cran: STAR | Projects | Ecosyste.ms: Papers

10.1016/j.cell.2021.03.062

Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: over 3 years ago

10.7150/ijbs.45693

Cancer stem cell property and gene signature in bone-metastatic Breast Cancer cells
Cited by: 7
Author(s): An Luo, Yue Xu, Shujun Li, Jinxia Bao, Jianrong Lu, Nan Ding, Qian Zhao, Yuting Fu, Fei Liu, William C. Cho, Xunbin Wei, Haiyun Wang, Zuoren Yu
Software Mentions: 5
Published: almost 5 years ago

10.3390/cancers12010037

Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 158
Author(s): Magdalena Niemira, François Collin, Anna Szałkowska, Agnieszka Bielska, Karolina Chwiałkowska, Joanna Reszeć, Jacek Nikliński, Mirosław Kwaśniewski, Adam Krętowski
Software Mentions: 5
Published: almost 5 years ago

10.12688/wellcomeopenres.14735.2

Mapping targets for small nucleolar RNAs in yeast
Cited by: 16
Author(s): Tatiana Dudnakova, Hywel Dunn-Davies, Rosie Peters, David Tollervey
Software Mentions: 5
Published: about 6 years ago

10.1038/s41396-020-0606-6

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava
Cited by: 12
Author(s): Romain Savary, Cindy Dupuis, Frédéric G. Masclaux, Ivan D. Mateus, Edward C. Rojas, Ian R. Sanders
Software Mentions: 5
Published: almost 5 years ago

10.1093/hmg/ddaa140

Motor neuron translatome reveals deregulation of SYNGR4 and PLEKHB1 in mutant TDP-43 amyotrophic lateral sclerosis models
Cited by: 13
Author(s): Rita F Marques, Jan Broder Engler, Katrin Küchler, Ross A. Jones, Thomas Lingner, Gabriela Salinas, Thomas H. Gillingwater, Manuel A. Friese, Kent E. Duncan
Software Mentions: 5
Published: over 4 years ago

10.1002/evl3.129

Methylation and gene expression differences between reproductive and sterile bumblebee workers
Cited by: 48
Author(s): Hollie Marshall, Zoë N. Lonsdale, Eamonn B. Mallon
Software Mentions: 5
Published: about 5 years ago

10.3389/fonc.2021.615234

Combined Analysis of RNA Sequence and Microarray Data Reveals a Competing Endogenous RNA Network as Novel Prognostic Markers in Malignant Pleural Mesothelioma
Cited by: 5
Author(s): Weicheng Duan, Kang Wang, Yijie Duan, Xiuyi Chen, Xufeng Chu, Ping Hu, Bo Xiong
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-02048-6

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Cited by: 289
Author(s): Elena Denisenko, Belinda Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, C Olivier, Rebecca K. Simmons, Ryan Lister, Alistair R.R. Forrest
Software Mentions: 5
Published: over 4 years ago

10.1038/s41389-020-0224-1

Desmoplastic small round cell tumor is dependent on the EWS-WT1 transcription factor
Cited by: 24
Author(s): Jenna M. Gedminas, Maggie H. Chassé, Mitchell McBrairty, Ian Beddows, Susan M. Kitchen-Goosen, Patrick J. Grohar
Software Mentions: 5
Published: over 4 years ago

10.1186/s13045-020-01005-x

RNA sequencing: new technologies and applications in cancer research
Cited by: 187
Author(s): Mingye Hong, Shuangping Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu‐Juan Xie, Zhilong Xiao, Hua Zhang
Software Mentions: 5
Published: almost 4 years ago

10.3390/genes12081291

Regional Specific Differentiation of Integumentary Organs: Regulation of Gene Clusters within the Avian Epidermal Differentiation Complex and Impacts of SATB2 Overexpression
Cited by: 3
Author(s): Gee-Way Lin, Yung-Chih Lai, Ya-Chen Liang, Randall B. Widelitz, Ping Wu, Cheng‐Ming Chuong
Software Mentions: 5
Published: over 3 years ago

10.1186/s13567-021-00972-4

Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis
Cited by: 8
Author(s): Hesham A. Ali, Shavahn C. Loux, Laura Kennedy, Kirsten E. Scoggin, Pouya Dini, Carleigh E. Fedorka, Theodore S. Kalbfleisch, A. Esteller-Vico, David W. Horohov, Erdal Erol, Craig N. Carter, Jon J. Smith, Barry A. Ball
Software Mentions: 5
Published: over 3 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/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/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: about 7 years ago

10.1126/sciadv.abd7819

High-resolution 3D imaging uncovers organ-specific vascular control of tissue aging
Cited by: 54
Author(s): Junyu Chen, Unnikrishnan Sivan, Sin Lih Tan, Luciana Lippo, Jessica De Angelis, Rossella Labella, Amit Singh, Alexandros Chatzis, Stanley Cheuk, Mino Medhghalchi, Jesús Gil, Georg A. Holländer, Brian D. Marsden, R. J. P. Williams, Saravana K. Ramasamy, Anjali P. Kusumbe
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.4619

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs
Cited by: 6
Author(s): Tianle Chao, Zhibin Ji, Lei Hou, Jin Wang, Chunlan Zhang, Guizhi Wang
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-019-1922-x

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Cited by: 31
Author(s): Zilu Zhou, Baocheng Xu, Andy J. Minn, Nancy R. Zhang
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-021-86002-x

Comprehensive transcriptomic analysis of COVID-19 blood, lung, and airway
Cited by: 102
Author(s): Andrea R. Daamen, Prathyusha Bachali, Katherine A. Owen, Kathryn M. Kingsmore, Erika L. Hubbard, Adam C. Labonte, Robert Robl, Sneha Shrotri, Amrie C. Grammer, Peter E. Lipsky
Software Mentions: 5
Published: over 3 years ago

10.3390/pharmaceutics13081105

Evaluation of an Intravitreal Rho-Associated Kinase Inhibitor Depot Formulation in a Rat Model of Diabetic Retinopathy
Cited by: 2
Author(s): Cécile Lebon, Heike Neubauer, Marianne Berdugo, Kimberley Delaunay, Elke Markert, Kolja Becker, Katja S. Baum-Kroker, J. Prestle, Holger Fuchs, Remko A. Bakker, Francine Behar‐Cohen
Software Mentions: 5
Published: over 3 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

10.1186/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

10.7717/peerj.3720

Atropos: specific, sensitive, and speedy trimming of sequencing reads
Cited by: 168
Author(s): John P. Didion, Marcel Martin, Francis S. Collins
Software Mentions: 5
Published: about 7 years ago

10.1038/s41598-021-84270-1

Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model
Cited by: 4
Author(s): Valentin Baloche, Julie Rivière, Thi Bao Tram Tran, Aurore Gelin, Olivia Bawa, Nicolas Signolle, Mouhamadou Diop, Philippe Dessen, Stéphanie Beq, Muriel D. David, P. Busson
Software Mentions: 5
Published: over 3 years ago

10.1080/15592294.2019.1710913

A regulatory role for CHD2 in myelopoiesis
Cited by: 5
Author(s): Farzaneh Shahin Varnoosfaderani, Anna M. Palau, Wenbo Dong, Jenna Persson, Mickaël Durand-Dubief, J. Peter Svensson, Andreas Lennartsson
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-019-1840-y

Genetic regulation of gene expression and splicing during a 10-year period of human aging
Cited by: 38
Author(s): Brunilda Balliu, Matthew G. Durrant, Olivia de Goede, Nathan S. Abell, Li X, Boxiang Liu, Michael J. Gloudemans, Naomi L. Cook, Kevin S. Smith, David A. Knowles, Mauro Pala, Francesco Cucca, David Schlessinger, Siddhartha Jaiswal, Chiara Sabatti, Lars Lind, Erik Ingelsson, Stephen B. Montgomery
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-021-86070-z

A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Cited by: 7
Author(s): Karen Davey, Daniel Wong, Filip A. Konopacki, Eugene Kwa, Tony Ly, Heike Fiegler, Christopher R. Sibley
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-021-00996-4

Reorganization of the 3D chromatin architecture of rice genomes during heat stress
Cited by: 39
Author(s): Zhe Liang, Qian Zhang, Changmian Ji, Guihua Hu, Pingxian Zhang, Yifan Wang, Liwen Yang, Xiaofeng Gu
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.32332

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex
Cited by: 131
Author(s): Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B. Huttner, Michael Hiller
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.30862

Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation
Cited by: 54
Author(s): Angela Halstead, Chiraag D Kapadia, Jennifer K. Bolzenius, Clarence E Chu, Andrew E. Schriefer, Lukas D. Wartman, Gregory R. Bowman, Vivek Arora
Software Mentions: 5
Published: about 7 years ago

10.1186/s12864-017-4031-9

unitas: the universal tool for annotation of small RNAs
Cited by: 83
Author(s): Daniel Gebert, Charlotte Hewel, David Rosenkranz
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.25125

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression
Cited by: 111
Author(s): Daniel Andergassen, Christoph P. Dotter, D. Wenzel, Verena Sigl, Philipp C. Bammer, Markus Muckenhuber, Daniela Mayer, Tomasz M. Kuliński, Hans-Christian Theussl, Josef Penninger, Christoph Bock, Denise P. Barlow, Florian M. Pauler, Quanah J. Hudson
Software Mentions: 5
Published: over 7 years ago

10.1186/s40478-017-0414-z

Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.62270

The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline
Cited by: 66
Author(s): Danielle Janosevic, Jered Myslinski, Thomas McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yunlong Liu, Kimberly S. Collins, Ying‐Hua Cheng, Seth Winfree, Tarek M. El‐Achkar, Bernhard Maier, Ricardo Melo Ferreira, Michael T. Eadon, Takashi Hato, Pierre C. Dagher
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.37816

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity
Cited by: 65
Author(s): Xue Song Zhang, Jackie Li, Kimberly A. Krautkramer, Michelle Badri, Thomas Battaglia, Timothy C. Borbet, Hyunwook Koh, Sandy Ng, Rachel A Sibley, Yuanyuan Li, Wimal Pathmasiri, Jindal Sk, Robin R. Shields-Cutler, Ben Hillmann, Gabriel A. Al‐Ghalith, Victoria Ruiz, Alexandra E. Livanos, Angélique B. van’t Wout, Nabeetha A. Nagalingam, Arlin B. Rogers, Susan Sumner, Dan Knights, John M. Denu, Huilin Li, Kelly V. Ruggles, Richard Bonneau, R. Anthony Williamson, Marcus Rauch, Martin J. Blaser
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.52004

Single cell transcriptional signatures of the human placenta in term and preterm parturition
Cited by: 173
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Edward Sendler, Yi Xu, Valeria Garcia‐Flores, Yaozhu Leng, Francesca Luca, Sonia S. Hassan, Nardhy Gomez-López
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.67714

The cryptic gonadotropin-releasing hormone neuronal system of human basal ganglia
Cited by: 13
Author(s): Katalin Skrapits, Miklós Sárvári, Imre Farkas, Balázs Göcz, Szabolcs Takács, Éva Rumpler, Viktória Váczi, Csaba Vastagh, Gergely Rácz, András Matolcsy, Norbert Solymosi, Szilárd Póliska, Blanka Tóth, Ferenc Erdélyi, Gábor Szabó, Michael D. Culler, Cécile Allet, Ludovica Cotellessa, Vincent Prévot, Paolo Giacobini, Erik Hrabovszky
Software Mentions: 5
Published: over 3 years ago

10.1007/s00395-021-00887-3

LncRNA LncHrt preserves cardiac metabolic homeostasis and heart function by modulating the LKB1-AMPK signaling pathway
Cited by: 24
Author(s): Ning Liu, Masaharu Kataoka, Yingchao Wang, Linbin Pu, Xiaoxuan Dong, Xuyang Fu, Feng Zhang, Feng Gao, Tian Liang, Jianqiu Pei, Changchen Xiao, Qiongzi Qiu, TingTing Hong, Qiming Chen, Jing Zhao, Long‐Guan Zhu, Junhua He, Xiaoyun Hu, Yu Nie, Wei Zhu, Hong Yu, Douglas B. Cowan, Xinyang Hu, Jianan Wang, Dazhi Wang, Jinghai Chen
Software Mentions: 5
Published: over 3 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.58659

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
Cited by: 22
Author(s): Bjoern Gaertner, Sebastiaan van Heesch, Valentin Schneider-Lunitz, Jana Felicitas Schulz, Franziska Witte, Susanne Blachut, Steven Nguyen, Richard L. Wong, Ileana Matta, Norbert Hübner
Software Mentions: 5
Published: over 4 years ago

10.3389/fcimb.2016.00136

The Transcriptome of Exophiala dermatitidis during Ex-vivo Skin Model Infection
Cited by: 22
Author(s): Caroline Poyntner, Barbara Blasi, Elsa Arcalís, Ursula Mirastschijski, Katja Sterflinger, Hakim Tafer
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.62850

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Cited by: 24
Author(s): Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash Ahmed, Rubin Be, Troy J. Comi, Shounak Bhogale, Syed Sameed Husain, Charles Blatti, Martin Middendorf, Saurabh Sinha, Sriram Chandrasekaran, Gene E. Robinson
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13229-020-00369-8

Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life
Cited by: 18
Author(s): Jessica A. Jiménez, Travis Ptacek, Alex H. Tuttle, Ralf S. Schmid, Sheryl S. Moy, Jeremy M. Simon, Mark J. Zylka
Software Mentions: 5
Published: about 4 years ago

10.18632/aging.101341

Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.63450

Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons
Cited by: 28
Author(s): Qijing Xie, Maria Brbić, Felix Horns, Sai Saroja Kolluru, Robert C. Jones, Jiefu Li, Anay R Reddy, Anthony Xie, Sayeh Kohani, Zhuoran Li, Colleen N. McLaughlin, Tongchao Li, Chuanyun Xu, David Vacek, David J. Luginbuhl, Jure Leskovec, Stephen R. Quake, Liqun Luo, Hongjie Li
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1006017

Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes
Cited by: 42
Author(s): Kévin Lebrigand, Le He, Nishant Thakur, Marie-Jeanne Arguel, Jolanta Polanowska, Bernard Henrissat, Éric Record, Ghislaine Magdelenat, Valérie Barbe, Sylvain Raffaele, Pascal Barbry, Jonathan J. Ewbank
Software Mentions: 5
Published: over 8 years ago

10.1186/s13100-018-0138-z

Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Cited by: 33
Author(s): Gavin Pereira, Laura Sánchez, Paul Schaughency, Alejandro Rubio-Roldán, Justin Choi, Evarist Planet, Ranjan Batra, Priscilla Turelli, Didier Trono, Lyle W. Ostrow, John Ravits, Haig H. Kazazian, Sarah J. Wheelan, Sara R. Heras, Jens Mayer, José L. García‐Pérez, John Goodier
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.54508

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation
Cited by: 24
Author(s): Ava C. Carter, Jin Xu, Meagan Y Nakamoto, Yuning Wei, Brian Zarnegar, Quanming Shi, James P. Broughton, Ryan C. Ransom, Ankit Salhotra, Surya Nagaraja, Rui Li, Diana R. Dou, Kathryn E. Yost, Seung Woo Cho, Anil Mistry, Michael T. Longaker, Paul A. Khavari, Robert T. Batey, Deborah S. Wuttke, Howard Y. Chang
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.27014

Regulation of life span by the gut microbiota in the short-lived African turquoise killifish
Cited by: 262
Author(s): Patrick M. Smith, David Willemsen, Miriam Popkes, Franziska Metge, Edson Gandiwa, Martin Reichard, Dario Riccardo Valenzano
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.48476

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
Cited by: 29
Author(s): Matteo D’Antonio, Joaquin Reyna, David Jakubosky, Maureen D. Donovan, Marc Jan Bonder, Hiroko Matsui, Oliver Stegle, Naoki Nariai, Agnieszka D’Antonio‐Chronowska, Kelly A. Frazer
Software Mentions: 5
Published: about 5 years ago

10.3389/fcell.2021.652408

Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver
Cited by: 21
Author(s): Xianliang Hou, Yane Yang, Ping Li, Zhipeng Zeng, Wenlong Hu, Ruilian Zhe, Xinqiong Liu, Donge Tang, Minglin Ou, Yong Dai
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: over 4 years ago

10.1242/bio.040683

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Cited by: 4
Author(s): Isabel Reuter, Jana Jäckels, Susanne Kneitz, Jochen Kuper, Klaus–Peter Lesch, Christina Lillesaar
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.669354

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation
Cited by: 7
Author(s): Geert Dom, Petr Dmitriev, Marie-Alexandra Lambot, Guy Van Vliet, Daniel Glinoer, Frédérick Libert, Anne Lefort, Jacques Emile Dumont, Carine Maenhaut
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.47214

In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation
Cited by: 15
Author(s): Daniel Andergassen, Zachary D. Smith, Jordan P. Lewandowski, Chiara Gerhardinger, Alexander Meissner, John L. Rinn
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.38795

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin
Cited by: 20
Author(s): Angela M Phillips, Michael B. Doud, Luna O Gonzalez, Vincent Butty, Yu‐Shan Lin, Jesse D. Bloom, Matthew D. Shoulders
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pgen.1006648

Adaptation of A-to-I RNA editing in Drosophila
Cited by: 56
Author(s): Yuange Duan, Shengqian Dou, Shiqi Luo, Hong Zhang, Jian Lü
Software Mentions: 5
Published: over 7 years ago

10.15252/emmm.202013162

The NFIB‐ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cells
Cited by: 23
Author(s): Federica Zilli, Pedro Marques Ramos, Priska Auf der Maur, Charly Jehanno, Atul Sethi, Marie–May Coissieux, Tobias Eichlisberger, Loïc Sauteur, Adelin Rouchon, Laura Bonapace, Joana Couto, Roland Rad, Michael Rugaard Jensen, Andrea Banfi, Michael Stadler, Mohamed Bentires‐Alj
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1008611

A non-canonical RNAi pathway controls virulence and genome stability in Mucorales
Cited by: 17
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Eusebio Navarro, Victoriano Garre
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-020-06911-5

Wild mice with different social network sizes vary in brain gene expression
Cited by: 2
Author(s): Patrícia C. Lopes, Barbara König
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.01009

RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development
Cited by: 22
Author(s): Siyuan Xing, Ranran Liu, Guiping Zhao, Lu Liu, M.A.M. Groenen, Ole Madsen, Maiqing Zheng, Xinting Yang, R.P.M.A. Crooijmans, Jie Wen
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.23253

Analogous mechanism regulating formation of neocortical basal radial glia and cerebellar Bergmann glia
Cited by: 32
Author(s): Xin Heng, Qiu Guo, Alan W. Leung, Kairong Li
Software Mentions: 5
Published: over 7 years ago

10.1038/cr.2017.121

5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers
Cited by: 229
Author(s): Wenshuai Li, Xu Zhang, Xingyu Lu, Lei You, Yanqun Song, Zhongguang Luo, Jun Zhang, Ji Nie, Wanwei Zheng, Diannan Xu, Yaping Wang, Yuanqiang Dong, Shulin Yu, Jun Hong, Jianping Shi, Hankun Hao, Fen Luo, Lingyang Hua, Peng Wang, Xiaoping Qian, Fang Yuan, Lian-Huan Wei, Ming Cui, Taiping Zhang, Quan Liao, Menghua Dai, Ziwen Liu, Ge Chen, Katherine Meckel, Sarbani Adhikari, Guifang Jia, Marc Bissonnette, Xin‐Xiang Zhang, Yupei Zhao, Wei Zhang, Chuan He, Jie Liu
Software Mentions: 5
Published: about 7 years ago

10.1186/s12863-018-0660-5

Skeletal muscle in aged mice reveals extensive transformation of muscle gene expression
Cited by: 45
Author(s): I‐Hsuan Lin, Junn-Liang Chang, Kate Hua, Wan-Chen Huang, Ming Hsu, Yifan Chen
Software Mentions: 5
Published: over 6 years ago

10.1101/2021.01.15.426908

Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules
Cited by: 2
Author(s): Jakub Jankowski, Hye Kyung Lee, Julia Wilflingseder, Lothar Hennighausen
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41398-021-01358-y

Zbtb16 regulates social cognitive behaviors and neocortical development
Cited by: 23
Author(s): Noriyoshi Usui, Stefano Berto, Ami Konishi, Makoto Kondo, Genevieve Konopka, Hideo Matsuzaki, Shoichi Shimada
Software Mentions: 5
Published: over 3 years ago

10.26508/lsa.201800171

LATS1 and LATS2 suppress breast cancer progression by maintaining cell identity and metabolic state
Cited by: 24
Author(s): Noa Furth, Ioannis S. Pateras, Ron Rotkopf, Vassiliki Vlachou, Irina Rivkin, Ina Schmitt, Deborah Bakaev, Anat Gershoni, Elena Ainbinder, Dena Leshkowitz, Randy L. Johnson, Vassilis G. Gorgoulis, Moshe Oren, Yael Aylon
Software Mentions: 5
Published: about 6 years ago

10.26508/lsa.202000709

Myeloid transformation by <i>MLL</i>-<i>ENL</i> depends strictly on C/EBP
Cited by: 4
Author(s): Radosław Wesołowski, Elisabeth Kowenz‐Leutz, Karin Zimmermann, Dorothea Dörr, Maria Hofstätter, Robert K. Slany, Alexander Mildner, Achim Leutz
Software Mentions: 5
Published: about 4 years ago

10.1016/j.tranon.2021.101107

3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Xinyuan Liu, Beate Gündel, Xidan Li, Jianping Liu, Andrew N. Wright, Matthias Löhr, Gustav Arvidsson, Rainer Heuchel
Software Mentions: 5
Published: over 3 years ago

10.1002/advs.202001402

TRADES: Targeted RNA Demethylation by SunTag System
Cited by: 25
Author(s): Jing Mo, Zonggui Chen, Shanshan Qin, Shu Li, Chuangang Liu, Lu Zhang, Ruoxi Ran, Ying Kong, Fang Wang, Song-Mei Liu, Yu Zhou, Xiaolian Zhang, Xiaocheng Weng, Xiang Zhou
Software Mentions: 5
Published: over 4 years ago

10.1038/s41398-020-00994-0

Presynaptic dysfunction in CASK-related neurodevelopmental disorders
Cited by: 25
Author(s): Martin Becker, Francesca Mastropasqua, Jan Philipp Reising, Simon Maier, Mai‐Lan Ho, Ielyzaveta Rabkina, Danyang Li, Janina Neufeld, Lea Ballenberger, Lynnea Myers, Viveka Moritz, Malin Kele, Josephine Wincent, Charlotte Willfors, Rouslan Sitnikov, Eric Herlenius, Britt‐Marie Anderlid, Anna Falk, Sven Bölte, Kristiina Tammimies
Software Mentions: 5
Published: about 4 years ago

10.7150/thno.53229

Neoantigen landscape in metastatic nasopharyngeal carcinoma
Cited by: 13
Author(s): Lin Mei, Xiaolong Zhang, Rui You, Qi Yang, Xiong Zou, Kai Yu, You‐Ping Liu, Ruhai Zou, Yi-Jun Hua, Pei‐Yu Huang, Jin Wang, Qi Zhao, Xiaobing Jiang, Jun Tang, Yeunhwa Gu, Tao Yu, Guangcun He, YuLong Xie, Zhi‐Qiang Wang, Ting Liu, Siyuan Chen, Zhixiang Zuo, Ming‐Yuan Chen
Software Mentions: 5
Published: almost 4 years ago

10.7150/thno.51795

Genome-wide CRISPR/Cas9 knockout screening uncovers a novel inflammatory pathway critical for resistance to arginine-deprivation therapy
Cited by: 11
Author(s): Cheng‐Ying Chu, Yi‐Ching Lee, Cheng-Han Hsieh, Chi‐Tai Yeh, Tsu‐Yi Chao, Po-Hung Chen, I-Hsuan Lin, Tsung‐Han Hsieh, Jing Wen Shih, Chia‐Hsiung Cheng, Che-Chang Chang, Po-Chuan Lin, Yuan‐Li Huang, Tsung-Ming Chen, Yun Yen, David K. Ann, Hsing-Jien Kung
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.ajhg.2021.04.024

Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder
Cited by: 6
Author(s): Holger Hengel, Shabab B. Hannan, Sarah Dyack, Sara MacKay, Ulrich Schatz, Martin Fleger, Andreas Kurringer, Ghassan Balousha, Zaïd Ghanim, Fowzan S. Alkuraya, Hamad Alzaidan, Hessa S. Alsaif, Tadahiro Mitani, Sevcan Tuğ Bozdoğan, Davut Pehlivan, James R. Lupski, Joseph J Gleeson, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Elliott H. Sherr, Kendall C. Parks, Emanuela Argilli, Amber Begtrup, Hamid Galehdari, Osama Balousha, Gholamreza Shariati, Neda Mazaheri, Reza Azizi Malamiri, Alistair T. Pagnamenta, Helen Kingston, Siddharth Banka, Adam Jackson, Mathew Osmond, Angelika Rieß, Tobias B. Haack, Thomas Nägele, Stefanie Schuster, Stefan Hauser, Jakob Admard, Nicolas Casadei, Ana Velić, Boris Maček, Stephan Ossowski, Henry Houlden, Reza Maroofian, Lüdger Schöls
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pgen.1007559

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Cited by: 141
Author(s): Rachel Kaletsky, Victoria Yao, April Williams, Alexi Runnels, Alicja Tadych, Shaoqiang Zhou, Olga G. Troyanskaya, Coleen T. Murphy
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-70131-w

Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy
Cited by: 6
Author(s): Paolo Montaldo, Aubrey J. Cunnington, Vânia Oliveira, Ravi Swamy, Prathik Bandya, Stuti Pant, Peter J Lally, Phoebe Ivain, Josephine Mendoza, Gaurav Atreja, Padmesh Vadakepat, Mythili Baburaj, Monica Sebastian, Indiramma Yasashwi, Chinnathambi Kamalarathnam, Rema Chandramohan, Mangalabharathi Sundaram, Kumutha Kumaraswami, Shobha Kumar, Naveen Benakappa, Swati Manerkar, Jayashree Mondhkar, Vinayagam Prakash, Mohammed Sajjid, Arasar Seeralar, Ismat Jahan, Sadeka Choudhury Moni, Mohammod Shahidullah, Radhika Sujatha, M Chandrasekaran, Siddarth Ramji, Seetha Shankaran, Myrsini Kaforou, Jethro Herberg, Sudhin Thayyil
Software Mentions: 5
Published: over 4 years ago

10.1242/dev.146811

Epigenetic resetting of human pluripotency
Cited by: 210
Author(s): Ge Guo, Ferdinand von Meyenn, Maria Rostovskaya, James Clarke, Sabine Dietmann, Duncan Baker, Anna Sahakyan, Samuel A. Myers, Paul Bertone, Wolf Reik, Kathrin Plath, Austin Smith
Software Mentions: 5
Published: over 7 years ago

10.1016/j.devcel.2018.12.026

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis
Cited by: 32
Author(s): Toni Beltran, Consuelo Barroso, T. Y. Birkle, Lewis Stevens, Hillel T. Schwartz, Paul W. Sternberg, Hélène Fradin, Kristin C. Gunsalus, Fabio Piano, Garima Sharma, Chiara Cerrato, Julie Ahringer, Enrique Martínez-Pérez, Mark Blaxter, Peter Sarkies
Software Mentions: 5
Published: over 5 years ago

10.1186/s13195-020-00716-0

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
Cited by: 27
Author(s): Daichi Shigemizu, Shintaro Akiyama, Sayuri Higaki, Toshiyuki Sugimoto, Takashi Sakurai, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takahiro Ochiya, Shumpei Niida, Kouichi Ozaki
Software Mentions: 5
Published: about 4 years ago

10.1128/mBio.03202-19

Reducing Aspergillus fumigatus Virulence through Targeted Dysregulation of the Conidiation Pathway
Cited by: 18
Author(s): James I P Stewart, Vinicius M. Fava, Joshua D. Kerkaert, Adithya S. Subramanian, Fabrice N. Gravelat, Mélanie Lehoux, P. Lynne Howell, Robert A. Cramer, Donald C. Sheppard
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-68949-5

Capsidiol-related genes are highly expressed in response to Colletotrichum scovillei during Capsicum annuum fruit development stages
Cited by: 10
Author(s): Viviane Yumi Baba, Adrian F. Powell, Suzana Tiemi Ivamoto, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Renata Mussoi Giacomin, Susan R. Strickler, Lukas A. Mueller, Rosana Rodrigues, Leandro Simões Azeredo Gonçalves
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-019-40867-1

Loss of the Polycomb group protein Rnf2 results in derepression of tbx-transcription factors and defects in embryonic and cardiac development
Cited by: 17
Author(s): Naomi D. Chrispijn, Dei M. Elurbe, Michaela Mickoleit, Marco Aben, Dennis E. M. de Bakker, Karolina M. Andralojc, Jan Huisken, Jeroen Bakkers, Leonie M. Kamminga
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008055

Loss of function mutations in essential genes cause embryonic lethality in pigs
Cited by: 38
Author(s): Martijn F.L. Derks, Arne B. Gjuvsland, Mirte Bosse, Marcos S. Lopes, Maren van Son, B. Harlizius, Beatrice Tan, Hanne Hamland, Eli Grindflek, Martien A. M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-07107-7

Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
Cited by: 13
Author(s): Stephanie Lam, J. Zeidan, F. Miglior, Aroa Suárez-Vega, Isabel Gómez-Redondo, Pablo Augusto de Souza Fonseca, Leluo Guan, Sinéad M. Waters, Ángela Cánovas
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-020-59808-4

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation
Cited by: 29
Author(s): Ian M. Traniello, Syed Bukhari, Jessica L. Kevill, Amy Cash Ahmed, Adam R. Hamilton, Nicholas L. Naeger, Declan C. Schroeder, Gene E. Robinson
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-019-57110-6

Single-cell transcriptional profiles in human skeletal muscle
Cited by: 160
Author(s): Aliza Rubenstein, Gregory R. Smith, Ulrika Raue, Gwénaëlle Begue, Kiril Minchev, Frederique Ruf-Zamojski, Venugopalan D. Nair, Xingyu Wang, Lan Zhou, Elena Zaslavsky, Todd A. Trappe, Scott Trappe, Stuart C. Sealfon
Software Mentions: 5
Published: almost 5 years ago

10.1038/s41598-020-60638-7

Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor
Cited by: 7
Author(s): Lukáš Rambousek, Tilo Gschwind, Carlos Lafourcade, Jean-Charles Paterna, Linda Dib, Jean‐Marc Fritschy, Adriano Fontana
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-020-6495-2

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features
Cited by: 8
Author(s): Yang Li, Menggen Dalai, Rongguo Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
Software Mentions: 5
Published: almost 5 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

10.3390/brainsci10050275

Transcriptome Analysis of Alcohol Drinking in Non-Dependent and Dependent Mice Following Repeated Cycles of Forced Swim Stress Exposure
Cited by: 10
Author(s): Sean P. Farris, Gayatri R. Tiwari, Olga N. Ponomareva, Marcelo F. López, R. Dayne Mayfield, Howard C. Becker
Software Mentions: 5
Published: over 4 years ago

10.3390/cells10061371

Single-Cell Transcriptional Heterogeneity of Lymphatic Endothelial Cells in Normal and Inflamed Murine Lymph Nodes
Cited by: 18
Author(s): Eliane Sibler, Yuliang He, Luca Ducoli, Nadja Keller, Noriki Fujimoto, Lothar C. Dieterich, Michael Detmar
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-019-2947-6

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
Cited by: 3
Author(s): Mohamed K. Gunady, Stephen M. Mount, Héctor Corrada Bravo
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-020-6769-8

High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maize
Cited by: 20
Author(s): Yuancong Wang, Jing Xu, Min Ge, Lei Ning, Meng-Mei Hu, Han Zhao
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-017-3810-7

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species
Cited by: 27
Author(s): Ezra Lencer, Wesley C. Warren, Richard G. Harrison, Amy R. McCune
Software Mentions: 5
Published: over 7 years ago

10.1186/s13058-019-1230-0

Elacestrant (RAD1901) exhibits anti-tumor activity in multiple ER+ breast cancer models resistant to CDK4/6 inhibitors
Cited by: 44
Author(s): Hemang Patel, Nianjun Tao, Kyung Min Lee, Mariela Huerta, Heike Arlt, Tara Mullarkey, Steven Troy, Carlos L. Arteaga, Teeru Bihani
Software Mentions: 5
Published: almost 5 years ago

10.3390/cells8080919

The Combination of IFN β and TNF Induces an Antiviral and Immunoregulatory Program via Non-Canonical Pathways Involving STAT2 and IRF9
Cited by: 11
Author(s): Mélissa K. Mariani, Pouria Dasmeh, Audray Fortin, Élise Caron, Mario Kalamujic, Alexander N. Harrison, Diana Ioana Hotea, Dacquin M. Kasumba, Sandra Cervantes-Ortiz, Espérance Mukawera, Adrian W.R. Serohijos, Nathalie Grandvaux
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-020-60065-8

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation
Cited by: 7
Author(s): Jessica Schira‐Heinen, A. Czapla, Marion Hendricks, Andreas Kloetgen, Wasco Wruck, James Adjaye, Gesine Kögler, Hans Müller, Kai Stühler, Hans‐Ingo Trompeter
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-019-51379-3

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium
Cited by: 9
Author(s): Les Kallestad, Seth Blackshaw, Ahmad M. Khalil, Krzysztof Palczewski
Software Mentions: 5
Published: about 5 years ago

Projects: cran: STAR

Papers Mentioning STAR 5,759