bioconductor: tximport | Projects

10.3390/genes11040415

Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep
Cited by: 14
Author(s): Kisun Pokharel, Jaana Peippo, Melak Weldenegodguad, Mervi Honkatukia, Menghua Li, Juha Kantanen
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-017-1332-x

Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7
Cited by: 71
Author(s): Katja Meyer, Tino Köster, Christiané Nolte, Claus Weinholdt, Martin Lewinski, Ivo Große, Dorothee Staiger
Software Mentions: 5
Published: about 7 years ago

10.3390/ijms21093229

A PIANO (Proper, Insufficient, Aberrant, and NO Reprogramming) Response to the Yamanaka Factors in the Initial Stages of Human iPSC Reprogramming
Cited by: 6
Author(s): Kejin Hu
Software Mentions: 5
Published: over 4 years ago

10.1093/gbe/evab110

Transcriptomic Analysis of Skin Color in Anole Lizards
Cited by: 5
Author(s): Pietro Longo Hollanda de Mello, Paul M Hime, Richard E. Glor
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giz145

Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples
Cited by: 31
Author(s): Hong Zheng, Kevin Brennan, Mikel Hernáez, Olivier Gevaert
Software Mentions: 5
Published: almost 5 years ago

10.3390/ijms21061938

Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis
Cited by: 8
Author(s): Dimitrios S. Kanakoglou, Theodora-Dafni Michalettou, Christina Vasileiou, Evangelos Gioukakis, Δωροθέα Μανέτα, Konstantinos Kyriakidis, Alexandros G. Georgakilas, Ioannis Michalopoulos
Software Mentions: 5
Published: over 4 years ago

10.1172/jci.insight.148694

Natural mucosal barriers and COVID-19 in children
Cited by: 113
Author(s): Carl A. Pierce, Sharlene Sy, Benjamin T. Galen, D. Yitzchak Goldstein, Erika P. Orner, Marla J. Keller, Kevan C. Herold, Betsy C. Herold
Software Mentions: 5
Published: over 3 years ago

10.1177/0748730418813785

LimoRhyde: A Flexible Approach for Differential Analysis of Rhythmic Transcriptome Data
Cited by: 47
Author(s): Jordan M. Singer, Jacob J. Hughey
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.ppat.1009443

Bacteria primed by antimicrobial peptides develop tolerance and persist
Cited by: 33
Author(s): Alexandro Rodríguez‐Rojas, Desiree Y. Baeder, Paul R. Johnston, Roland R. Regoes, Jens Rolff
Software Mentions: 5
Published: over 3 years ago

10.3390/ijms21051894

The Polymorphic PolyQ Tail Protein of the Mediator Complex, Med15, Regulates the Variable Response to Diverse Stresses
Cited by: 7
Author(s): Gallagher Jeg, Ser Sl, Michael C. Ayers, C Nassif, Amaury Pupo
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms20246207

Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27
Cited by: 11
Author(s): Xiaojun Hu, Suranjana Goswami, Ju Qiu, Qian Chen, Sylvain Laverdure, Brad T. Sherman, Tomozumi Imamichi
Software Mentions: 5
Published: almost 5 years ago

10.1002/btm2.10198

Transcriptomic response of brain tissue to focused <scp>ultrasound‐mediated blood–brain</scp> barrier disruption depends strongly on anesthesia
Cited by: 12
Author(s): Alexander S. Mathew, Catherine M. Gorick, E. Andrew Thim, William J. Garrison, Alexander L. Klibanov, G. Wilson Miller, Natasha D. Sheybani, Richard J. Price
Software Mentions: 5
Published: almost 4 years ago

10.1093/brain/awaa242

Functional gene networks reveal distinct mechanisms segregating in migraine families
Cited by: 14
Author(s): Anne Marie Rasmussen, Lisette J. A. Kogelman, David M. Kristensen, Mona Ameri Chalmer, Jes Olesen, Thomas Folkmann Hansen
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.64977

Unique integrated stress response sensors regulate cancer cell susceptibility when Hsp70 activity is compromised
Cited by: 11
Author(s): Sara Sannino, Megan E. Yates, Mark E. Schurdak, Steffi Oesterreich, Adrian V. Lee, Peter Wipf, Jeffrey L. Brodsky
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-021-01001-8

Evolution of the codling moth pheromone via an ancient gene duplication
Cited by: 9
Author(s): Jean-Marc Lassance, Bao‐Jian Ding, Christer Löfstedt
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.53600

MEIS-mediated suppression of human prostate cancer growth and metastasis through HOXB13-dependent regulation of proteoglycans
Cited by: 30
Author(s): Calvin VanOpstall, Padma Srikanth, Hannah Brechka, Marc Gillard, Sophia Lamperis, Baizhen Zhu, Roger Brown, Raj Bhanvadia, Donald Vander Griend
Software Mentions: 5
Published: over 4 years ago

10.1186/s13071-020-04424-4

Molecular signatures of the rediae, cercariae and adult stages in the complex life cycles of parasitic flatworms (Digenea: Psilostomatidae)
Cited by: 3
Author(s): Maksim A. Nesterenko, Viktor V. Starunov, Sergei V. Shchenkov, Anna R. Maslova, Sofia Denisova, Andrey I. Granovich, Andrej A. Dobrovolskij, Konstantin Khalturin
Software Mentions: 5
Published: about 4 years ago

10.1002/ps.6061

Toxicological and molecular profiling of insecticide resistance in a Brazilian strain of fall armyworm resistant to Bt Cry1 proteins
Cited by: 24
Author(s): Debora Boaventura, Benjamin Buer, Niklas Hamaekers, Frank Maiwald, Ralf Nauen
Software Mentions: 5
Published: about 4 years ago

10.1007/s00424-021-02582-7

Abnormal neonatal sodium handling in skin precedes hypertension in the SAME rat
Cited by: 2
Author(s): L. J. Mullins, Jessica R. Ivy, Mairi Ward, Olav Tenstad, Helge Wiig, Kento Kitada, Jonathan Manning, Natalia Rakova, Dominik N. Müller, John J. Mullins
Software Mentions: 5
Published: over 3 years ago

10.1164/rccm.202003-0510OC

Whole-Blood RNA Profiles Associated with Pulmonary Arterial Hypertension and Clinical Outcome
Cited by: 36
Author(s): Christopher J. Rhodes, Pablo Otero-Núñez, John Wharton, Emilia M. Swietlik, Sokratis Kariotis, Lars Harbaum, Mark J. Dunning, Jason M. Elinoff, Niamh Errington, A. A. Roger Thompson, James Iremonger, J. Gerry Coghlan, Paul A. Corris, Luke Howard, David G. Kiely, Colin Church, Joanna Pepke‐Zaba, Mark Toshner, Stephen J. Wort, Ankit A. Desai, Marc Humbert, William C. Nichols, Laura Southgate, David‐Alexandre Trégouët, Richard Trembath, Inga Prokopenko, Stefan Gräf, Nicholas W. Morrell, Dennis Wang, Allan Lawrie, Martin R. Wilkins
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1007114

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus
Cited by: 62
Author(s): Steven P. Barrett, Kevin R. Parker, Caroline Horn, Miguel A. Mata, Julia Salzman
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.62857

TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex
Cited by: 23
Author(s): Nicole Merritt, Keith Garcia, Dushyandi Rajendran, Zhen‐Yuan Lin, Xiaomeng Zhang, Katrina A. Mitchell, Nicholas Borcherding, Colleen Fullenkamp, Michael S. Chimenti, Anne‐Claude Gingras, Kieran F. Harvey, Munir R. Tanas
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.63745

Perinatal granulopoiesis and risk of pediatric asthma
Cited by: 2
Author(s): Benjamin A. Turturice, Juliana Theorell, Mary Dawn Koenig, Lisa Tussing‐Humphreys, Diane R. Gold, Augusto A. Litonjua, Emily Oken, Sheryl L. Rifas–Shiman, David L. Perkins, Patricia W. Finn
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0231695

Genetic algorithm-based personalized models of human cardiac action potential
Cited by: 18
Author(s): Dmitrii Smirnov, Andrey Pikunov, Roman Syunyaev, Ruslan Deviatiiarov, Oleg Gusev, Kedar Aras, Anna Gams, Aaron C. Koppel, Igor R. Efimov
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.35788

A promoter interaction map for cardiovascular disease genetics
Cited by: 111
Author(s): Lindsey Montefiori, Débora R. Sobreira, Noboru Jo Sakabe, Ivy Aneas, Amelia C Joslin, Grace Hansen, Grazyna Bozek, Ivan P. Moskowitz, Elizabeth M. McNally, Marcelo A. Nóbrega
Software Mentions: 5
Published: over 6 years ago

10.3390/ijms22179470

Mammalian and Invertebrate Models as Complementary Tools for Gaining Mechanistic Insight on Muscle Responses to Spaceflight
Cited by: 13
Author(s): Thomas J. Cahill, Henry Cope, Joseph J. Bass, Eliah Overbey, Rachel Gilbert, Willian A. da Silveira, Amber M. Paul, Tejaswini Mishra, Raúl Herranz, Sigrid Reinsch, Sylvain V. Costes, Gary Hardiman, Nathaniel J. Szewczyk, Candice Tahimic
Software Mentions: 5
Published: about 3 years ago

10.1038/s41388-021-01940-0

Human cell transformation by combined lineage conversion and oncogene expression
Cited by: 10
Author(s): Biswajyoti Sahu, Päivi Pihlajamaa, Kaiyang Zhang, Kimmo Palin, Saija Ahonen, Alejandra Cervera, Ari Ristimäki, Lauri A. Aaltonen, Sampsa Hautaniemi, Jussi Taipale
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-019-6024-3

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods
Cited by: 14
Author(s): Polina Drozdova, Lorena Rivarola-Duarte, Daria Bedulina, Denis V. Axenov-Gribanov, S Schreiber, Anton Gurkov, Z. M. Shatilina, Kseniya Vereshchagina, Yulia Lubyaga, Ekaterina Madyarova, Christian Otto, Frank Jühling, Wibke Busch, Lena Jakob, Magnus Lucassen, Franz-Josef Sartoris, Jörg Hackermüller, Steve Hoffmann, Hans‐Otto Pörtner, Till Luckenbach, Maxim A. Timofeyev, Peter F. Stadler
Software Mentions: 5
Published: about 5 years ago

10.1038/s41388-021-02005-y

Intron retention-induced neoantigen load correlates with unfavorable prognosis in multiple myeloma
Cited by: 19
Author(s): Chuanpeng Dong, Annamaria Cesarano, Giuseppe Bombaci, Jill L. Reiter, Christina Y. Yu, Yue Wang, Zhaoyang Jiang, Mohammad Abu Zaid, Kun Huang, Xiongbin Lu, Brian A Walker, Fabiana Perna, Yunlong Liu
Software Mentions: 5
Published: about 3 years ago

10.3390/cells8101196

Genome-Wide Distribution of Nascent Transcripts in Sperm DNA, Products of a Late Wave of General Transcription
Cited by: 6
Author(s): Leila Kianmehr, Homayoun Khazali, Hassan Rajabi‐Maham, Ali Sharifi‐Zarchi, François Cuzin, Minoo Rassoulzadegan
Software Mentions: 5
Published: about 5 years ago

10.1128/mSystems.00550-20

A Comprehensive Coexpression Network Analysis in Vibrio cholerae
Cited by: 4
Author(s): Cory D. DuPai, Claus O. Wilke, Bryan William Davies
Software Mentions: 5
Published: about 4 years ago

10.1016/j.joca.2018.12.015

Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage
Cited by: 30
Author(s): Bola Ajekigbe, Kathleen Cheung, Yaobo Xu, Andrew Skelton, Andreas Panagiotopoulos, Jamie Soul, Timothy E. Hardingham, David J. Deehan, M.J. Barter, David A. Young
Software Mentions: 5
Published: over 5 years ago

10.1128/mBio.01165-19

A Central Small RNA Regulatory Circuit Controlling Bacterial Denitrification and N 2 O Emissions
Cited by: 12
Author(s): Hannah Gaimster, Claire L. Hews, Ryan D. Griffiths, Manuel J. Soriano-Laguna, Mark Alston, David J. Richardson, Andrew J. Gates, Gary Rowley
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-92838-0

Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta
Cited by: 4
Author(s): Gust Bilcke, Lore Van Craenenbroeck, Alexandre Castagna, Cristina Maria Osuna-Cruz, Klaas Vandepoele, Koen Sabbe, Lieven De Veylder, Wim Vyverman
Software Mentions: 5
Published: about 3 years ago

10.12688/f1000research.18276.2

Using equivalence class counts for fast and accurate testing of differential transcript usage
Cited by: 9
Author(s): Marek Cmero, N. Davidson, Alicia Oshlack
Software Mentions: 5
Published: over 5 years ago

10.3389/fncel.2020.00131

Loss of Arid1a Promotes Neuronal Survival Following Optic Nerve Injury
Cited by: 3
Author(s): Xue-Qi Peng, Shang-Kun Dai, Changping Li, Peipei Li, Zhimeng Wang, Heng Du, Zhao‐Qian Teng, Shuguang Yang, Chang‐Mei Liu
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2019.01386

Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection
Cited by: 17
Author(s): Thomas J. Hall, Douglas Vernimmen, John Andrew Browne, Michael P. Mullen, Stephen V. Gordon, David E. MacHugh, Alan M. O’Doherty
Software Mentions: 5
Published: almost 5 years ago

10.3390/ijms22031073

Machine Learning Analysis of Longevity-Associated Gene Expression Landscapes in Mammals
Cited by: 6
Author(s): Anton Kulaga, Eugen Ursu, Dmitri Toren, Vladyslava Tyshchenko, Rodrigo Guinea, Malvina Pushkova, Vadim E. Fraifeld, Robi Tăcutu
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-020-07228-z

Differential gene expression analysis reveals pathways important in early post-traumatic osteoarthritis in an equine model
Cited by: 6
Author(s): Annette M. McCoy, Ann M. Kemper, M. Boyce, M. P. Brown, Troy N. Trumble
Software Mentions: 5
Published: almost 4 years ago

10.3389/fimmu.2021.670309

Comparative Immunogenomics of Canine Natural Killer Cells as Immunotherapy Target
Cited by: 7
Author(s): Alicia A. Gingrich, Taylor Reiter, Sean J Judge, Daniel York, Mio Yanagisawa, Aryana Razmara, Ian R. Sturgill, Ugur Nur Basmaci, Rachel Brady, Kevin Stoffel, William J. Murphy, Robert B. Rebhun, C. Titus Brown, Robert J. Canter
Software Mentions: 5
Published: about 3 years ago

10.3389/fimmu.2021.645446

Antiretroviral Treatment-Induced Decrease in Immune Activation Contributes to Reduced Susceptibility to Tuberculosis in HIV-1/Mtb Co-infected Persons
Cited by: 4
Author(s): Katalin A. Wilkinson, Deborah Schneider-Luftman, Rachel Lai, Christopher Barrington, Nishtha Jhilmeet, David M. Lowe, Gavin Kelly, Robert J. Wilkinson
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-75128-z

Novel genomic targets of valosin-containing protein in protecting pathological cardiac hypertrophy
Cited by: 5
Author(s): Ning Zhou, Xin Chen, Jing Xi, Ben Ma, Christiana Leimena, Shaunrick Stoll, Gangjian Qin, Charles Wang, Hongyu Qiu
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-019-6444-0

The transcriptome of Pinus pinaster under Fusarium circinatum challenge
Cited by: 18
Author(s): Laura Hernandez‐Escribano, Erik A. Visser, Eugenia Iturritxa, Rosa Raposo, Sanushka Naidoo
Software Mentions: 5
Published: almost 5 years ago

10.3389/fpls.2018.01309

A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics
Cited by: 17
Author(s): Chuanmei Zhu, Jiani Yang, Mathew S. Box, Elizabeth A. Kellogg, Andrea L. Eveland
Software Mentions: 5
Published: about 6 years ago

10.1093/g3journal/jkaa055

Transcriptome analysis of Caenorhabditis elegans lacking heme peroxidase SKPO-1 reveals an altered response to Enterococcus faecalis
Cited by: 4
Author(s): Yi Liu, Daniel Martínez-Martínez, Clara L. Essmann, Melissa R. Cruz, Filipe Cabreiro, Danielle A. Garsin
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.celrep.2021.109105

Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins
Cited by: 24
Author(s): Joseph Hiatt, Devin A. Cavero, Michael McGregor, Weihao Zheng, Jonathan M. Budzik, Theodore L. Roth, Kelsey M. Haas, David Wu, Ujjwal Rathore, Anke Meyer-Franke, Mohamed S. Bouzidi, Eric Shifrut, Youjin Lee, Vigneshwari Easwar Kumar, Eric V. Dang, David E. Gordon, Jason A. Wojcechowskyj, Judd F. Hultquist, Krystal A. Fontaine, Satish K. Pillai, Jeffery S. Cox, Joel D. Ernst, Nevan J. Krogan, Alexander Marson
Software Mentions: 4
Published: over 3 years ago

10.3390/cancers12102844

Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples
Cited by: 6
Author(s): Susana Iraola-Guzmán, Anna Brunet-Vega, Cinta Pegueroles, Ester Saus, Hrant Hovhannisyan, Àlex Casalots, Carles Pericay, Toni Gabaldón
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.52621

FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences
Cited by: 78
Author(s): Raeann Goering, Laura I. Hudish, Bryan B. Guzman, Nisha Raj, Gary J. Bassell, Holger A. Russ, Daniel Domínguez, J. Matthew Taliaferro
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12040963

Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington’s Disease
Cited by: 14
Author(s): Müge Yalçin, Rukeia El-Athman, Koliane Ouk, Josef Priller, Angela Relógio
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-54782-y

Investigating the energy crisis in Alzheimer disease using transcriptome study
Cited by: 21
Author(s): S. Akila Parvathy Dharshini, Y-h. Taguchi, M. Michael Gromiha
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.66749

Murine muscle stem cell response to perturbations of the neuromuscular junction are attenuated with aging
Cited by: 11
Author(s): Jacqueline Larouche, Mahir Mohiuddin, Jeongmoon J. Choi, Peter Ulintz, Paula Fraczek, Kaitlyn Sabin, Sethuramasundaram Pitchiaya, Sarah J Kurpiers, Jesus A. Castor-Macias, Wenxuan Liu, Robert Louis Hastings, Lemuel A. Brown, James F. Markworth, Kanishka de Silva, Benjamin Levi, Sofía D. Merajver, Gregorio Valdez, Joe V. Chakkalakal, Young C. Jang, Susan V. Brooks, Carlos A. Aguilar
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0178532

Integrative genomic analyses for identification and prioritization of long non-coding RNAs associated with autism
Cited by: 21
Author(s): Brian Gudenas, Anand Srivastava, Liangjiang Wang
Software Mentions: 4
Published: over 7 years ago

10.1016/j.joca.2020.06.001

Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
Cited by: 18
Author(s): Antony K. Sorial, Ines M.J. Hofer, M. Tselepi, Kathleen Cheung, Eleanor Parker, David J. Deehan, S.J. Rice, John Loughlin
Software Mentions: 4
Published: about 4 years ago

10.3389/fbioe.2020.00035

Dynamic Alternative Splicing During Mouse Preimplantation Embryo Development
Cited by: 13
Author(s): Yongzhong Xing, Weihao Yang, Guoqing Liu, Xiangjun Cui, Hu Meng, Hongyu Zhao, Xingbo Zhao, Jun Li, Zhe Liu, Michael Q. Zhang, Liang Cai
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0240975

RNA sequencing of whole blood in dogs with primary immune-mediated hemolytic anemia (IMHA) reveals novel insights into disease pathogenesis
Cited by: 5
Author(s): Corie Borchert, Adam Herman, Megan Roth, Aimee C. Brooks, Steven G. Friedenberg
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0228514

Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events
Cited by: 12
Author(s): Benjamin Young, Xaymara M. Serrano, Stephanie M. Rosales, Margaret W. Miller, Dana E. Williams, Nikki Traylor-Knowles
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pmed.1002309

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis
Cited by: 231
Author(s): Alexandra Snyder, Tavi Nathanson, Samuel A. Funt, Arun Ahuja, Jacqueline L. Buros, Matthew D. Hellmann, Eliza Chang, Bülent Arman Aksoy, Hikmat Al‐Ahmadie, Erik Yusko, Marissa Vignali, Sharon Benzeno, Mariel Elena Boyd, Meredith Maisie Moran, Gopa Iyer, Harlan Robins, Elaine R. Mardis, Taha Merghoub, Jeff Hammerbacher, Jonathan E. Rosenberg, Dean F. Bajorin
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.671806

Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript Switching
Cited by: 6
Author(s): Danai Georgiadou, Souad Boussata, Remco Keijser, Dianta Janssen, Gijs B. Afink, Marie van Dijk
Software Mentions: 4
Published: over 3 years ago

10.1093/gbe/evab075

Transcriptomic Signatures of Ageing Vary in Solitary and Social Forms of an Orchid Bee
Cited by: 8
Author(s): Alice Séguret, Eckart Stolle, Fernando A. Fleites-Ayil, José Javier G. Quezada‐Euán, Klaus Hartfelder, Karen Meusemann, Mark C. Harrison, Antonella Soro, Robert J. Paxton
Software Mentions: 4
Published: over 3 years ago

10.3390/genes10100745

Differential Gene Expression in Articular Cartilage and Subchondral Bone of Neonatal and Adult Horses
Cited by: 4
Author(s): Ann M. Kemper, Jenny Drnevich, Molly E. McCue, Annette M. McCoy
Software Mentions: 4
Published: about 5 years ago

10.3389/fgene.2020.556418

Transcriptional Programs Underlying Cold Acclimation of Common Carp (Cyprinus carpio L.)
Cited by: 14
Author(s): Yong Long, Xixi Li, Fengyang Li, Guodong Ge, Ran Liu, Guangliang Song, Qing Li, Zhengxue Qiao
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.66417

Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19
Cited by: 56
Author(s): Courtney Tindle, MacKenzie Fuller, Ayden G. Fonseca, Sahar Taheri, Stella‐Rita Ibeawuchi, Nathan Beutler, Gajanan D. Katkar, Amanraj Claire, Vanessa Castillo, Moises Hernandez, Hana Russo, Jason Duran, Laura E. Crotty Alexander, Ann Tipps, Grace Lin, Patricia A. Thistlethwaite, Ranajoy Chattopadhyay, Thomas F. Rogers, Debashis Sahoo, Pradipta Ghosh, Soumita Das
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pbio.3000591

Yap suppresses T-cell function and infiltration in the tumor microenvironment
Cited by: 50
Author(s): Eleni Stampouloglou, Nan Cheng, Anthony Federico, Emily M. Slaby, Stefano Monti, Gregory L. Szeto, Xaralabos Varelas
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-96055-7

Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR
Cited by: 6
Author(s): Gilbert O. Silveira, Murilo Sena Amaral, Helena S. Coelho, Lucas F. Maciel, Adriana S. A. Pereira, Giovanna G. O. Olberg, Patrícia A. Miyasato, Eliana Nakano, Sérgio Verjovski-Almeida
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-42560-9

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats
Cited by: 22
Author(s): Diana D. Moreno-Santillán, Carlos Machaín-Williams, Georgina Hernández-Montes, Jorge Ortega
Software Mentions: 4
Published: over 5 years ago

10.1016/j.isci.2021.102361

NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data
Cited by: 17
Author(s): Eliah Overbey, Amanda Saravia-Butler, Zhe Zhang, Komal S. Rathi, Homer Fogle, Willian A. da Silveira, Richard Barker, Joseph J. Bass, Afshin Beheshti, Daniel C. Berrios, Elizabeth A. Blaber, Egle Cekanaviciute, Helio A. Costa, Laurence Davin, Kathleen M. Fisch, Samrawit Gebre, Matthew Geniza, Rachel Gilbert, Simon Gilroy, Gary Hardiman, Raúl Herranz, Yared H. Kidane, Colin Kruse, Michael Lee, Ted Liefeld, Norman Lewis, J. Tyson McDonald, Robert Meller, Tejaswini Mishra, Imara Y. Perera, Shayoni Ray, Sigrid Reinsch, Sara Brin Rosenthal, Michael Strong, Nathaniel J. Szewczyk, Candice Tahimic, Deanne Taylor, Joshua P. Vandenbrink, Alicia Villacampa, Silvio Weging, Chris Wolverton, Sarah E. Wyatt, Luis Zea, Sylvain V. Costes, Jonathan M. Galazka
Software Mentions: 4
Published: over 3 years ago

10.1111/tpj.14299

Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
Cited by: 46
Author(s): Xiaoming Wang, Siyuan Chen, Song Xue, Danni Liu, Peng Zhao, Yunze Lu, Yanbing Cheng, Zhenshan Liu, Xiaojun Nie, Weining Song, Qixin Sun, Shengbao Xu, Chuang Ma
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-90540-9

Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)
Cited by: 3
Author(s): Candace J. Grimes, Lene H. Petersen, Anja Schulze
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.68714

Deep learning detects cardiotoxicity in a high-content screen with induced pluripotent stem cell-derived cardiomyocytes
Cited by: 17
Author(s): Francis Grafton, Jaclyn J. Ho, Sara Ranjbarvaziri, Farshad Farshidfar, Anastasiia Budan, Stephanie Steltzer, Mahnaz Maddah, Kevin E. Loewke, Kristina Green, Snahel Patel, Tim Hoey, Mohammad A. Mandegar
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-89366-2

Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes
Cited by: 9
Author(s): Cecília Ártico Banho, Vincent Mérel, Thiago Y. Oliveira, Claudia M. A. Carareto, Cristina Vieira
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.6985

Simphony: simulating large-scale, rhythmic data
Cited by: 7
Author(s): Jordan M. Singer, Darwin Y. Fu, Jacob J. Hughey
Software Mentions: 4
Published: over 5 years ago

10.1038/s41380-020-00955-5

Temporal unsnarling of brain’s acute neuroinflammatory transcriptional profiles reveals panendothelitis as the earliest event preceding microgliosis
Cited by: 24
Author(s): Mahesh Chandra Kodali, Hao Chen, Francesca‐Fang Liao
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41380-018-0271-6

Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma
Cited by: 106
Author(s): Katharina Gapp, Gretchen van Steenwyk, Pierre-Luc Germain, Wayo Matsushima, Konrad L. M. Rudolph, Francesca Manuella, Martin Roszkowski, Grégoire Vernaz, Tanay Ghosh, Paweł Pelczar, Isabelle M. Mansuy, Eric A. Miska
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-41298-8

Regeneration associated transcriptional signature of retinal microglia and macrophages
Cited by: 54
Author(s): Diana Mitchell, Chi Sun, Samuel S. Hunter, Daniel D. New, Deborah L. Stenkamp
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.49178

Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell
Cited by: 107
Author(s): Eran Mick, Denis V. Titov, Owen S. Skinner, Rohit Sharma, Alexis A. Jourdain, Vamsi K. Mootha
Software Mentions: 4
Published: over 4 years ago

10.1038/srep45125

Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis
Cited by: 42
Author(s): Matthew D. MacManes, Suzanne H. Austin, Andrew S. Lang, April M. Booth, Victoria S. Farrar, Rebecca M. Calisi
Software Mentions: 4
Published: over 7 years ago

10.3390/microorganisms7090315

Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts
Cited by: 17
Author(s): Erik A. Visser, Jill L. Wegrzyn, Emma Theodora Steenkamp, Alexander Andrew Myburg, Sanushka Naidoo
Software Mentions: 4
Published: about 5 years ago

10.3389/fimmu.2017.01221

PI3Kδ Inhibition Enhances the Antitumor Fitness of Adoptively Transferred CD8+ T Cells
Cited by: 56
Author(s): Jacob S. Bowers, Kinga Majchrzak, Michelle H. Nelson, Bülent Arman Aksoy, Megan Wyatt, Aubrey S. Smith, Stefanie R. Bailey, Lillian R. Neal, Jeff Hammerbacher, Chrystal M. Paulos
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.43738

Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice
Cited by: 66
Author(s): Mina Kojima, Dirk G. de Rooij, David C. Page
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2019.01063

α7 Nicotinic Acetylcholine Receptor Signaling Modulates Ovine Fetal Brain Astrocytes Transcriptome in Response to Endotoxin
Cited by: 16
Author(s): Mingju Cao, James W. MacDonald, Hai L. Liu, Molly Weaver, Marina Farrel Cortês, Lucien Daniel Durosier, Patrick Burns, Gilles Fecteau, André Desrochers, Jay Schulkin, Marta C. Antonelli, Raphael Bernier, Michael O. Dorschner, Theo K. Bammler, Martin G. Frasch
Software Mentions: 4
Published: over 5 years ago

10.1534/g3.118.200810

Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression
Cited by: 13
Author(s): Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan Archibald, David Hume, Emily L. Clark
Software Mentions: 4
Published: almost 6 years ago

10.1186/s40168-019-0724-4

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight
Cited by: 65
Author(s): Peng Jiang, Stefan J. Green, George E. Chlipala, Fred W. Turek, Martha Hotz Vitaterna
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-76137-8

Evolution from adherent to suspension: systems biology of HEK293 cell line development
Cited by: 41
Author(s): Magdalena Malm, Rasool Saghaleyni, Magnus Lundqvist, Marco Giudici, Véronique Chotteau, Ray Field, Paul Varley, Diane Hatton, Luigi Grassi, Thomas Svensson, Jens Nielsen, Johan Rockberg
Software Mentions: 4
Published: about 4 years ago

10.1534/g3.119.400998

A Collection of Pre-mRNA Splicing Mutants in Arabidopsis thaliana
Cited by: 20
Author(s): Tohru Kanno, Peter Venhuizen, Ming‐Tsung Wu, Phebe Chiou, Chia-Liang Chang, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.60546

Acquisition of innate odor preference depends on spontaneous and experiential activities during critical period
Cited by: 13
Author(s): Qiang Qiu, Yunming Wu, Limei Ma, Wenjing Xu, Max Hills, Vivekanandan Ramalingam, Chong Yu
Software Mentions: 4
Published: over 3 years ago

10.3389/fnmol.2019.00241

A TBR1-K228E Mutation Induces Tbr1 Upregulation, Altered Cortical Distribution of Interneurons, Increased Inhibitory Synaptic Transmission, and Autistic-Like Behavioral Deficits in Mice
Cited by: 21
Author(s): Chaehyun Yook, Kyungdeok Kim, Doyoun Kim, Hyojin Kang, Sun-Gyun Kim, Eunjoon Kim, Soo Young Kim
Software Mentions: 4
Published: about 5 years ago

10.3390/ijms21249478

Toll-Like Receptor 7 Is Required for Lacrimal Gland Autoimmunity and Type 1 Diabetes Development in Male Nonobese Diabetic Mice
Cited by: 8
Author(s): Ivy L. Debreceni, Michael S. Chimenti, David Serreze, Aron M. Geurts, Yi-Guang Chen, Scott M. Lieberman
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms20102570

Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard
Cited by: 35
Author(s): Prarthana Shankar, Mitra C. Geier, Lisa Truong, Ryan McClure, Paritosh Pande, Katrina M. Waters, Robert L. Tanguay
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms20174094

Mice Exposed to Combined Chronic Low-Dose Irradiation and Modeled Microgravity Develop Long-Term Neurological Sequelae
Cited by: 18
Author(s): Eliah Overbey, Amber M. Paul, Willian A. da Silveira, Candice Tahimic, Sigrid Reinsch, Nathaniel J. Szewczyk, Seta Stanbouly, Charles Wang, Jonathan M. Galazka, Xiao Wen Mao
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-67432-5

Differential expression of polyamine biosynthetic pathways in skin lesions and in plasma reveals distinct profiles in diffuse cutaneous leishmaniasis
Cited by: 7
Author(s): Hayna Malta‐Santos, Jaqueline França‐Costa, Amanda Ferreira Macedo, Artur T. L. Queiroz, Kiyoshi F. Fukutani, Sandra Márcia Muxel, Ricardo Khouri, Johan Van Weyenbergh, Viviane Boaventura, Aldina Barral, Jackson Maurício Lopes Costa, Eny Iochevet Segal Floh, Bruno B. Andrade, Lucile Maria Floeter‐Winter, Valéria M. Borges
Software Mentions: 4
Published: over 4 years ago

10.1534/genetics.118.301515

PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana
Cited by: 17
Author(s): Tohru Kanno, Peter Venhuizen, Wen Teng, Wen-Dar Lin, Phebe Chiou, Maria Kalyna, A. J. M. Matzke, Marjori Matzke
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-021-03149-5

Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant
Cited by: 6
Author(s): Maya Khasin, Lois F. Bernhardson, Patrick M. O’Neill, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Deanna L. Funnell‐Harris
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.ppat.1009659

Sickle-trait hemoglobin reduces adhesion to both CD36 and EPCR by Plasmodium falciparum-infected erythrocytes
Cited by: 5
Author(s): Jens E. V. Petersen, Joseph W. Saelens, Elizabeth Freedman, Louise Turner, Thomas Lavstsen, Rick M. Fairhurst, Mahamadou Diakité, Steve M. Taylor
Software Mentions: 4
Published: over 3 years ago

10.1080/15476286.2020.1729594

LncRNAs in molluscan and mammalian stages of parasitic schistosomes are developmentally-regulated and coordinately expressed with protein-coding genes
Cited by: 13
Author(s): Hyung Chul Kim, Ahmad M. Khalil, Emmitt R. Jolly
Software Mentions: 4
Published: over 4 years ago

10.1186/s12870-020-2251-7

A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Cited by: 17
Author(s): Grant R. Cramer, Noé Cochetel, Ryan Ghan, Agnès Destrac-Irvine, Serge Delrot
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12870-021-02997-5

Low nitrogen availability inhibits the phosphorus starvation response in maize (Zea mays ssp. mays L.)
Cited by: 10
Author(s): J. Vladimir Torres-Rodríguez, M. Nancy Salazar-Vidal, Ricardo A. Chávez Montes, Julio A. Massange‐Sánchez, C. Stewart Gillmor, Ruairidh J. H. Sawers
Software Mentions: 4
Published: over 3 years ago

10.1098/rsos.181453

Behavioural and transcriptional changes in post-mating females of an egg parasitoid wasp species
Cited by: 19
Author(s): Pengcheng Liu, Dejun Hao
Software Mentions: 4
Published: almost 6 years ago

10.1172/jci.insight.145029

Nrf2 overexpression rescues the RPE in mouse models of retinitis pigmentosa
Cited by: 30
Author(s): David M. Wu, Xuke Ji, Maryna V. Ivanchenko, M. S. Chung, Mary E. Piper, Parimal Rana, Sean K. Wang, Y. Y. Xue, Emma R. West, Sophia R. Zhao, Hongbin Xu, Marcelo Cicconet, Wenjun Xiong, Constance L. Cepko
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13073-020-00787-6

Molecular correlates and therapeutic targets in T cell-inflamed versus non-T cell-inflamed tumors across cancer types
Cited by: 21
Author(s): Riyue Bao, Daniel Stapor, Jason J. Luke
Software Mentions: 4
Published: about 4 years ago

10.1242/dev.175265

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs
Cited by: 21
Author(s): Alexandra L. McCorkindale, Philipp Wahle, Irwin Jungreis, Peter Menzel, Chinmay Shukla, Rúben Lopes Pereira Abreu, Rafael A. Irizarry, Irmtraud M. Meyer, M Kellis, Robert P. Zinzen
Software Mentions: 4
Published: over 5 years ago

Projects: bioconductor: tximport

Papers Mentioning tximport 367