cran: STAR | Projects | Ecosyste.ms: Papers

10.7554/eLife.37184

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Cited by: 68
Author(s): Ji Li, Peter S. Choi, Christine L. Chaffer, Katherine Labella, Justin Hwang, Andrew O. Giacomelli, Jong Wook Kim, Nina Ilić, John G. Doench, Seav Huong Ly, Chao Dai, Kimberly R. Hagel, Andrew L. Hong, Ole Gjoerup, Shom Goel, Jennifer Y Ge, David E. Root, Jean J. Zhao, Angela N. Brooks, Robert A. Weinberg, William C. Hahn
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.49673

Rbfox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels
Cited by: 25
Author(s): Francesco Tomassoni-Ardori, Gianluca Fulgenzi, Jodi Becker, Colleen Barrick, Mary Ellen Palko, Skyler Kuhn, Vishal N. Kopardé, Maggie Cam, Sudhirkumar Yanpallewar, Shalini Oberdoerffer, Lino Tessarollo
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.46327

Identification of RBPMS as a mammalian smooth muscle master splicing regulator via proximity of its gene with super-enhancers
Cited by: 21
Author(s): Erick E Nakagaki-Silva, Clare Gooding, Miriam Llorian, Aishwarya G. Jacob, Fred Richards, Adrian Buckroyd, Sanjay Sinha, Christopher W.J. Smith
Software Mentions: 5
Published: about 7 years ago

10.7554/eLife.63856

Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila
Cited by: 60
Author(s): Colleen N. McLaughlin, Maria Brbić, Qijing Xie, Tongchao Li, Felix Horns, Sai Saroja Kolluru, Justus M. Kebschull, David Vacek, Anthony Xie, Jiefu Li, Robert C. Jones, Jure Leskovec, Stephen R. Quake, Liqun Luo, Hongjie Li
Software Mentions: 5
Published: over 5 years ago

10.1155/2020/3817573

Diet Modifies Pioglitazone’s Influence on Hepatic PPARγ-Regulated Mitochondrial Gene Expression
Cited by: 5
Author(s): Sakil Kulkarni, Jiansheng Huang, Eric Tycksen, Paul Cliften, David A. Rudnick
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.44161

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Cited by: 30
Author(s): Andrew L. Hong, Yuen-Yi Tseng, Jeremiah A. Wala, Won-Jun Kim, Bryan D. Kynnap, Mihir B. Doshi, Guillaume Kugener, Gabriel J. Sandoval, Thomas P. Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine Clinton, Alanna J. Church, Brian D. Crompton, Katherine A. Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A. Clemons, Stuart L. Schreiber, David E. Root, Prafulla C. Gokhale, N. Susan, Elizabeth Mullen, Charles W.M. Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L. Ligon, Jesse S. Boehm, William C. Hahn
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.52611

Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides
Cited by: 108
Author(s): Jamie R Wangen, Rachel Green
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.60326

Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation
Cited by: 15
Author(s): Amanjot Singh, Joern Hulsmeier, Arvind Reddy Kandi, Sai Shruti Pothapragada, Jens Hillebrand, Arnas Petrauskas, Khushboo Agrawal, Krishnan Rt, Devasena Thiagarajan, Deepa Jayaprakashappa, K. VijayRaghavan, Mani Ramaswami, Baskar Bakthavachalu
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.60191

MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor–1
Cited by: 33
Author(s): Tessa M. Popay, Jing Wang, Clare M. Adams, Gregory C. Howard, Simona G. Codreanu, Stacy D. Sherrod, John A. McLean, Lance R. Thomas, Shelly L. Lorey, Yuichi Machida, April M. Weissmiller, Christine M. Eischen, Qi Liu, William P. Tansey
Software Mentions: 5
Published: over 5 years ago

10.3389/fphys.2019.00278

Weighted Gene Co-expression Network Analysis for RNA-Sequencing Data of the Varicose Veins Transcriptome
Cited by: 14
Author(s): Jianbin Zhang, Qiangqiang Nie, Chaozeng Si, Wang Cheng, Yang Chen, Weiliang Sun, Pei Lin, Jing Guo, Jie Kong, Yiyao Cui, Feng Wang, Xueqiang Fan, Zhidong Ye, Jianyan Wen, Peng Liu
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.38619

Mapping the transcriptional diversity of genetically and anatomically defined cell populations in the mouse brain
Cited by: 52
Author(s): Ken Sugino, Erin Clark, Anton Schulmann, Yasuyuki Shima, Lihua Wang, David Hunt, Bryan M. Hooks, Dimitri Tränkner, Jayaram Chandrashekar, Serge Picard, Andrew Lemire, Nelson Spruston, Adam W. Hantman, Sacha B. Nelson
Software Mentions: 5
Published: over 7 years ago

10.1073/pnas.2005330117

Nuclear receptor REVERBα is a state-dependent regulator of liver energy metabolism
Cited by: 31
Author(s): Louise Hunter, Charlotte E Pelekanou, Antony Adamson, Polly Downton, Nichola J Barron, Thomas Cornfield, Toryn Poolman, Neil Humphreys, Peter Cunningham, Leanne Hodson, A. S. I. Loudon, Mudassar Iqbal, David A. Bechtold, David Ray
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.21476

Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated
Cited by: 67
Author(s): Ximena Ibarra-Soria, Thiago S. Nakahara, Jingtao Lilue, Yue Jiang, Casey Trimmer, Mateus A.A. Souza, Paulo H.M. Netto, Kentaro Ikegami, Nicolle R. Murphy, Mairi Kusma, Andrea Kirton, Luís R. Saraiva, Thomas Keane, Hiroaki Matsunami, Joel D. Mainland, Fábio Papes, Darren W. Logan
Software Mentions: 5
Published: over 9 years ago

10.1073/pnas.2110758118

TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia
Cited by: 22
Author(s): Maike Bensberg, Olof Rundquist, Aida Selimović, Cathrine Lagerwall, Mikael Benson, Mika Gustafsson, Hartmut Vogt, Antonio Lentini, Colm E. Nestor
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.63324

Adipocyte NR1D1 dictates adipose tissue expansion during obesity
Cited by: 20
Author(s): Louise Hunter, Charlotte E Pelekanou, Nichola J Barron, Rebecca C Northeast, M Grudzień, Antony Adamson, Polly Downton, Thomas Cornfield, Peter Cunningham, Jean-Noël Billaud, Leanne Hodson, Andrew S. I. Loudon, Richard D. Unwin, Mudassar Iqbal, David Ray, David A. Bechtold
Software Mentions: 5
Published: about 5 years ago

10.1098/rsos.200792

Tissue-specific developmental regulation and isoform usage underlie the role ofdoublesexin sex differentiation and mimicry inPapilioswallowtails
Cited by: 13
Author(s): Riddhi Deshmukh, Dhanashree Lakhe, Krushnamegh Kunte
Software Mentions: 5
Published: almost 6 years ago

10.21203/rs.3.rs-25639/v1

A potential role for AHR in SARS-CoV-2 pathology
Cited by: 12
Author(s): Federico Giovannoni, Zhaorong Li, Cybele C. Garcı́a, Francisco J. Quintana
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.14997

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
Cited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: over 10 years ago

10.7554/eLife.49044

NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress
Cited by: 22
Author(s): Dongdong Han, Lars Schomacher, Katrin M. Schüle, Medhavi Mallick, Michael U. Musheev, Emil Karaulanov, Laura Krebs, Annika von Seggern, Christof Niehrs
Software Mentions: 5
Published: almost 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: over 5 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: over 5 years ago

10.1038/sdata.2015.51

De novo transcriptome profiling of highly purified human lymphocytes primary cells
Cited by: 34
Author(s): Raoul Jean Pierre Bonnal, Valeria Ranzani, Alberto Arrigoni, Serena Maria Curti, Ilaria Panzeri, Paola Gruarin, Sergio Abrignani, Grazisa Rossetti, Massimiliano Pagani
Software Mentions: 5
Published: almost 11 years ago

10.1038/sdata.2016.51

Comprehensive RNA-Seq profiling to evaluate lactating sheep mammary gland transcriptome
Cited by: 40
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, J. J. Arranz
Software Mentions: 5
Published: about 10 years ago

10.1038/sdata.2018.142

A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research
Cited by: 306
Author(s): Philip L. De Jager, Yiyi Ma, Cristin McCabe, Jishu Xu, Badri N. Vardarajan, Daniel Felsky, Hans‐Ulrich Klein, Charles C. White, Mette A. Peters, Ben Lodgson, Parham Nejad, Ao Tang, Lara M. Mangravite, Lei Yu, Chris Gaiteri, Sara Mostafavi, Julie A. Schneider, David A. Bennett
Software Mentions: 5
Published: about 8 years ago

10.7554/eLife.60100

Sequential perturbations to mouse corticogenesis following in utero maternal immune activation
Cited by: 15
Author(s): Cesar P Canales, Myka L. Estes, Karol Cichewicz, Kartik Angara, John Paul Aboubechara, Scott A. Cameron, Kathryn Prendergast, Linda Su-Feher, Iva Zdilar, Ellie J Kreun, Emma C Connolly, Jin Myeong Seo, Jack B Goon, Kathleen Farrelly, Tyler W. Stradleigh, Deborah van der List, Lori Haapanen, Judy Van de Water, Daniel Vogt, A. Kimberley McAllister, A. Nord
Software Mentions: 5
Published: over 5 years ago

10.1038/sdata.2018.290

Transcriptome profiling of a beach-adapted wild legume for dissecting novel mechanisms of salinity tolerance
Cited by: 5
Author(s): Hengyou Zhang, Christine Zuelsdorf, Darin S. Penneys, Shoujin Fan, Janice Kofsky, Bao‐Hua Song
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: about 9 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: over 6 years ago

10.1038/s41597-020-0527-2

Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain
Cited by: 6
Author(s): Kimberly A. Aldinger, Andrew E. Timms, James W. MacDonald, Hanna K. McNamara, Jennifer Herstein, Theo K. Bammler, Oleg V. Evgrafov, James A. Knowles, Pat Levitt
Software Mentions: 5
Published: about 6 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: about 8 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: about 5 years ago

10.7554/eLife.49577

The Mars1 kinase confers photoprotection through signaling in the chloroplast unfolded protein response
Cited by: 40
Author(s): Karina Perlaza, Hannah Toutkoushian, Morgane Boone, Mable Lam, Masakazu Iwai, Martin C. Jonikas, Peter Walter, Silvia Ramundo
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.49424

Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei
Cited by: 164
Author(s): Jing Ren, Alina Isakova, Drew Friedmann, Jiawei Zeng, Sophie M. Grutzner, Albert Pun, Grace Zhao, Sai Saroja Kolluru, Ruiyu Wang, Rui Lin, Pengcheng Li, Anan Li, Jennifer L. Raymond, Qi Luo, Minmin Luo, Stephen R. Quake, Liqun Luo
Software Mentions: 5
Published: almost 7 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: almost 7 years ago

10.7554/eLife.54385

Polyploidy in the adult Drosophila brain
Cited by: 30
Author(s): Shyama Nandakumar, Olga Grushko, Laura Buttitta
Software Mentions: 5
Published: almost 6 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: about 6 years ago

10.3389/fpls.2021.695439

Genome-Wide Identification and Characterization of Small Peptides in Maize
Cited by: 15
Author(s): Yan Liang, Wanchao Zhu, Sijia Chen, Qidong Jia, Li Lin
Software Mentions: 5
Published: about 5 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: over 5 years ago

10.7554/eLife.68967

Spatially patterned excitatory neuron subtypes and projections of the claustrum
Cited by: 17
Author(s): Sarah R. Erwin, Brianna N. Bristow, Kaitlin E Sullivan, Rennie M Kendrick, Brian A. Marriott, Lihua Wang, Jody Clements, Andrew L. Lemire, Jesse Jackson, Mark S. Cembrowski
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.55792

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
Cited by: 56
Author(s): Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Küçükural, Lihua Julie Zhu
Software Mentions: 5
Published: almost 6 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: almost 7 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 6 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: almost 9 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: over 6 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: over 6 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: almost 8 years ago

10.7554/eLife.33480

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
Cited by: 86
Author(s): David A. Knowles, Courtney K Burrows, John Blischak, Kristen Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard, Yoav Gilad
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: over 6 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 5 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: almost 9 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: about 6 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: over 9 years ago

10.1371/journal.pbio.3000710

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice
Cited by: 18
Author(s): Virlana M. Shchuka, Luis E. Abatti, Huayun Hou, Nawrah Khader, Anna Dorogin, Michael D. Wilson, Oksana Shynlova, Jennifer A. Mitchell
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: about 9 years ago

10.1002/ece3.6930

Immunogenetic and tolerance strategies against a novel parasitoid of wild field crickets
Cited by: 0
Author(s): Kristin L. Sikkink, Nathan W. Bailey, Marlene Zuk, Susan L. Balenger
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-019-5496-5

OMICfpp: a fuzzy approach for paired RNA-Seq counts
Cited by: 1
Author(s): Alberto Berral-González, Ángela L. Riffo‐Campos, Guillermo Ayala
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-018-38209-8

Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers
Cited by: 30
Author(s): Manal H. Saad, Matthew Rumschlag, Michael H. Guerra, Candace Savonen, Alaina M Jaster, Philip D. Olson, Adnan Alazizi, Francesca Luca, Roger Piqué-Regi, Carl J. Schmidt, Michael J. Bannon
Software Mentions: 5
Published: over 7 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: over 6 years ago

10.15252/msb.20177728

The landscape of human mutually exclusive splicing
Cited by: 50
Author(s): Klas Hatje, Raza-Ur Rahman, Ramón Vidal, Dominic Simm, Björn Hammesfahr, V. Bansal, Ashish Rajput, Michel‐Edwar Mickael, Ting Sun, Stefan Bonn, Martin Kollmar
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-018-29993-4

Analysis of diet-induced differential methylation, expression, and interactions of lncRNA and protein-coding genes in mouse liver
Cited by: 10
Author(s): José P. Silva, Derek Van Booven
Software Mentions: 5
Published: about 8 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: over 5 years ago

10.1038/s41598-018-27078-w

Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage
Cited by: 19
Author(s): Kátia de Paiva Lopes, Tatiana Vinasco-Sandoval, Ricardo Assunção Vialle, Fernando Mendes Paschoal, Vanessa Albuquerque Paschoal Aviz Bastos, Edson Bor‐Seng‐Shu, Manoel Jacobsen Teixeira, Elizabeth Sumi Yamada, Pablo Diego do Carmo Pinto, Amanda Ferreira Vidal, André M. Ribeiro-dos-Santos, Fabiano Cordeiro Moreira, Sidney Emanuel Batista dos Santos, Eric Homero Albuquerque Paschoal, Ândrea Ribeiro‐dos‐Santos
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-021-07937-z

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments
Cited by: 13
Author(s): Stephanie De Vos, Stéphane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer, Peter Bossier
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: over 9 years ago

10.15252/msb.20199012

Sex‐dependent and sex‐independent regulatory systems of size variation in natural populations
Cited by: 4
Author(s): Hirokazu Okada, Ryuta Yagi, Vincent Gardeux, Bart Deplancke, Ernst Hafen
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.ppat.1009674

Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection
Cited by: 5
Author(s): Michelle Y.H. Lee, Amit A. Upadhyay, Hasse Walum, Chi N. Chan, Reem A. Dawoud, Christine Grech, Justin Harper, Kirti A. Karunakaran, Sydney A. Nelson, Ernestine Mahar, Kyndal Goss, Diane G. Carnathan, Barbara Cervasi, Kiran Gill, Gregory K. Tharp, Elizabeth R. Wonderlich, Vijayakumar Velu, Simon M. Barratt‐Boyes, Mirko Paiardini, Guido Silvestri, Jacob D. Estes, Steven E. Bosinger
Software Mentions: 5
Published: about 5 years ago

10.15252/msb.20209888

Gene expression profiling reveals insights into infant immunological and febrile responses to group B meningococcal vaccine
Cited by: 6
Author(s): Daniel O’Connor, Marta Pinto, Dylan Sheerin, Adriana Tomić, Ruth Drury, Samuel Channon‐Wells, Ushma Galal, Christina Dold, Hannah Robinson, Simon Kerridge, Emma Plested, Henry J. Hughes, Lisa Stockdale, Manish Sadarangani, Matthew D. Snape, Christine S. Rollier, Michael Levin, Andrew J. Pollard
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 5 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 9 years ago

10.1371/journal.pgen.1007631

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic
Cited by: 16
Author(s): Peter A. Combs, Hunter B. Fraser
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.ppat.1008346

Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells
Cited by: 28
Author(s): Tzu‐Chun Chen, Marc Talló-Parra, Qian M. Cao, Sebastián Kadener, René Böttcher, Gemma Pérez‐Vilaró, Pakpoom Boonchuen, Kunlaya Somboonwiwat, Juana Díez, Peter Sarnow
Software Mentions: 5
Published: about 6 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: about 6 years ago

10.1186/s13024-020-00405-4

Integrated analysis of the aging brain transcriptome and proteome in tauopathy
Cited by: 20
Author(s): Carl Grant Mangleburg, Timothy Wu, Hari Krishna Yalamanchili, Caiwei Guo, Yi-Cheng Hsieh, Duc Duong, Eric B. Dammer, Philip L. De Jager, Nicholas T. Seyfried, Zhandong Liu, Zhandong Liu
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.ppat.1007050

Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses
Cited by: 48
Author(s): William H. Palmer, Nathan Medd, Philippa M. Beard, Darren J. Obbard
Software Mentions: 5
Published: about 8 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: over 6 years ago

10.1242/dev.184143

A single cell transcriptome atlas of the developing zebrafish hindbrain
Cited by: 33
Author(s): Monica Tambalo, Richard Mitter, David Wilkinson
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1008444

Surfing motility is a complex adaptation dependent on the stringent stress response in Pseudomonas aeruginosa LESB58
Cited by: 16
Author(s): Daniel Pletzer, Evelyn Sun, Caleb Ritchie, Lauren Wilkinson, Leo T. Liu, Michael J. Trimble, Heidi Wolfmeier, Travis M. Blimkie, Robert E. W. Hancock
Software Mentions: 5
Published: over 6 years ago

10.1242/dev.174557

Lgr5+ stem/progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool
Cited by: 46
Author(s): Nicole Prior, Christopher J. Hindley, Fabian Rost, Elena Meléndez, Winnie Lau, Berthold Göttgens, Steffen Rulands, Benjamin D. Simons, Meritxell Huch
Software Mentions: 5
Published: over 7 years ago

10.1172/JCI91363

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes
Cited by: 70
Author(s): Bon Ham Yip, Violetta Steeples, Emmanouela Repapi, Richard N. Armstrong, Miriam Llorian, S. Roy, Jacqueline Shaw, Hamid Dolatshad, Stephen Taylor, Amit Verma, Matthias Bartenstein, Paresh Vyas, Nicholas C. P. Cross, Luca Malcovati, Mario Cazzola, Eva Hellström‐Lindberg, Seishi Ogawa, Christopher W.J. Smith, Andrea Pellagatti, Jacqueline Boultwood
Software Mentions: 5
Published: over 9 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 7 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13073-021-00952-5

Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes
Cited by: 39
Author(s): Bethany Barnes, Louisa Nelson, Anthony Tighe, George J. Burghel, I‐Hsuan Lin, Sudha Desai, Joanne C. McGrail, Robert D. Morgan, Stephen S. Taylor
Software Mentions: 5
Published: almost 5 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: about 6 years ago

10.1186/s13073-021-00924-9

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Cited by: 8
Author(s): Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander, Micah T. McClain
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-020-00747-0

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Cited by: 37
Author(s): Soumaya Zlitni, Alex Bishara, Eli L. Moss, Е. И. Ткаченко, Joyce B. Kang, Rebecca Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami S. Bhatt
Software Mentions: 5
Published: about 6 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-020-00783-w

The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Cited by: 50
Author(s): Florent Petitprez, Sacha Lévy, Chengming Sun, Maxime Meylan, Christophe Linhard, Étienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catheriné Sautès-Fridman, Aurélien de Reyniès
Software Mentions: 5
Published: almost 6 years ago

10.3390/cells10040876

Stability of Imprinting and Differentiation Capacity in Naïve Human Cells Induced by Chemical Inhibition of CDK8 and CDK19
Cited by: 0
Author(s): Raquel Bernad, Cian J. Lynch, Rocío G. Urdinguio, Camille Stephan‐Otto Attolini, Mario F. Fraga, Manuel Serrano
Software Mentions: 5
Published: over 5 years ago

10.1093/molbev/msz099

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Cited by: 72
Author(s): Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D Garcia, Martine Bérubé, Nader Pourmand, Tomàs Marquès-Bonet, Mary J. O’Connell, Per Palsbøll, Carlo C. Maley
Software Mentions: 5
Published: over 7 years ago

10.1186/s13059-021-02494-w

Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization
Cited by: 12
Author(s): Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell, Ania Wilczynska
Software Mentions: 5
Published: almost 5 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: about 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 7 years ago

10.1093/molbev/msy198

Phylotranscriptomic Insights into the Diversification of EndothermicThunnusTunas
Cited by: 13
Author(s): Adam Ciezarek, Owen G. Osborne, Oliver N. Shipley, Edward J. Brooks, S Tracey, Jaime D. McAllister, Luke D. Gardner, Michael J.E. Sternberg, Barbara A. Block, Vincent Savolainen
Software Mentions: 5
Published: almost 8 years ago

10.1186/s13059-021-02505-w

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Cited by: 23
Author(s): Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Yahan Liang, B Wold, A Mortazavi
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: about 5 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: about 8 years ago

10.1371/journal.pgen.1007268

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans
Cited by: 106
Author(s): Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk
Software Mentions: 5
Published: over 8 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: almost 5 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: almost 6 years ago

10.1186/s13059-021-02348-5

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
Cited by: 65
Author(s): Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Pedro Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Software Mentions: 5
Published: over 5 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759