiuh Peña Centeno, Orr Shomroni, Magali Hennion, Rashi Halder, Ramón Vidal, Raza-Ur Rahman, Stefan Bonn
Software Mentions: 7
Published: about 10 years ago

10.1186/s12864-021-07595-1

Dynamics of rumen gene expression, microbiome colonization, and their interplay in goats
Cited by: 15
Author(s): Xiangyu Pan, Zongjun Li, Bibo Li, Chen Zhao, Yu Wang, Yulin Chen, Yu Jiang
Software Mentions: 7
Published: over 5 years ago

10.3390/plants9121700

Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots
Cited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pbio.3000797

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability
Cited by: 15
Author(s): Corey E. Hayford, Darren R. Tyson, Charles J. Robbins, Peter L. Frick, Vito Quaranta, Leonard A. Harris
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-018-2353-5

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data
Cited by: 81
Author(s): Roelof J.C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji‐Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper, Oscar Krijgsman
Software Mentions: 7
Published: about 8 years ago

10.21203/rs.3.rs-380803/v1

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
Cited by: 9
Author(s): Alexandra Tsitsiklis, Beth Shoshana Zha, Ashley Byrne, Catherine DeVoe, Sophia Levan, Elze Rackaityte, Sara Sunshine, Eran Mick, Rajani Ghale, Alejandra Jauregui, Norma Neff, Aartik Sarma, Paula Hayakawa Serpa, Thomas Deiss, Amy Kistler, Sidney Carrillo, K. Mark Ansel, Aleksandra Leligdowicz, S. Christenson, Nicola L. Jones, Benjamin Wu, Spyros Darmanis, Michael A. Matthay, Susan V. Lynch, Joseph L. DeRisi, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Prescott G. Woodruff, David J. Erle, O. A. Rosenberg, Carolyn S. Calfee, Charles Langelier
Software Mentions: 7
Published: over 5 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 7 years ago

10.21203/rs.3.rs-131380/v2

Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets
Cited by: 3
Author(s): Young Il Kim, Kwang-Min Yu, June-Young Koh, Eunha Kim, Se‐Mi Kim, Young Ho Kim, Mark Anthony B. Casel, Rare Rollon, Seung-Gyu Jang, Min‐Suk Song, Su‐Jin Park, Hye Won Jeong, Eung‐Gook Kim, Ok-Jun Lee, Younho Choi, Shin-Ae Lee, Su–Hyung Park, Jae U. Jung, Young Ki Choi
Software Mentions: 7
Published: over 5 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: over 8 years ago

10.1186/s12864-018-4805-8

Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq
Cited by: 14
Author(s): Karel Sedlář, Pavlína Koščová, Maryna Vasylkivska, Barbora Branská, Jan Kolek, Kristyna Kupkova, Petra Patáková, Ivo Provazník
Software Mentions: 7
Published: over 8 years ago

10.1038/s41597-019-0095-5

Multi omics analysis of fibrotic kidneys in two mouse models
Cited by: 25
Author(s): Mira Pavkovic, Lorena Pantano, Cory V. Gerlach, Sergine Brutus, Sarah A. Boswell, Robert A. Everley, Jagesh V. Shah, Shannan Ho Sui, Vishal S. Vaidya
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: over 5 years ago

10.1073/pnas.1819788116

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs
Cited by: 48
Author(s): Zhangming Yan, Norman Huang, Weixin Wu, Weizhong Chen, Yiqun Jiang, Jingyao Chen, Xuerui Huang, Xingzhao Wen, Jie Xu, Qiushi Jin, Kang Zhang, Zhe Chen, Shu Chien, Sheng Zhong
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.ppat.1009875

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis
Cited by: 14
Author(s): Ian J. Groves, Emma L A Drane, Marco Michalski, Jack Monahan, Cinzia G. Scarpini, Stephen Smith, Giovanni Bussotti, Csilla Várnai, Stefan Schoenfelder, Peter Fraser, Anton J. Enright, Nicholas Coleman
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-020-6502-7

Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies
Cited by: 23
Author(s): Xiaohong Li, Nigel G. F. Cooper, Timothy E. O’Toole, Eric C. Rouchka
Software Mentions: 6
Published: over 6 years ago

10.1186/s13100-019-0180-5

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
Cited by: 20
Author(s): Nicky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Software Mentions: 6
Published: about 7 years ago

10.1172/jci.insight.149185

Th1 polarization defines the synovial fluid T cell compartment in oligoarticular juvenile idiopathic arthritis
Cited by: 16
Author(s): Amélie M. Julé, Kacie J. Hoyt, Kevin Wei, María Gutiérrez‐Arcelus, Maria Taylor, Julie Ng, James A. Lederer, Siobhan Case, Margaret H. Chang, Ezra Cohen, Fatma Dedeoğlu, Melissa Hazen, Jonathan S Hausmann, Olha Halyabar, Erin Janssen, Jeffrey Lo, Mindy S. Lo, Esra Meidan, Jay Roberts, Mary Beth Son, Robert P. Sundel, Pui Y. Lee, Talal Chatila, Peter A. Nigrović, Lauren A. Henderson
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-020-6714-x

DolphinNext: a distributed data processing platform for high throughput genomics
Cited by: 61
Author(s): Onur Yukselen, Osman Turkyilmaz, Ahmet Öztürk, Manuel Garber, Alper Küçükural
Software Mentions: 6
Published: over 6 years ago

10.1038/s41423-021-00647-2

The microbiota is dispensable for the early stages of peripheral regulatory T cell induction within mesenteric lymph nodes
Cited by: 16
Author(s): Carolin Wiechers, Mangge Zou, Eric Galvez, Michael Beckstette, Maria F. Ebel, Till Strowig, Jochen Huehn, Joern Pezoldt
Software Mentions: 6
Published: over 5 years ago

10.1016/j.immuni.2021.08.011

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses
Cited by: 58
Author(s): Qingli Tang, Rachel E. Rigby, George R. Young, Astrid Korning Hvidt, Tanja Davis, Tiong Kit Tan, Anne Bridgeman, Alain Townsend, George Kassiotis, Jan Rehwinkel
Software Mentions: 6
Published: about 5 years ago

10.1016/j.immuni.2020.09.015

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
Cited by: 143
Author(s): Travis Hughes, Marc H. Wadsworth, Todd M. Gierahn, Tran Do, David I. Weiss, Priscila Ribeiro Andrade, Feiyang Ma, Bruno Jorge de Andrade Silva, Shuai Shao, Lam C. Tsoi, José Ordovás-Montañés, Jóhann E. Guðjónsson, Robert L. Modlin, J. Christopher Love, Alex K. Shalek
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.ppat.1009280

Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Cited by: 29
Author(s): TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlöf, Jennifer A. Cundiff, Zeus Saldaña‐Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Software Mentions: 6
Published: about 5 years ago

10.1016/j.ajhg.2019.05.010

Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver
Cited by: 33
Author(s): Minal Çalışkan, Elisabetta Manduchi, Harish Rao, Julian A. Segert, Márcia Holsbach Beltrame, Marco Trizzino, YoSon Park, Samuel White Baker, Alessandra Chesi, Matthew E. Johnson, Kenyaita M. Hodge, Michelle E. Leonard, Bao‐Li Loza, Xin Dong, Andrea M. Berrido, Nicholas J. Hand, Robert C. Bauer, Andrew D. Wells, Kim M. Olthoff, Abraham Shaked, Daniel J. Rader, Struan F.A. Grant, Christopher D. Brown
Software Mentions: 6
Published: over 7 years ago

10.1093/gigascience/giab003

long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data
Cited by: 25
Author(s): Shanika L. Amarasinghe, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 6
Published: over 5 years ago

10.1038/s41438-021-00488-0

Cytokinin but not gibberellin application had major impact on the phenylpropanoid pathway in grape
Cited by: 23
Author(s): Kamal Tyagi, Itay Maoz, Bettina Kochanek, Noa Sela, Larry Lerno, Susan E. Ebeler, Amnon Lichter
Software Mentions: 6
Published: over 5 years ago

10.1093/gigascience/giz022

Digital expression explorer 2: a repository of uniformly processed RNA sequencing data
Cited by: 41
Author(s): Mark Ziemann, Antony Kaspi, Assam El‐Osta
Software Mentions: 6
Published: over 7 years ago

10.1093/gigascience/giz037

GenPipes: an open-source framework for distributed and scalable genomic analyses
Cited by: 107
Author(s): Mathieu Bourgey, Rola Dali, Robert Eveleigh, Kuang Chung Chen, Louis Létourneau, Joël Fillon, Marc Michaud, Maxime Caron, Johanna Sandoval, François Lefebvre, Gary Leveque, Eloi Mercier, David Bujold, Pascale Marquis, Patrick Tran Van, David Anderson de Lima Morais, Julien Tremblay, Xiaojian Shao, Édouard Henrion, Emmanuel González, Pierre-Olivier Quirion, B. Caron, Guillaume Bourque
Software Mentions: 6
Published: over 7 years ago

10.1186/s12864-018-4670-5

Circular RNA expression and regulatory network prediction in posterior cingulate astrocytes in elderly subjects
Cited by: 28
Author(s): Shobana Sekar, Lori Cuyugan, Jonathan Adkins, Philipp Geiger, Winnie S. Liang
Software Mentions: 6
Published: over 8 years ago

10.1098/rsos.191480

Mid and hindgut transcriptome profiling analysis of Atlantic salmon ( Salmon salar ) under unpredictable chronic stress
Cited by: 2
Author(s): Signe Dille Løvmo, Angelico Madaro, Paul Whatmore, Tora Bardal, Mari‐Ann Östensen, Simen Rød Sandve, Rolf Erik Olsen
Software Mentions: 6
Published: over 6 years ago

10.1093/g3journal/jkab177

New genomic resources and comparative analyses reveal differences in floral gene expression in selfing and outcrossing Collinsia sister species
Cited by: 8
Author(s): Lauren J. Frazee, Joanna L. Rifkin, Dinusha C. Maheepala, Alannie‐Grace Grant, Stephen I. Wright, Susan Kalisz, Amy Litt, Rachel B. Spigler
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0218458

p73 regulates epidermal wound healing and induced keratinocyte programming
Cited by: 18
Author(s): J. Scott Beeler, Clayton B. Marshall, Paula I. González-Ericsson, Timothy M. Shaver, Gabriela L. Santos Guasch, Spencer Lea, Kimberly N. Johnson, Hailing Jin, Bryan J. Venters, Melinda E. Sanders, Jennifer A. Pietenpol
Software Mentions: 6
Published: over 7 years ago

10.3390/cancers12113457

Exploring the Role of Osteosarcoma-Derived Extracellular Vesicles in Pre-Metastatic Niche Formation and Metastasis in the 143-B Xenograft Mouse Osteosarcoma Model
Cited by: 19
Author(s): Alekhya Mazumdar, Joaquín Urdínez, Aleksandar Boro, Matthias Arlt, Fabian E. Egli, Barbara Niederöst, Patrick K. Jaeger, Greta Moschini, Roman Muff, Bruno Fuchs, Jess G. Snedeker, Ana Gvozdenovic
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12859-020-3399-8

iSeqQC: a tool for expression-based quality control in RNA sequencing
Cited by: 15
Author(s): Gaurav Kumar, Adam Ertel, George J. Feldman, Joan Kupper, Paolo Fortina
Software Mentions: 6
Published: over 6 years ago

10.1093/g3journal/jkaa043

Global translational landscape of the Candida albicans morphological transition
Cited by: 8
Author(s): Vasanthakrishna Mundodi, Saket Choudhary, Andrew D. Smith, David Kadosh
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12864-021-07469-6

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
Cited by: 5
Author(s): Andreas Hoek, Katharina Maibach, Ebru Özmen, Ana Ivonne Vazquez‐Armendariz, Jan Philipp Mengel, Torsten Hain, Susanne Herold, Alexander Goesmann
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-017-1808-4

QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model
Cited by: 36
Author(s): Lian Liu, Shao Wu Zhang, Yufei Huang, Jia Meng
Software Mentions: 6
Published: about 9 years ago

10.1371/journal.pone.0175657

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts
Cited by: 28
Author(s): Wolfgang Kaisers, Petra Boukamp, Hans Jürgen Stark, Holger Schwender, Julia Tigges, Jean Krutmann, Heiner Schaal
Software Mentions: 6
Published: over 9 years ago

10.26508/lsa.201800175

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Cited by: 16
Author(s): Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson
Software Mentions: 6
Published: almost 8 years ago

10.1186/s12864-017-3630-9

Interferon signaling in ascites-associated macrophages is linked to a favorable clinical outcome in a subgroup of ovarian carcinoma patients
Cited by: 42
Author(s): Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller‐Brüsselbach, Silke Reinartz, Rolf Müller
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0205406

Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: A prospective observational study
Cited by: 10
Author(s): Andrew P Zammit, Rohit Anthony Sinha, Caroline Cooper, Christopher Perry, Ian H. Frazer, Zewen Kelvin Tuong
Software Mentions: 6
Published: about 8 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759