10.3389/fimmu.2020.588411

Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains
Cited by: 6
Author(s): Elisa Crisci, Marco Moroldo, Thien‐Phong Vu Manh, Ammara Mohammad, Laurent Jourdren, Céline Urien, Edwige Bouguyon, Elise Bordet, Claudia Bevilacqua, Mickaël Bourge, Jérémy Pezant, Alexis Pléau, Olivier Boulesteix, Isabelle Schwartz, Nicolas Bertho, Elisabetta Giuffra
Software Mentions: 7
Published: almost 6 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

10.1186/s13059-021-02321-2

Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach
Cited by: 23
Author(s): Oriana Genolet, Anna A. Monaco, Ilona Dunkel, Michael Boettcher, Edda G. Schulz
Software Mentions: 7
Published: over 5 years ago

10.1186/s13195-020-00654-x

Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through RNA sequencing analysis
Cited by: 44
Author(s): Daichi Shigemizu, Tomohisa Mori, Shintaro Akiyama, Sayuri Higaki, Hiroshi Watanabe, Takashi Sakurai, Shumpei Niida, Kouichi Ozaki
Software Mentions: 7
Published: over 6 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

10.1038/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

10.1186/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

10.1186/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

10.1186/1472-6807-13-2

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

10.1371/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/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

10.3389/fimmu.2021.665312

An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells
Cited by: 8
Author(s): James Davies, Andrés F. Vallejo, Sofía Sirvent, Gemma Porter, Kalum Clayton, Yamkela Qumbelo, Patrick S. Stumpf, Jonathan West, Clive M. Gray, Nyaradzo T. L. Chigorimbo‐Murefu, Ben D. MacArthur, Marta E. Polak
Software Mentions: 7
Published: over 5 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

10.1186/s12864-016-3300-3

Assessing characteristics of RNA amplification methods for single cell RNA sequencing
Cited by: 32
Author(s): Hannah Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian–Bing Fan, Stephen Fisher, Jennifer Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin, Rui Li, William J. Mack, Sean McGroty, Joseph Nguyen, Neeraj Salathia, Jamie Shallcross, Tade Souaiaia, Jennifer M. Spaethling, Christopher Walker, Jinhui Wang, Kai Wang, Wei Wang, André Wildberg, Lina Zheng, Robert H. Chow, James Eberwine, James A. Knowles, Kun Zhang, Junhyong Kim
Software Mentions: 7
Published: almost 10 years ago

10.1371/journal.pbio.3000988

The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures
Cited by: 9
Author(s): Hiroyuki Mori, Colleen E. Dugan, Akira Nishii, Ameena Benchamana, Ziru Li, Thomas S. Cadenhead, Arun K. Das, Charles R. Evans, Katherine A. Overmyer, Steven M. Romanelli, Sydney K. Peterson, Devika P. Bagchi, Callie A.S. Corsa, Julie Hardij, Brian S. Learman, Mahmoud El Azzouny, Joshua J. Coon, Ken Inoki, Ormond A. MacDougald
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: almost 6 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

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: almost 6 years ago

10.3389/fimmu.2018.01553

Single Cell RNA Sequencing of Rare Immune Cell Populations
Cited by: 88
Author(s): Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I. Croucher, Tri Giang Phan
Software Mentions: 7
Published: over 8 years ago

10.1186/s13059-020-02156-3

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Cited by: 42
Author(s): Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne, Hendrik Marks, Hendrik G. Stunnenberg, Wout Megchelenbrink
Software Mentions: 7
Published: about 6 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

10.1186/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

10.15252/msb.20167507

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation
Cited by: 43
Author(s): Margaux Michel, Carina Demel, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur, Patrick Cramer
Software Mentions: 7
Published: over 9 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

10.1038/s41598-017-13397-x

The effect of insecticide synergist treatment on genome-wide gene expression in a polyphagous pest
Cited by: 28
Author(s): Simon Snoeck, Robert Greenhalgh, Luc Tirry, Richard M. Clark, Thomas Van Leeuwen, Wannes Dermauw
Software Mentions: 7
Published: about 9 years ago

10.3389/fimmu.2020.578505

Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life
Cited by: 18
Author(s): Tue Bjerg Bennike, Benoit Fatou, Asimenia Angelidou, Joann Diray‐Arce, Reza Falsafi, Rebecca Ford, Erin E. Gill, Simon D. van Haren, Olubukola T. Idoko, Ahwon Lee, Rym Ben‐Othman, William Pomat, Casey P. Shannon, Kinga K. Smolen, Scott J. Tebbutt, Al Ozonoff, Peter Richmond, Anita H. J. van den Biggelaar, Robert E. W. Hancock, Beate Kampmann, Tobias R. Kollmann, Ofer Levy, Hanno Steen
Software Mentions: 7
Published: about 6 years ago

10.1186/s12967-021-02936-w

TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Cited by: 114
Author(s): Yingdong Zhao, Ming-Chung Li, Mariam M. Konaté, Li Chen, Biswajit Das, Chris Karlovich, P. Mickey Williams, Yvonne A. Evrard, James H. Doroshow, Lisa M. McShane
Software Mentions: 7
Published: over 5 years ago

10.1016/j.isci.2021.102870

Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance
Cited by: 14
Author(s): Katharina Gapp, Guillermo E. Parada, Fridolin Groß, Alberto Corcoba, Jasmine Kaur, Evelyn Grau, Martin Hemberg, Johannes Bohacek, Eric A. Miska
Software Mentions: 7
Published: about 5 years ago

10.3389/fimmu.2020.596514

Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic Salmon
Cited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13059-020-02087-z

DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance
Cited by: 34
Author(s): Flora D’Anna, Laurien Van Dyck, Jieyi Xiong, Hui Zhao, Rebecca Berrens, Junbin Qian, Paweł Bieniasz-Krzywiec, Vikas Chandra, Luc Schoonjans, Jason Matthews, Jonathan De Smedt, Liesbeth Minnoye, Ricardo Amorim, Sepideh Khorasanizadeh, Qian Yu, Liyun Zhao, Marie De Borre, Savvas N. Savvides, M. Celeste Simon, Peter Carmeliet, Wolf Reik, Fraydoon Rastinejad, Massimiliano Mazzone, Bernard Thienpont, Diether Lambrechts
Software Mentions: 7
Published: about 6 years ago

10.1186/s13073-019-0657-3

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases
Cited by: 67
Author(s): Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Àlex Arenas, B. Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan‐Erik Karlsson, Mattias Köpsén, Eun Jung Lee, Antonio Lentini, Xinxiu Li, Mattias Magnusson, David Martínez-Enguita, Andreas Matussek, Colm E. Nestor, Samuel Schäfer, Oliver Seifert, Ceylan Sonmez, Henrik Stjernman, Andreas Tjärnberg, Simon Wu, Karin Åkesson, Alexander K Shalek, Margaretha Stenmarker, Huan Zhang, Mika Gustafsson, Mikael Benson
Software Mentions: 7
Published: about 7 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

10.1016/j.molcel.2021.03.013

Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression
Cited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: over 5 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

10.1002/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

10.1186/1471-2105-16-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

10.1016/j.molcel.2019.01.017

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection
Cited by: 122
Author(s): Manuel García-Moreno, Marko Noerenberg, Shuai Ni, Aino I Järvelin, Esther González-Almela, Caroline E. Lenz, Marcel Bach-Pagés, Victoria Cox, Rosario Avolio, Thomas W. Davis, Svenja Hester, Thibault J.M. Sohier, Bingnan Li, Gregory Heikel, Gracjan Michlewski, Miguel Á. Sanz, Luís Carrasco, Emiliano P. Ricci, Vicent Pelechano, Ilan Davis, Bernd Fischer, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 7
Published: over 7 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

10.7554/eLife.55794

Intra-species differences in population size shape life history and genome evolution
Cited by: 31
Author(s): David Willemsen, Rongfeng Cui, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 7
Published: about 6 years ago

10.3389/fmicb.2021.631889

DWV Infection in vitro Using Honey Bee Pupal Tissue
Cited by: 3
Author(s): Yunfei Wu, Xuye Yuan, Jing Li, Tatsuhiko Kadowaki
Software Mentions: 7
Published: over 5 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

10.3389/fimmu.2021.568729

Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid
Cited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.49658

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Cited by: 278
Author(s): Matthew T Parker, Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D Gould, Anthony Hall, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 7
Published: almost 7 years ago

10.1093/molbev/msz154

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

10.1038/s41419-021-04067-y

Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4
Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: about 5 years ago

10.1002/mc.23147

Loss of myeloid‐specific lamin A/C drives lung metastasis through Gfi‐1 and C/EBPε‐mediated granulocytic differentiation
Cited by: 3
Author(s): Hiroki Ishii, Woo‐Yong Park, Jae-Young So, Skyler Kuhn, Vishal N. Kopardé, Yanli Pang, Tim F. Greten, M. Christine Hollander, Li Yang
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0201830

Exposure to a firefighting overhaul environment without respiratory protection increases immune dysregulation and lung disease risk
Cited by: 14
Author(s): Stephen J. Gainey, Gavin P. Horn, Albert E. Towers, Maci L. Oelschlager, Vincent L. Tir, Jenny Drnevich, Kenneth W. Fent, Stephen Kerber, Denise L. Smith, Gregory G. Freund
Software Mentions: 7
Published: about 8 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

10.1002/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/s12915-021-01062-9

Exposure to ethanol leads to midfacial hypoplasia in a zebrafish model of FASD via indirect interactions with the Shh pathway
Cited by: 12
Author(s): Alfire Sidik, Groves Dixon, Desirè M. Buckley, Hannah G. Kirby, Suwan Sun, Johann K. Eberhart
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

10.1186/s12864-021-07509-1

Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer’s disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis
Cited by: 7
Author(s): Yang Dong, Morgan Newman, Stephen Pederson, Karissa Barthelson, Nhi Hin, Michael Lardelli
Software Mentions: 7
Published: over 5 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

10.3390/microorganisms8101528

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria
Cited by: 14
Author(s): Mathilde Lebas, Peggy Garault, Daniel Carrillo, Francisco M. Codoñer, Muriel Derrien
Software Mentions: 7
Published: about 6 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

10.1038/s41598-019-52584-w

Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data
Cited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0173115

Altered regulation and expression of genes by BET family of proteins in COPD patients
Cited by: 11
Author(s): Rajneesh Malhotra, Nisha Kurian, Xin Zhou, Fang Jiang, Susan J. Monkley, Amy DeMicco, Ib Groth Clausen, Göran Dellgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg, Elisabeth Israelsson, Graham Belfield, Outi Vaarala
Software Mentions: 7
Published: over 9 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

10.1111/1751-7915.13634

Soil microbiota influences clubroot disease by modulating <i>Plasmodiophora brassicae</i> and <i>Brassica napus</i> 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/s12870-020-02808-3

Integrated Transcriptomic and Metabolomic analysis reveals a transcriptional regulation network for the biosynthesis of carotenoids and flavonoids in ‘Cara cara’ navel Orange
Cited by: 18
Author(s): Haipeng Zhang, Jiajing Chen, Zhaoxin Peng, Meiyan Shi, Xiao Liu, Wen Huang, Youwu Jiang, Yunjiang Cheng, Juan Xu, Hongyan Zhang
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-017-05927-4

Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity
Cited by: 35
Author(s): Handan Melike Dönertaş, Hamit İzgi, Altuğ Kamacıoğlu, Zhisong He, Philipp Khaitovich, Mehmet Somel
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-017-05377-y

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes
Cited by: 33
Author(s): Zupeng Wang, Yifei Liu, Li Li, Dawei Li, Qiong Zhang, Yangtao Guo, Shuaibin Wang, Caihong Zhong, Hongwen Huang
Software Mentions: 7
Published: over 9 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

10.1186/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

10.1016/j.molcel.2020.01.007

Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation
Cited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: over 6 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

10.3390/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

10.7554/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

10.7554/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

10.3390/genes11040400

Combining Experimental Evolution and Genomics to Understand How Seed Beetles Adapt to a Marginal Host Plant
Cited by: 7
Author(s): Alexandre Rêgo, Samridhi Chaturvedi, Amy L. Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Software Mentions: 7
Published: over 6 years ago

10.1002/jcsm.12665

Myogenesis modelled by human pluripotent stem cells: a multi‐omic study of Duchenne myopathy early onset
Cited by: 28
Author(s): Virginie Mournetas, Emmanuelle Massouridès, Jean-Baptiste Dupont, Étienne Kornobis, Hélène Polveche, Margot Jarrige, Alan R L Dorval, Maxime R. F. Gosselin, Antigoni Manousopoulou, Spiros D. Garbis, Dariusz C. Górecki, Christian Pinset
Software Mentions: 7
Published: over 5 years ago

10.3390/ijms221910451

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance
Cited by: 1
Author(s): Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka, Ellen Zuther
Software Mentions: 7
Published: about 5 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

10.7554/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

10.1371/journal.ppat.1009130

Infection of human Nasal Epithelial Cells with SARS-CoV-2 and a 382-nt deletion isolate lacking ORF8 reveals similar viral kinetics and host transcriptional profiles
Cited by: 90
Author(s): Akshamal M Gamage, Kai Sen Tan, Wharton Chan, Jing Liu, Chee Wah Tan, Yew Kwang Ong, Mark Thong, Anand Kumar Andiappan, Danielle E. Anderson, De Yun Wang, Lin‐Fa Wang
Software Mentions: 7
Published: almost 6 years ago

10.3389/fcimb.2021.733619

Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures
Cited by: 8
Author(s): Elizabeth H. Byrne, M Fărcăşanu, Seth M. Bloom, Nondumiso Xulu, Jiawu Xu, Barry L. Hykes, Nomfuneko A. Mafunda, Matthew R. Hayward, Mary Dong, Krista Dong, Thandeka Gumbi, Fransisca Xolisile Ceasar, Nasreen Ismail, Thumbi Ndung’u, Christina Gosmann, Musie Ghebremichael, Scott A. Handley, Caroline Mitchell, Alexandra Chloé Villani, Douglas S. Kwon
Software Mentions: 7
Published: about 5 years ago

10.3389/fmolb.2020.565530

Cross-Sectional Transcriptional Analysis of the Aging Murine Heart
Cited by: 4
Author(s): Matthew Greenig, Andrew Melville, Derek Huntley, Mark Isalan, Michał Mielcarek
Software Mentions: 7
Published: about 6 years ago

10.1534/g3.114.011759

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: about 12 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the <i>Vespula</i> 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

10.1534/g3.119.0011

Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode <i>Auanema rhodensis</i>
Cited by: 31
Author(s): Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, André Pires-daSilva
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

10.7554/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

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: over 5 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

10.7554/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

10.3389/fonc.2019.00523

Comprehensive Gene Expression Analysis in NMIBC Using RNA-seq Reveals New Therapy Strategies
Cited by: 11
Author(s): Xiaoliang Chen, Fuquan Jiang, Jia Chen, Ming Liu, Yong-Hao Nan, Licheng Qu, Qingkuo Kong, Fangfang Hou, Wenshan Luo, Wanli Na, Xin Jin, Jiufeng Tan
Software Mentions: 7
Published: over 7 years ago

10.3389/fcell.2021.702046

Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast
Cited by: 17
Author(s): Robert Morey, Omar Farah, Sampada Kallol, Daniela F. Requena, Morgan Meads, Matteo Moretto-Zita, Francesca Soncin, Louise C. Laurent, Mana M. Parast
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2021.684002

Regulation of Long Non-coding RNA KCNQ1OT1 Network in Colorectal Cancer Immunity
Cited by: 5
Author(s): Junjie Liu, Wei Lv, Shuling Li, Jingwen Deng
Software Mentions: 7
Published: about 5 years ago

10.3390/genes11091107

Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina
Cited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 10 years ago

10.3390/genes11101165

OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
Cited by: 21
Author(s): Rui Li, Kai Hu, Haibo Liu, Michael R. Green, Lihua Julie Zhu
Software Mentions: 7
Published: about 6 years ago

10.1093/g3journal/jkab255

Improved draft reference genome for the Glassy-winged Sharpshooter (<i>Homalodisca vitripennis</i>), a vector for Pierce’s disease
Cited by: 8
Author(s): Cassandra L. Ettinger, Frank J. Byrne, Matthew A. Collin, Derreck Carter-House, Linda L. Walling, Peter W. Atkinson, Rick A Redak, Jason E. Stajich
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

10.1093/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

10.1186/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

10.1371/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

10.3390/cancers12061453

DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage
Cited by: 16
Author(s): Jamal Elhasnaoui, Valentina Miano, Giulio Ferrero, Elena Doria, Antonette E. Leon, Aline S C Fabrício, Laura Annaratone, Isabella Castellano, Anna Sapino, Michele De Bortoli
Software Mentions: 7
Published: over 6 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

10.1038/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

10.1038/s41597-021-00809-x

A multi-center cross-platform single-cell RNA sequencing reference dataset
Cited by: 14
Author(s): Xin Chen, Zujun Yang, Wanqiu Chen, Yongmei Zhao, Andrew Farmer, Bao Tran, Vyacheslav Furtak, Malcolm Moos, Wenming Xiao, Charles Wang
Software Mentions: 7
Published: over 5 years ago