pypi: salmon | Projects | Ecosyste.ms: Papers

10.1038/s41421-021-00274-1

Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19
Cited by: 21
Author(s): Yun Tan, Wei Zhang, Zhaoqin Zhu, Na Qiao, Yun Ling, Mingquan Guo, Tong Yin, Hai Fang, Xiaoguang Xu, Gang Lu, Peipei Zhang, Shuangshuang Yang, Ziyu Fu, Dongguo Liang, Yinyin Xie, Ruihong Zhang, Lu Jiang, Shuting Yu, Jing Lu, Fang-Ying Jiang, Jian Chen, Chenlu Xiao, Shengyue Wang, Shuo Chen, Xiu‐Wu Bian, Hongzhou Lu, Feng Liu, Sai‐Juan Chen
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.59073

Re-expression of SMARCA4/BRG1 in small cell carcinoma of ovary, hypercalcemic type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism
Cited by: 15
Author(s): Krystal A. Orlando, Amber K Douglas, Aierken Abudu, Yemin Wang, Basile Tessier‐Cloutier, Weiping Su, Alec Peters, Larry S. Sherman, Regan P. Moore, Vinh Nguyen, Gian Luca Negri, Shane Colborne, Gregg B. Morin, Friedrich Kommoss, Jessica D. Lang, William P.D. Hendricks, Elizabeth A. Raupach, Patrick Pirrotte, David G. Huntsman, Jeffrey M. Trent, Joel S. Parker, Jesse R. Raab, Bernard E. Weissman
Software Mentions: 9
Published: about 4 years ago

10.1186/s13059-021-02363-6

Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Cited by: 24
Author(s): Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas, Soren Charmsaz, Nicole Groß, Skylar Woolman, Kayla Cruz, Rebecca M Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan, Elizabeth D. Thompson, Elizabeth M. Jaffee, Elana J. Fertig
Software Mentions: 9
Published: over 3 years ago

10.1186/s40168-019-0684-8

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Cited by: 38
Author(s): Luís Pedro Coelho, Renato Alves, Paulo P. Monteiro, Jaime Huerta-Cepas, Ana T. Freitas, Peer Bork
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: almost 7 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: 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: about 6 years ago

10.3390/ijms21051720

Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana
Cited by: 27
Author(s): Stephanie Schaarschmidt, Axel Fischer, Ellen Zuther, Dirk K. Hincha
Software Mentions: 5
Published: almost 5 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: over 5 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

10.7554/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

10.15252/msb.20188591

Widespread inter‐individual gene expression variability in <i>Arabidopsis thaliana</i>
Cited by: 48
Author(s): Sandra Cortijo, Zeynep Gökçe Gayretli Aydın, Sebastian E. Ahnert, James Locke
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-80145-z

Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes
Cited by: 10
Author(s): Michelle M. Stein, Mitchell Conery, Kevin M. Magnaye, Selene M. Clay, Christine Billstrand, Raluca Nicolae, Katherine A. Naughton, Carole Ober, Emma E. Thompson
Software Mentions: 4
Published: almost 4 years ago

10.3390/ijms21041337

Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus
Cited by: 29
Author(s): Weida Lin, Yueling Li, Qiuwei Lu, Hongfei Lü, Junmin Li
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0157022

SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data
Cited by: 660
Author(s): Hugo Varet, Loraine Brillet-Guéguen, Jean‐Yves Coppée, Marie‐Agnès Dillies
Software Mentions: 4
Published: over 8 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: about 4 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

10.1186/s12864-020-6522-3

Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments
Cited by: 13
Author(s): Federico Vita, Beatrice Giuntoli, Edoardo Bertolini, Cosimo Taiti, Elettra Marone, Chiara D’Ambrosio, Emanuela Trovato, Danilo Sciarrone, Mariosimone Zoccali, Raffaella Balestrini, Andrea Scaloni, Luigi Mondello, Stefano Mancuso, Massimo Alessio, Amedeo Alpi
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-97257-9

Microglial ASD-related genes are involved in oligodendrocyte differentiation
Cited by: 4
Author(s): Yuta Takanezawa, Shihori Tanabe, Daiki Kato, Rie Ozeki, Masayo Komoda, Tatsunori Suzuki, Hiroko Baba, Rieko Muramatsu
Software Mentions: 3
Published: over 3 years ago

10.3389/fendo.2021.616339

Case Report: Temozolomide Treatment of Refractory Prolactinoma Resistant to Dopamine Agonists
Cited by: 9
Author(s): Hao Tang, Yijun Cheng, Jinyan Huang, Jianfeng Li, Benyan Zhang, Zhe Wu
Software Mentions: 3
Published: almost 4 years ago

10.3390/ijms22073767

Characterization of Type I Interferon-Associated Chemokines and Cytokines in Lacrimal Glands of Nonobese Diabetic Mice
Cited by: 5
Author(s): Merri-Grace Allred, Michael S. Chimenti, Ashley E. Ciecko, Yi-Guang Chen, Scott M. Lieberman
Software Mentions: 3
Published: over 3 years ago

10.1155/2019/7976382

High Concentration of Low-Density Lipoprotein Results in Disturbances in Mitochondrial Transcription and Functionality in Endothelial Cells
Cited by: 8
Author(s): Stefanie Gonnissen, Johannes Ptok, Christine Goy, Kirsten Jander, Philipp Jakobs, Olaf Eckermann, Wolfgang Kaisers, Florian von Ameln, Jörg Timm, Niloofar Ale‐Agha, Judith Haendeler, Heiner Schaal, Joachim Altschmied
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-020-01606-7

Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex
Cited by: 2
Author(s): Nicole L. Garrison, Michael S. Brewer, Jason E. Bond
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1009485

Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA
Cited by: 28
Author(s): Heejin Choi, Zhengpin Wang, Jurrien Dean
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0239730

Global gene expression profile under low-temperature conditions in the brain of the grass carp (Ctenopharyngodon idellus)
Cited by: 5
Author(s): Minjun Shi, Qiangxiang Zhang, Yongming Li, Wanting Zhang, Lanjie Liao, Yingyin Cheng, Yanxin Jiang, Xiaoli Huang, You Duan, L. Xia, Weidong Ye, Yaping Wang, Xiao-Qin Xia
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0247227

Transcriptome and metabolome analysis of crGART, a novel cell model of de novo purine synthesis deficiency: Alterations in CD36 expression and activity
Cited by: 2
Author(s): Randall C. Mazzarino, Veronika Barešová, Marie Zikánová, Nathan Duval, Terry G. Wilkinson, David Patterson, Guido N. Vacano
Software Mentions: 2
Published: over 3 years ago

10.1038/s42003-021-02062-9

A synthetic RNA editing factor edits its target site in chloroplasts and bacteria
Cited by: 21
Author(s): Santana Royan, Bernard Gutmann, Catherine Colas des Francs‐Small, Suvi Honkanen, J.W. Schmidberger, Ashley Soet, Yueming K. Sun, Lilian Vincis Pereira Sanglard, Charles S. Bond, Ian Small
Software Mentions: 2
Published: over 3 years ago

10.3389/fonc.2021.635237

A Case Series of Metastatic Metaplastic Breast Carcinoma Treated With Anti-PD-1 Therapy
Cited by: 14
Author(s): Isaac Kim, Venkatesh Rajamanickam, Brady Bernard, Brie Chun, Yaping Wu, Maritza Martel, Zhaoyu Sun, William L. Redmond, Katherine Sanchez, Reva Basho, Heather L. McArthur, David B. Page
Software Mentions: 2
Published: over 3 years ago

10.3390/genes12050692

Nanopore Sequencing and Hi-C Based De Novo Assembly of Trachidermus fasciatus Genome
Cited by: 0
Author(s): Gangcai Xie, Xu Zhang, Feng Lv, Mengmeng Sang, Hairong Hu, Jinqiu Wang, Dong Liu
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-021-83748-2

Thermal reaction norms of key metabolic enzymes reflect divergent physiological and behavioral adaptations of closely related amphipod species
Cited by: 7
Author(s): Lena Jakob, Kseniya Vereshchagina, Anette Tillmann, Lorena Rivarola-Duarte, Denis V. Axenov-Gribanov, Daria Bedulina, Anton Gurkov, Polina Drozdova, Maxim A. Timofeyev, Peter F. Stadler, Till Luckenbach, Hans‐Otto Pörtner, Franz-Josef Sartoris, Magnus Lucassen
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.52976

Selective egg cell polyspermy bypasses the triploid block
Cited by: 15
Author(s): Yanbo Mao, Alexander Gabel, Thomas Nakel, Prisca Viehöver, Thomas Baum, Dawit G. Tekleyohans, Dieu Vo, Ivo Große, Rita Groß‐Hardt
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.45396

Translation affects mRNA stability in a codon-dependent manner in human cells
Cited by: 149
Author(s): Qiushuang Wu, Santiago Gerardo Medina, Gopal Kushawah, Michelle Lynn DeVore, Luciana Andrea Castellano, Jacqelyn M. Hand, Matthew Wright, Ariel Bazzini
Software Mentions: 2
Published: over 5 years ago

10.3390/antiox10091427

Selenoprotein T Protects Endothelial Cells against Lipopolysaccharide-Induced Activation and Apoptosis
Cited by: 2
Author(s): Dennis Merk, Johannes Ptok, Philipp Jakobs, Florian von Ameln, Jan Greulich, Pia Kluge, Kathrin Semperowitsch, Olaf Eckermann, Heiner Schaal, Niloofar Ale‐Agha, Joachim Altschmied, Judith Haendeler
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0204045

Versican is differentially regulated in the adventitial and medial layers of human vein grafts
Cited by: 5
Author(s): Richard D. Kenagy, Shinsuke Kikuchi, Steve P. Evanko, Matthijs S. Ruiter, Marco Piola, Alban Longchamp, Maurizio Pesce, Monica Soncini, Sébastien Déglise, Gianfranco Beniamino Fiore, Jacques-Antoine Haefliger, Tannin A. Schmidt, Mark W. Majesky, Michael Sobel, Thomas N. Wight
Software Mentions: 1
Published: about 6 years ago

10.1186/s12915-020-00846-9

LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data
Cited by: 8
Author(s): Benedict Hew, Qiao Wen Tan, Wooi-Boon Goh, Jonathan Wei Xiong Ng, Marek Mutwil
Software Mentions: 1
Published: over 4 years ago

10.1038/s41389-021-00349-4

IL-6 promotes drug resistance through formation of polyploid giant cancer cells and stromal fibroblast reprogramming
Cited by: 25
Author(s): Na Niu, Jun Yao, Robert C. Bast, Anil K. Sood, Jinsong Liu
Software Mentions: 1
Published: about 3 years ago

Ecosyste.ms: Papers

Projects: pypi: salmon

Papers Mentioning salmon 36