cran: rsem | Projects | Ecosyste.ms: Papers

10.7554/eLife.38579

FoxA1 and FoxA2 drive gastric differentiation and suppress squamous identity in NKX2-1-negative lung cancer
Cited by: 52
Author(s): Soledad A. Camolotto, S. R. Pattabiraman, Timothy Mosbruger, Alex Jones, Veronika K Belova, Grace Orstad, Mitchell Streiff, Lydia Salmond, Chris Stubben, Klaus H. Kaestner, Eric L. Snyder
Software Mentions: 12
Published: about 6 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: over 9 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

10.1111/eva.13120

Comparative transcriptomics of ice‐crawlers demonstrates cold specialization constrains niche evolution in a relict lineage
Cited by: 4
Author(s): Sean D. Schoville, Sabrina Simon, Ming Bai, Zachary T. Beethem, R. Yu. Dudko, Monika J. B. Eberhard, Paul B. Frandsen, Simon Küpper, Ryuichiro Machida, Max Verheij, Peter Willadsen, Xin Zhou, Benjamin Wipfler‍
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0153782

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
Cited 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

10.1002/1873-3468.14180

Genome‐scale metabolic modelling of SARS‐CoV‐2 in cancer cells reveals an increased shift to glycolytic energy production
Cited by: 13
Author(s): Elisabeth Yaneske, Guido Zampieri, Loris Bertoldi, Giuseppe Benvenuto, Claudio Angione
Software Mentions: 7
Published: over 3 years ago

10.1002/1878-0261.12569

Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progression
Cited by: 34
Author(s): Bo Pang, Jiu Hua Xu, Jing Hu, Fenghua Guo, Linyun Wan, Mingjiang Cheng, Lin Pang
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.ppat.1007518

Comprehensive profiling of translation initiation in influenza virus infected cells
Cited by: 22
Author(s): Heather M. Machkovech, Jesse D. Bloom, Arvind R. Subramaniam
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-018-1589-8

Enhancers in the Peril lincRNA locus regulate distant but not local genes
Cited by: 20
Author(s): Abigail F. Groff, A. Rasim Barutcu, Jordan P. Lewandowski, John L. Rinn
Software Mentions: 6
Published: about 6 years ago

10.1002/1878-0261.12654

Programmed death‐ligand 1 gene expression is a prognostic marker in early breast cancer and provides additional prognostic value to 21‐gene and 70‐gene signatures in estrogen receptor‐positive disease
Cited by: 18
Author(s): Ioannis Zerdes, Emmanouil G. Sifakis, Alexios Matikas, Sebastian Chrétien, Nicholas P. Tobin, Johan Hartman, George Z. Rassidakis, Jonas Bergh, Theodoros Foukakis
Software Mentions: 5
Published: almost 5 years ago

10.3389/fgene.2019.00689

Transcription Profiling of Monocyte-Derived Macrophages Infected In Vitro With Two Strains of Streptococcus agalactiae Reveals Candidate Pathways Affecting Subclinical Mastitis in Cattle
Cited by: 6
Author(s): Anna Lewandowska-Sabat, Е. В. Кирсанова, Christophe Klopp, T. R. Solberg, B. Heringstad, Olav Østerås, Preben Boysen, I. Olsaker
Software Mentions: 5
Published: over 5 years ago

10.1038/srep43793

Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome
Cited by: 24
Author(s): Guogui Ning, Cheng Xu, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0188415

Physiological effects of a novel artificially synthesized antimalarial cyclic peptide: Mahafacyclin B
Cited by: 2
Author(s): Yūkō Fujita, Panpaki Seekaki, Naoya Ogata, Kazuhiro Chiba
Software Mentions: 5
Published: about 7 years ago

10.1111/mec.13113

Variation in promiscuity and sexual selection drives avian rate of Faster‐Z evolution
Cited by: 74
Author(s): Alison E. Wright, Peter W. Harrison, Fabian Zimmer, Stephen H. Montgomery, Marie A. Pointer, Judith E. Mank
Software Mentions: 5
Published: almost 10 years ago

10.1002/1878-0261.12478

Identification of tumor suppressor miRNAs by integrative miRNA and mRNA sequencing of matched tumor–normal samples in lung adenocarcinoma
Cited by: 38
Author(s): Namhee Yu, Seunghui Yong, Hong Kwan Kim, Yoon La Choi, Yeonjoo Jung, Doyeon Kim, Jihae Seo, Ye Eun Lee, Daehyun Baek, Jinseon Lee, Seungjae Lee, Jong Eun Lee, Jaesang Kim, Young Tae Kim, Sanghyuk Lee
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-12-323

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
Cited by: 14,016
Author(s): Bo Li, Colin N. Dewey
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-019-5947-z

Small RNA discovery in the interaction between barley and the powdery mildew pathogen
Cited by: 26
Author(s): Matt Hunt, Sagnik Banerjee, Priyanka Surana, Meiling Liu, Greg Fuerst, Sandra M. Mathioni, Blake C. Meyers, Dan Nettleton, Roger P. Wise
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-862

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes
Cited by: 51
Author(s): Peter J.P. Croucher, Michael S. Brewer, Christopher J. Winchell, Geoff Oxford, Rosemary G. Gillespie
Software Mentions: 4
Published: almost 12 years ago

10.1099/mgen.0.000319

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses
Cited by: 22
Author(s): Yu Chen, Chen Yuan, Christopher A. Desjardins, Jennifer L. Tenor, Dena L. Toffaletti, Charles Giamberardino, Anastasia P. Litvintseva, John R. Perfect, Christina A. Cuomo
Software Mentions: 4
Published: almost 5 years ago

10.1111/mec.15216

Sex‐specific changes in the aphid DNA methylation landscape
Cited by: 32
Author(s): Thomas C. Mathers, Sam T. Mugford, Lawrence Percival‐Alwyn, Yazhou Chen, Gemy Kaithakottil, David Swarbreck, Saskia A. Hogenhout, Cock van Oosterhout
Software Mentions: 4
Published: over 5 years ago

10.1002/1878-0261.12769

KDM3A/Ets1 epigenetic axis contributes to PAX3/FOXO1‐driven and independent disease‐promoting gene expression in fusion‐positive Rhabdomyosarcoma
Cited by: 3
Author(s): Lays Martin Sobral, Hannah M. Hicks, Janet K. Parrish, Tyler McCann, Joseph Hsieh, Andrew Goodspeed, James C. Costello, Joshua C. Black, Paul Jedlicka
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.2988

Compacting and correcting Trinity and Oases RNA-Seq <i>de novo</i> assemblies
Cited by: 84
Author(s): Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
Software Mentions: 4
Published: almost 8 years ago

10.15252/embj.2019104185

Timeless couples G‐quadruplex detection with processing by <scp>DDX</scp> 11 helicase during <scp>DNA</scp> replication
Cited by: 42
Author(s): Letícia Koch Lerner, Sandro Holzer, M.L. Kilkenny, Saša Šviković, Pierre Murat, Davide Schiavone, Cara Bernadette Eldridge, Alice Bittleston, Joseph D. Maman, Dana Branzei, Katherine Stott, Luca Pellegrini, Julian E. Sale
Software Mentions: 4
Published: over 4 years ago

10.3389/fnmol.2018.00363

Assessing Transcriptome Quality in Patch-Seq Datasets
Cited by: 33
Author(s): Shreejoy J. Tripathy, Lilah Toker, Claire Bomkamp, B. Ogan Mancarci, Manuel Belmadani, Paul Pavlidis
Software Mentions: 4
Published: about 6 years ago

10.3389/fonc.2021.653902

Fucoidan Inhibits the Progression of Hepatocellular Carcinoma via Causing lncRNA LINC00261 Overexpression
Cited by: 10
Author(s): Danhui Ma, Jiayi Wei, Sinuo Chen, Heming Wang, Ning Lv, Shihua Luo, Chieh-Lun Liu, Guangqi Song, Qunyan Yao
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-014-0410-6

Corset: enabling differential gene expression analysis for de novoassembled transcriptomes
Cited by: 278
Author(s): N. Davidson, Alicia Oshlack
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-015-0746-6

Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
Cited by: 74
Author(s): Adler R. Dillman, Marissa Macchietto, Camille F. Porter, Alicia K. Rogers, Brian A. Williams, Igor Antoshechkin, Ming Min Lee, Z. Goodwin, Xiaojun Lu, Edwin E. Lewis, Heidi Goodrich-Blair, S. Patricia Stock, Byron J. Adams, Paul W. Sternberg, A Mortazavi
Software Mentions: 4
Published: over 9 years ago

10.3390/jcm10132973

Meteorin Is a Novel Therapeutic Target for Wet Age-Related Macular Degeneration
Cited by: 4
Author(s): Kimberley Delaunay, Alexandre Sellam, Virginie Dinet, Alexandre Moulin, Min Zhao, Emmanuelle Gélizé, Jérémie Canonica, Marie‐Christine Naud, Patricia Crisanti-Lassiaz, Francine Behar‐Cohen
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1006302

Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Cited by: 87
Author(s): Dihong Lu, Marissa Macchietto, Dennis Chang, Mirayana M. Barros, J. G. Baldwin, A Mortazavi, Adler R. Dillman
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-72291-1

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng
Cited by: 9
Author(s): Dan Zhang, Wei Li, Zhongjian Chen, Fang Wei, Yunlong Liu, Li‐Zhi Gao
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.20023

Nematophagous fungus Arthrobotrys oligospora mimics olfactory cues of sex and food to lure its nematode prey
Cited by: 68
Author(s): Yu-Ting Hsueh, Matthew R. Gronquist, Erich M. Schwarz, Ravi D. Nath, Ching-Han Lee, Shalha Gharib, Frank C. Schroeder, Paul W. Sternberg
Software Mentions: 4
Published: almost 8 years ago

10.3389/fpls.2016.01920

Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax
Cited by: 45
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Natalya V. Kishlyan, Alexander V. Zyablitsin, А. Ф. Садритдинова, Anastasiya V. Snezhkina, Maria Fedorova, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pgen.1009044

NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation
Cited by: 18
Author(s): Yuta Hiraike, Hironori Waki, Kana Miyake, Takahito Wada, Misato Oguchi, Kaede Saito, Sadami Tsutsumi, Hiroyuki Aburatani, Toshimasa Yamauchi, Takashi Kadowaki
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-14-220

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data
Cited by: 15
Author(s): Xinyun Ma, Xuegong Zhang
Software Mentions: 3
Published: over 11 years ago

10.1186/s12920-019-0551-2

Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines
Cited by: 28
Author(s): Xing Yi Woo, Anuj Srivastava, Joel H. Graber, Vinod Kumar Yadav, Vishal Kumar Sarsani, Al Simons, Glen L. Beane, Stephen C. Grubb, Guruprasad Ananda, Rangjiao Liu, Grace A. Stafford, Jeffrey H. Chuang, Susan D. Airhart, R. Krishna Murthy Karuturi, Joshy George, Carol J. Bult
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-019-5795-x

Transcriptional analysis of renal dopamine-mediated Na+ homeostasis response to environmental salinity stress in Scatophagus argus
Cited by: 10
Author(s): Maoliang Su, Jia Zhou, Zhengyu Duan, Junbin Zhang
Software Mentions: 3
Published: over 5 years ago

10.1002/2211-5463.13239

Role of sericin 1 in the immune system of silkworms revealed by transcriptomic and proteomic analyses after gene knockout
Cited by: 3
Author(s): Xiaogang Ye, Shuo Zhao, Meiyu Wu, Jinghua Ruan, Xiaoli Tang, Xiaoxiao Wang
Software Mentions: 2
Published: over 3 years ago

10.1111/1751-7915.12735

Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds
Cited by: 47
Author(s): Olaf Tyc, Victor C. L. de Jager, Marlies van den Berg, Saskia Gerards, Thierry Janssens, Niels Zaagman, Marco Kai, Aleš Svatoš, Hans Zweers, C.A. Hordijk, Harrie Besselink, Wietse de Boer, Paolina Garbeva
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.03209

Genome Sequencing and Comparative Transcriptomics Provide a Holistic View of 4-Nitrophenol Degradation and Concurrent Fatty Acid Catabolism by Rhodococcus sp. Strain BUPNP1
Cited by: 19
Author(s): Kriti Sengupta, Martin Swain, Paul Livingstone, David E. Whitworth, Pradipta Saha
Software Mentions: 2
Published: almost 6 years ago

10.1038/srep14015

Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis
Cited by: 84
Author(s): Shu Huang, Chenghui Wang, Wucheng Yue, Jiao Chen, Sarah Gaughan, Wei Lu, Guoqing Lu, Chenghui Wang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0209496

Inflammation and transcriptional responses of peripheral blood mononuclear cells in classic ataxia telangiectasia
Cited by: 17
Author(s): Sharon A. McGrath‐Morrow, Roland Ndeh, Joseph M. Collaco, Cynthia Rothblum-Oviatt, Jonathan H. Wright, Michael A. O’Reilly, Benjamin D. Singer, Howard M. Lederman
Software Mentions: 2
Published: about 6 years ago

10.1111/mec.15241

Exposure to environmental radionuclides is associated with altered metabolic and immunity pathways in a wild rodent
Cited by: 22
Author(s): Jenni Kesäniemi, Toni Jernfors, Anton Lavrinienko, Kati Kivisaari, Mikko Kiljunen, Johanna Mappes, Phillip C. Watts
Software Mentions: 2
Published: over 5 years ago

10.1016/j.cell.2019.01.018

Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence
Cited by: 311
Author(s): Gabriel E. Neurohr, Rachel Terry, Jette Lengefeld, Megan Bonney, Gregory Brittingham, Fabien Moretto, Teemu P. Miettinen, Laura Pontano Vaites, Luis M. Soares, João A. Paulo, J. Wade Harper, Stephen Buratowski, Scott R. Manalis, Folkert J. van Werven, Liam J. Holt, Angelika Amon
Software Mentions: 2
Published: almost 6 years ago

10.1002/ece3.5724

Differential gene expression in chronic wasting disease‐positive white‐tailed deer (<i>Odocoileus virginianus</i>)
Cited by: 5
Author(s): Emma K. Trone-Launer, Chenghui Wang, Guoqing Lu, Nohra E. Mateus‐Pinilla, Paige R. Zick, James T. Lamer, Paul Shelton, Christopher N. Jacques
Software Mentions: 2
Published: about 5 years ago

10.1111/mec.13882

Insecticide resistance mediated by an exon skipping event
Cited by: 43
Author(s): Madeleine Berger, Alin M. Puinean, Emma Randall, Christoph Zimmer, Wellington Marcos da Silva, Pablo Bielza, L. M. Field, David Hughes, Ian R. Mellor, Keywan Hassani‐Pak, Herbert A.A. Siqueira, Martin S. Williamson, Chris Bass
Software Mentions: 2
Published: about 8 years ago

10.1186/s12870-017-1192-2

Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.)
Cited by: 37
Author(s): Alexey A. Dmitriev, George S. Krasnov, Tatiana A. Rozhmina, Roman O. Novakovskiy, Anastasiya V. Snezhkina, Maria S. Fedorova, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Anna V. Kudryavtseva, Nataliya V. Melnikova
Software Mentions: 2
Published: about 7 years ago

10.1002/1878-0261.12630

Cancer‐associated V‐ATPase induces delayed apoptosis of protumorigenic neutrophils
Cited by: 16
Author(s): Safaa A. Ibrahim, Arpita Kulshrestha, Gajendra K. Katara, Valerie Riehl, Manoranjan Sahoo, Kenneth D. Beaman
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12915-020-00773-9

Integrating evolutionarily novel horns within the deeply conserved insect head
Cited by: 6
Author(s): David M. Linz, Armin P. Moczek
Software Mentions: 1
Published: over 4 years ago

10.1186/s13100-016-0064-x

The endonuclease domain of the LINE-1 ORF2 protein can tolerate multiple mutations
Cited by: 14
Author(s): Kristine J. Kines, Mark J. Sokolowski, Dawn deHaro, Claiborne M. Christian, Melody Baddoo, Madison E. Smither, Victoria P. Belancio
Software Mentions: 1
Published: over 8 years ago

10.1186/s12870-016-0927-9

Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress
Cited by: 42
Author(s): Alexey A. Dmitriev, Anna V. Kudryavtseva, George S. Krasnov, N. V. Koroban, Anna S. Speranskaya, A.A. Krinitsina, Maxim S. Belenikin, Anastasiya V. Snezhkina, А. Ф. Садритдинова, Natalya V. Kishlyan, Tatiana A. Rozhmina, Olga Yu. Yurkevich, Olga V. Muravenko, Nadezhda L. Bolsheva, Nataliya V. Melnikova
Software Mentions: 1
Published: about 8 years ago

10.3389/fpsyg.2017.01286

Evaluating Fit Indices for Multivariate t-Based Structural Equation Modeling with Data Contamination
Cited by: 7
Author(s): Mark H. C. Lai, Jiaqi Zhang
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms221910404

Heterogeneity of Response to Iron-Based Metallodrugs in Glioblastoma Is Associated with Differences in Chemical Structures and Driven by FAS Expression Dynamics and Transcriptomic Subtypes
Cited by: 11
Author(s): Anne Vessières, Emie Quissac, Nolwenn Lemaire, Agustí Alentorn, Patrycja Domeracka, Pascal Pigeon, Marc Sanson, Ahmed Idbaïh, Maïté Verreault
Software Mentions: 1
Published: over 3 years ago

Projects: cran: rsem

Papers Mentioning rsem 53