cran: STAR | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-80334-w

Mitochondrial gene expression in single cells shape pancreatic beta cells' sub-populations and explain variation in insulin pathway
Cited by: 9
Author(s): Hadar Medini, T. Cohen, Dan Mo
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-79948-x

Role of PAI-1 in hepatic steatosis and dyslipidemia
Cited by: 44
Author(s): Joshua A. Levine, Carlota Oleaga, Mesut Eren, Ansel P. Amaral, Shu Meng, Elizabeth Lux, Sadiya S. Khan, Sanjiv J. Shah, Yasuhiro Omura, Nathalie Pamir, Joshua Hay, Grant D. Barish, Toshio Miyata, Hagai Tavori, Sergio Fazio, Douglas E. Vaughan
Software Mentions: 2
Published: almost 4 years ago

10.1038/oncsis.2017.56

Effects of proton versus photon irradiation on (lymph)angiogenic, inflammatory, proliferative and anti-tumor immune responses in head and neck squamous cell carcinoma
Cited by: 41
Author(s): Marilena Lupu-Plesu, Audrey Claren, Sonia Martial, Ndiaye Pd, Kévin Lebrigand, Nicolas Pons, Damien Ambrosetti, Isabelle Peyrottes, J. Feuillade, J. Hérault, Maeva Dufies, J. Doyen, Gilles Pagès
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0126416

Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep
Cited by: 15
Author(s): Aroa Suárez-Vega, Julio Benavides, Valentín Pérez Pérez, Gwenola Tosser‐Klopp, Christophe Klopp, Stephen J. Keennel, Juan José Arranz
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-021-85230-5

Modeling preeclampsia using human induced pluripotent stem cells
Cited by: 25
Author(s): Mariko Horii, Robert Morey, Tony Bui, Ojeni Touma, Katelyn N. Nelson, Hee-Young Cho, Hannah Rishik, Louise C. Laurent, Mana M. Parast
Software Mentions: 2
Published: over 3 years ago

10.1093/hmg/ddab154

Placental endocrine insufficiency programs anxiety, deficits in cognition and atypical social behaviour in offspring
Cited by: 6
Author(s): David J. Harrison, Hugo Creeth, Hannah R. Tyson, Raquel Boqué-Sastre, Susan Hunter, Dominic M. Dwyer, Anthony R Isles, John Roshan
Software Mentions: 2
Published: over 3 years ago

10.1038/oncsis.2017.32

The prohibitin-repressive interaction with E2F1 is rapidly inhibited by androgen signalling in prostate cancer cells
Cited by: 17
Author(s): Sarah Koushyar, G Economides, S Zaat, Wen Guo Jiang, Charlotte Bevan, Dafydd Alwyn Dart
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers12123518

MiR-215-5p Reduces Liver Metastasis in an Experimental Model of Colorectal Cancer through Regulation of ECM-Receptor Interactions and Focal Adhesion
Cited by: 29
Author(s): Táňa Macháčková, Petra Vychytilova-Faltejskova, Kamila Součková, Karolína Trachtová, Dominika Brchnelová, Marek Svoboda, Igor Kiss, Vladimír Procházka, Zdeněk Kala, Ondřej Slabý
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0207255

MMP-9 inhibition promotes anti-tumor immunity through disruption of biochemical and physical barriers to T-cell trafficking to tumors
Cited by: 54
Author(s): Vladi Juric, Chris O’Sullivan, Erin Stefanutti, М. А. Коваленко, Andrew E. Greenstein, Vivian Barry-Hamilton, Igor Mikaelian, Jeremiah D. Degenhardt, Yue Peng, Victoria Smith, Amanda Mikels‐Vigdal
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13059-019-1910-1

Transcriptome assembly from long-read RNA-seq alignments with StringTie2
Cited by: 734
Author(s): Sam Kovaka, Aleksey V. Zimin, Geo Pertea, Roham Razaghi, Steven L. Salzberg, Mihaela Pertea
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13059-019-1919-5

The somatic mutation landscape of the human body
Cited by: 76
Author(s): Pablo E. García-Nieto, Ashby J. Morrison, Hunter B. Fraser
Software Mentions: 2
Published: almost 5 years ago

10.1093/hmg/ddz169

Disease modeling of core pre-mRNA splicing factor haploinsufficiency
Cited by: 19
Author(s): Karen L. Wood, Charlie F. Rowlands, Wasay Mohiuddin Shaikh Qureshi, Huw B. Thomas, Weronika A. Buczek, Tracy A Briggs, Simon J. Hubbard, Kathryn E. Hentges, William G. Newman, Raymond T. O’Keefe
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12123597

Abemaciclib, A Selective CDK4/6 Inhibitor, Restricts the Growth of Pediatric Ependymomas
Cited by: 8
Author(s): Muh Lii Liang, Chun‐Han Chen, Yun Ru Liu, Man Hsu Huang, Yu Chen Lin, Tai-Tong Wong, Sey‐En Lin, Shing Shiung Chu, Yi Ding, Tsung Han Hsieh
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41388-020-1210-y

Phosphorylation independent eIF4E translational reprogramming of selective mRNAs determines tamoxifen resistance in breast cancer
Cited by: 17
Author(s): Chun Gong, Ho Tsoi, Ka Chun Mok, J.T. K. Cheung, Ellen P.S. Man, Keiji Fujino, Ashely Wong, Eric W.‐F. Lam, Ui‐Soon Khoo
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0064312

Assessing Phylogenetic Relationships among Galliformes: A Multigene Phylogeny with Expanded Taxon Sampling in Phasianidae
Cited by: 74
Author(s): Ning Wang, Rebecca T. Kimball, Edward L. Braun, Bin Liang, Zhengwang Zhang
Software Mentions: 2
Published: over 11 years ago

10.1038/s41388-019-0680-2

Isolation and characterization of patient-derived CNS metastasis-associated stromal cell lines
Cited by: 9
Author(s): Ben Yi Tew, Christophe Legendre, Gerald C. Gooden, Kyle N. Johnson, Rae Anne Martinez, Jeff Kiefer, Mark Bernstein, Jennifer Glen, Loren Butry, Aleksander Hinek, Steven Toms, Bodour Salhia
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0199740

Potential involvement of neutrophils in human thyroid cancer
Cited by: 45
Author(s): Maria Rosaria Galdiero, Gilda Varricchi, Stefania Loffredo, Claudio Bellevicine, Tiziana Lansione, Anne Lise Ferrara, Raffaella Iannone, Sarah Di Somma, Francesco Borriello, Eduardo Clery, Maria Triassi, Giancarlo Troncone, Gianni Marone
Software Mentions: 2
Published: over 6 years ago

10.1038/s41388-019-0712-y

The induction of core pluripotency master regulators in cancers defines poor clinical outcomes and treatment resistance
Cited by: 48
Author(s): Anastasia C. Hepburn, R.E. Steele, Rajan Veeratterapillay, Laura Wilson, Evangelia E. Kounatidou, Amy Barnard, Philip Berry, James Cassidy, Mohammad Moad, A El-Sherif, Luke Gaughan, Ian G. Mills, Craig Robson, Rakesh Heer
Software Mentions: 2
Published: almost 6 years ago

10.1136/jitc-2020-000832

Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy
Cited by: 18
Author(s): Natasa Prokopi, Christoph H. Tripp, Bart Tummers, Florian Hornsteiner, Sarah Spoeck, Jeremy Chase Crawford, Derek R. Clements, Mirjana Efremova, Katharina Hutter, Lydia Bellmann, Giuseppe Cappellano, Bruno L. Cadilha, Sebastian Kobold, Louis Boon, Daniela Ortner, Zlatko Trajanoski, Suzie Chen, Tanja D. de Gruijl, Juliana Idoyaga, Douglas R. Green, Patrizia Stoitzner
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0127985

Altered Interactions between the Gut Microbiome and Colonic Mucosa Precede Polyposis in APCMin/+ Mice
Cited by: 45
Author(s): Joshua S. Son, Shanawaj Khair, Donald W. Pettet, Nengtai Ouyang, Xinyu Tian, Yuanhao Zhang, Wei Zhu, Gerardo G. Mackenzie, Charles E. Robertson, Diana Ir, Daniel N. Frank, Basil Rigas, Ellen Li
Software Mentions: 2
Published: over 9 years ago

10.1186/s40425-019-0747-1

Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes
Cited by: 54
Author(s): Olga I. Isaeva, Г. В. Шаронов, Ekaterina O. Serebrovskaya, Maria A. Turchaninova, Andrew R. Zaretsky, Mikhail Shugay, Dmitriy M. Chudakov
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-80741-z

Gene expression and functional abnormalities in XX/Sry Leydig cells
Cited by: 3
Author(s): Shogo Yanai, Takashi Baba, Kai Inui, Kanako Miyabayashi, Seongwoo Han, Miki Inoue, Fumiya Takahashi, Masami Kanai‐Azuma, Yasuyuki Ohkawa, Man Ho Choi, Ken Ichirou Morohashi
Software Mentions: 2
Published: almost 4 years ago

10.1186/s40425-018-0406-y

Ibuprofen supports macrophage differentiation, T cell recruitment, and tumor suppression in a model of postpartum breast cancer
Cited by: 39
Author(s): Nathan D. Pennock, Holly A. Martinson, Qiuchen Guo, Courtney B. Betts, Sonali Jindal, Takahiro Tsujikawa, Lisa M. Coussens, Virginia F. Borges, Pepper Schedin
Software Mentions: 2
Published: about 6 years ago

10.1186/s13059-020-02033-z

Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients
Cited by: 4
Author(s): Daniel Spakowicz, Shaoke Lou, Brian Barron, José L. Gómez, Tianxiao Li, Qing Liu, Nicole Grant, Xiting Yan, Rebecca Hoyd, George M. Weinstock, Geoffrey Chupp, Mark Gerstein
Software Mentions: 2
Published: over 4 years ago

10.1186/s13059-020-02043-x

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data
Cited by: 68
Author(s): Liqing Tian, Yongjin Li, Michael N. Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael Rusch, John Easton, Jing Ma, Eric M. Davis, Austyn Trull, J. Robert Michael, Karol Szlachta, Charles G. Mullighan, Suzanne J. Baker, James R. Downing, David W. Ellison, Jinghui Zhang
Software Mentions: 2
Published: over 4 years ago

10.1016/j.mce.2021.111220

AKR1C2 and AKR1C3 expression in adipose tissue: Association with body fat distribution and regulatory variants
Cited by: 9
Author(s): Giada Ostinelli, Jinchu Vijay, Marie‐Claude Vohl, Elin Grundberg, André Tchernof
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-020-02085-1

Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance
Cited by: 53
Author(s): Christine E. Eyler, Hironori Matsunaga, Volker Hovestadt, Samantha J. Vantine, Peter van Galen, B Bernstein
Software Mentions: 2
Published: over 4 years ago

10.2196/28684

Interrupting Sitting Time in Postmenopausal Women: Protocol for the Rise for Health Randomized Controlled Trial
Cited by: 1
Author(s): Sheri J. Hartman, Lindsay Dillon, Andrea Z. LaCroix, Loki Natarajan, Dorothy D. Sears, Neville Owen, David W. Dunstan, James F. Sallis, Simon Schenk, Matthew A. Allison, Michelle Takemoto, Alexandra Herweck, Bao Nguyen, Dori E. Rosenberg
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0065923

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)
Cited by: 248
Author(s): Brant C. Faircloth, Laurie Sorenson, Francesco Santini, Michael E. Alfaro
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1009581

Biogenesis of P-TEFb in CD4+ T cells to reverse HIV latency is mediated by protein kinase C (PKC)-independent signaling pathways
Cited by: 12
Author(s): Uri Mbonye, Konstantin Leskov, Meenakshi Shukla, Saba Valadkhan, Jonathan Karn
Software Mentions: 2
Published: about 3 years ago

10.3390/ijerph18020634

Adverse Birth Outcomes Due to Exposure to Household Air Pollution from Unclean Cooking Fuel among Women of Reproductive Age in Nigeria
Cited by: 12
Author(s): Jamie Roberman, Theophilus I. Emeto, Oyelola A. Adegboye
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-80178-4

A role for orphan nuclear receptor liver receptor homolog-1 (LRH-1, NR5A2) in primordial follicle activation
Cited by: 11
Author(s): Marie-Charlotte Meinsohn, Camilla H K Hughes, Anthony Estienne, Hatice D. Saatcioglu, David Pépin, Raj Duggavathi, Bruce D. Murphy
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-79356-1

Late p65 nuclear translocation in glioblastoma cells indicates non-canonical TLR4 signaling and activation of DNA repair genes
Cited by: 6
Author(s): Isabele Fattori Moretti, Antônio M. Lerário, Marina Trombetta-Lima, Paula R. Sola, Roseli da Silva Soares, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie
Software Mentions: 2
Published: almost 4 years ago

10.1098/rspb.2020.1429

De novo biosynthesis of simple aromatic compounds by an arthropod ( Archegozetes longisetosus )
Cited by: 3
Author(s): Adrian Brückner, Martin Kaltenpoth, Michael Heethoff
Software Mentions: 2
Published: about 4 years ago

10.1016/j.molcel.2021.02.021

Structural basis for conformational equilibrium of the catalytic spliceosome
Cited by: 21
Author(s): Max E. Wilkinson, Sebastian M. Fica, Wojciech P. Galej, Kiyoshi Nagai
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0175943

Transcriptome and proteome responses in RNAlater preserved tissue of Arabidopsis thaliana
Cited by: 34
Author(s): Colin Kruse, Proma Basu, Darron R. Luesse, Sarah E. Wyatt
Software Mentions: 2
Published: over 7 years ago

10.1073/pnas.1907883116

Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians
Cited by: 177
Author(s): Kosuke Hashimoto, Tsukasa Kouno, Tomokatsu Ikawa, Norihito Hayatsu, Yurina Miyajima, Haruka Yabukami, Tommy Terooatea, Takashi Sasaki, Tsuyoshi Suzuki, Matthew Valentine, Giovanni Pascarella, Yasushi Okazaki, Harukazu Suzuki, Jay W. Shin, Aki Minoda, Ichiro Taniuchi, Hideyuki Okano, Yasumichi Arai, Nobuyoshi Hirose, Piero Carninci
Software Mentions: 2
Published: about 5 years ago

10.1073/pnas.2012288117

Phosphoglycolate salvage in a chemolithoautotroph using the Calvin cycle
Cited by: 27
Author(s): Nico J. Claassens, Giovanni Scarinci, Axel Fischer, Avi I. Flamholz, William R. Newell, Stefan Frielingsdorf, Oliver Lenz, Arren Bar‐Even
Software Mentions: 2
Published: over 4 years ago

10.1016/j.molcel.2019.07.037

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability
Cited by: 71
Author(s): Diana Zatreanu, Zhong Chao Han, Richard Mitter, Emanuela Tumini, Hannah Williams, Lea H. Gregersen, A. Barbara Dirac-Svejstrup, Stefania Roma, Aengus Stewart, Andrés Aguilera, Jesper Q. Svejstrup
Software Mentions: 2
Published: about 5 years ago

10.1186/s13052-018-0521-x

Egg introduction during complementary feeding according to allergic risk: not just for peanuts!
Cited by: 3
Author(s): Elvira Verduci, Annamaria Bianchi, Marta Brambilla, Mauro Calvani
Software Mentions: 2
Published: over 6 years ago

10.1167/iovs.61.10.13

Identification and Characterization of N<sup>6</sup>-Methyladenosine CircRNAs and Methyltransferases in the Lens Epithelium Cells From Age-Related Cataract
Cited by: 24
Author(s): Pengfei Li, Hualin Yu, Guowei Zhang, Lihua Kang, Bai Qin, Yu Cao, Jiawei Luo, Xiaojuan Chen, Ying Wang, Miaomiao Qin, Jian Wu, Yemeng Huang, Xi Zou, Huaijin Guan, Yong Wang
Software Mentions: 2
Published: over 4 years ago

10.1167/iovs.62.12.16

Dual Inhibition of Histone Deacetylases and the Mechanistic Target of Rapamycin Promotes Apoptosis in Cell Line Models of Uveal Melanoma
Cited by: 3
Author(s): Ruchi P. Patel, Joanna R. Thomas, Katherine M. Curt, Christina M. Fitzsimmons, Pedro J. Batista, Susan E. Bates, Michael M. Gottesman, Robert W. Robey
Software Mentions: 2
Published: about 3 years ago

10.1016/j.pneurobio.2020.101903

Uncovering memory-related gene expression in contextual fear conditioning using ribosome profiling
Cited by: 5
Author(s): Konstanze Simbriger, Inês S. Amorim, Gilliard Lach, Kleanthi Chalkiadaki, Stella Kouloulia, Seyed Mehdi Jafarnejad, Arkady Khoutorsky, Christos G. Gkogkas
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0153311

Identification of Differentially Expressed Genes Associated with Litter Size in Berkshire Pig Placenta
Cited by: 31
Author(s): Seul Gi Kwon, Jung Hye Hwang, Da Hye Park, Tae Wan Kim, Dong Jin Kang, Kyung Hee Kang, Il-Suk Kim, Hwa Chun Park, Chong-Sam Na, Ji Hee Ha, Chul Wook Kim
Software Mentions: 2
Published: over 8 years ago

10.1007/s13238-019-0630-3

Mutations in foregut SOX2+ cells induce efficient proliferation via CXCR2 pathway
Cited by: 3
Author(s): Tomoaki Hishida, Eric Vazquez-Ferrer, Yuriko Hishida-Nozaki, Ignacio Sancho‐Martinez, Yuta Takahashi, Fumiyuki Hatanaka, Jun Wu, Alejandro Ocampo, Pradeep Reddy, Min-Zu Wu, Laurie Gerken, Reuben J. Shaw, Concepción Rodrı́guez Esteban, Chris Benner, Hiroshi Nakagawa, Pedro Guillén García, Estrella Núñez-Delicado, Antoni Castells, Josep M. Campistol, Guanghui Liu, Juan Carlos Izpisúa Belmonte
Software Mentions: 2
Published: over 5 years ago

10.1002/pro.3628

Function and solution structure of the <scp> <i>Arabidopsis thaliana</i> </scp> RALF8 peptide
Cited by: 10
Author(s): Ronnie O. Frederick, Miyoshi Haruta, Marco Tonelli, Woonghee Lee, Gabriel Cornilescu, Claudia C. Cornilescu, Michael R. Sussman, John L. Markley
Software Mentions: 2
Published: over 5 years ago

10.1177/2045894021996190

Extracellular matrix degradation pathways and fatty acid metabolism regulate distinct pulmonary vascular cell types in pulmonary arterial hypertension
Cited by: 8
Author(s): Sharon Mumby, Frédèric Perros, Chee‐Kin Hui, Bo Xu, Weiqing Xu, Vahid Elyasigomari, Aurélie Hautefort, Grégoire Manaud, Marc Humbert, Kian Fan Chung, SJ Wort, Ian M. Adcock
Software Mentions: 2
Published: almost 4 years ago

10.1080/15476286.2018.1532253

RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B
Cited by: 9
Author(s): Laura Broglia, Solange Lise Materne, Anne-Laure Lécrivain, Karin Hahnke, Anaïs Le Rhun, Emmanuelle Charpentier
Software Mentions: 2
Published: about 6 years ago

10.1002/jmd2.12201

Selective screening for lysosomal storage disorders in a large cohort of minorities of African descent shows high prevalence rates and novel variants
Cited by: 5
Author(s): Renuka P. Limgala, Vyacheslav Furtak, Margarita Ivanova, Erk Changsila, Floyd Wilks, Marie Fidélia-Lambert, Özlem Göker-Alpan, Marjorie C. Gondré‐Lewis
Software Mentions: 2
Published: almost 4 years ago

10.1093/hmg/ddy127

Mutations in glycyl-tRNA synthetase impair mitochondrial metabolism in neurons
Cited by: 26
Author(s): Veronika Boczonadi, Kathrin Meyer, Humberto Gonczarowska-Jorge, Helen Griffin, Andreas Roos, Marina Bartsakoulia, Boglárka Bánsági, Giulia Ricci, Fanni Palinkas, René P. Zahedi, Francesco Bruni, Brian K. Kaspar, Hanns Lochmüller, Kym M. Boycott, Juliane S. Müller, Rita Horvath
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-81794-4

Valproic acid influences the expression of genes implicated with hyperglycaemia-induced complement and coagulation pathways
Cited by: 17
Author(s): Marina Barreto Felisbino, Mark Ziemann, Ishant Khurana, Jun Okabe, Keith Al-Hasani, Scott Maxwell, K N Harikrishnan, C. Oliveira, Maria Luiza S. Mello, Assam El‐Osta
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.redox.2020.101450

Mitochondrial complex I derived ROS regulate stress adaptation in Drosophila melanogaster
Cited by: 37
Author(s): Filippo Scialò, Ashwin Sriram, Rhoda Stefanatos, Ruth V. Spriggs, Samantha H. Y. Loh, L. Miguel Martins, Alberto Sanz
Software Mentions: 2
Published: over 4 years ago

10.1016/j.redox.2020.101654

Genome-wide transcriptional effects of deletions of sulphur metabolism genes in Drosophila melanogaster
Cited by: 9
Author(s): Olga G. Zatsepina, Dmitry S. Karpov, Lyubov N. Chuvakova, Alexander P. Rezvykh, S. Yu. Funikov, S. Yu. Sorokina, Alexey S. Zakluta, Д. Г. Гарбуз, Victoria Shilova, Michael B. Evgen’ev
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0154947

Transcriptome Characterization and Functional Marker Development in Sorghum Sudanense
Cited by: 7
Author(s): Jieqin Li, Lihua Wang, Qiuwen Zhan, Yanlong Liu, Xiaocui Yang
Software Mentions: 2
Published: over 8 years ago

10.1093/hmg/ddz038

Cellular α-synuclein pathology is associated with bioenergetic dysfunction in Parkinson’s iPSC-derived dopamine neurons
Cited by: 91
Author(s): Federico Zambon, Marta Cherubini, Hugo J. R. Fernandes, Charmaine Lang, Brent J. Ryan, Viola Volpato, Nora Bengoa-Vergniory, Siv Vingill, Moustafa Attar, Heather Booth, Walther Haenseler, Jane Vowles, Rory Bowden, Caleb Webber, Sally A. Cowley, Richard Wade‐Martins
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13045-020-00933-y

The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma
Cited by: 17
Author(s): Samrat Roy Choudhury, Cody Ashby, Ruslana G. Tytarenko, Michael Bauer, Yan Wang, Shayu Deshpande, Judith Den, Carolina Schinke, Maurizio Zangari, Sharmilan Thanendrarajan, Faith E. Davies, Frits van Rhee, Gareth J. Morgan, Brian A Walker
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0250669

Distinct expression of select and transcriptome-wide isolated 3’UTRs suggests critical roles in development and transition states
Cited by: 1
Author(s): Shaoyi Ji, Zihui Yang, Leonardi Gozali, Thomas Kenney, Arif Kocabas, Carolyn Jinsook Park, Mary Hynes
Software Mentions: 2
Published: over 3 years ago

10.1038/s41366-020-00716-y

Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity
Cited by: 9
Author(s): Diana Le Duc, Lin Chen, Yulia Popkova, Zuqin Yang, Akhil Velluva, Mehmet Volkan Çakır, Sonja Grunewald, Jan C. Simon, Andreas Dietz, Dirk Dannenberger, Antje Garten, Johannes R. Lemke, Jürgen Schiller, Matthias Blüher, Pamela A. Nono Nankam, Ulrike Rolle-Kampczyk, Martin von Bergen, Janet Kelso, Torsten Schöneberg
Software Mentions: 2
Published: about 4 years ago

10.1038/s41366-020-00694-1

Type 2 diabetes is associated with impaired jejunal enteroendocrine GLP-1 cell lineage in human obesity
Cited by: 23
Author(s): Céline Osinski, Léa Le Gleau, Christine Poitou, Juan de Toro‐Martín, Laurent Genser, Magali Fradet, Hédi Soula, Armelle Leturque, Corinne Blugeon, Laurent Jourdren, Edwige-Ludiwyne Hubert, Karine Clément, Patricia Serradas, Agnès Ribeiro
Software Mentions: 2
Published: about 4 years ago

10.21203/rs.3.rs-133494/v1

Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells
Cited by: 1
Author(s): David A. Hafler, Tomokazu Sumida, Shai Dulberg, J.C. Schupp, Helen Stillwell, Pierre-Paul Axisa, Michela Comi, Matthew R. Lincoln, Avraham Unterman, Naftali Kaminski, Asaf Madi, Vijay K. Kuchroo
Software Mentions: 2
Published: over 3 years ago

10.7150/ijms.48014

circRNA expression pattern and ceRNA network in the pathogenesis of aseptic loosening after total hip arthroplasty
Cited by: 4
Author(s): Shenghui Ni, Tianlong Jiang, Shimin Hao, Peng Luo, Penghao Wang, Yaser Almatari, Yu Wang, Zhe Zhang, Lei Guo
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12931-018-0861-5

Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells
Cited by: 29
Author(s): L. Cody Smith, Santiago Moreno, Lauren Robertson, Sarah Robinson, Kristal Gant, Andrew J. Bryant, Tara Sabo‐Attwood
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0223212

Regulatory interaction between the ZPBP2-ORMDL3/Zpbp2-Ormdl3 region and the circadian clock
Cited by: 3
Author(s): Matthew L. Chang, Sanny Moussette, Enrique Gamero-Estévez, José Héctor Gálvez, Victoria Chiwara, Indra R. Gupta, Aimee K. Ryan, Anna K. Naumova
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-021-81340-2

Screening for potential targets to reduce stenosis in bioprosthetic heart valves
Cited by: 3
Author(s): Rudi Foth, Orr Shomroni, Matthias Sigler, Jürgen Hörer, Julie Cleuziou, Thomas Paul, Katja Eildermann
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0234913

Perm1 regulates cardiac energetics as a downstream target of the histone methyltransferase Smyd1
Cited by: 11
Author(s): Shinichi Oka, Amira D. Sabry, A Horiuchi, Keiko M. Cawley, Sean O’Very, Maria A. Zaitsev, Thirupura S. Shankar, Jaemin Byun, Risa Mukai, Xiaoyong Xu, Natalia S. Torres, Anil Kumar, Masayuki Yazawa, Ling Jing, Iosif Taleb, Yukio Saijoh, Stavros G. Drakos, Junichi Sadoshima, Jason G. Warren
Software Mentions: 2
Published: over 4 years ago

10.1186/s12977-018-0394-5

Ribosome profiling of the retrovirus murine leukemia virus
Cited by: 15
Author(s): Nerea Irigoyen, Adam M. Dinan, Ian Brierley, Andrew E. Firth
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0041317

Asian Dust Storm Elevates Children’s Respiratory Health Risks: A Spatiotemporal Analysis of Children’s Clinic Visits across Taipei (Taiwan)
Cited by: 43
Author(s): Hwa‐Lung Yu, Lung-Chang Chien, Chen-Cheng Yang
Software Mentions: 2
Published: over 12 years ago

10.1155/2016/4503840

Profiling of the Predicted Circular RNAs in Ductal In Situ and Invasive Breast Cancer: A Pilot Study
Cited by: 30
Author(s): Marco Galasso, Giorgio Costantino, Lorenzo Pasquali, Linda Minotti, Federica Baldassari, Fabio Corrà, Chiara Agnoletto, Stefano Volinia
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12284-020-00387-3

Production Assessment and Genome Comparison Revealed High Yield Potential and Novel Specific Alleles Associated with Fertility and Yield in Neo-Tetraploid Rice
Cited by: 15
Author(s): Hang Yu, Muhammad Qasim Shahid, Qihang Li, Yudi Li, Cong Liu, Zengjun Lu, Jinwen Wu, Zemin Zhang, Xiangdong Liu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12284-020-00421-4

Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains
Cited by: 11
Author(s): Tai‐Hsi Wu, Marlen Müller, Wilhelm Gruissem, Navreet K. Bhullar
Software Mentions: 2
Published: about 4 years ago

10.1186/s12284-021-00502-y

Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress
Cited by: 21
Author(s): Qiqun Cheng, Peng Wang, Guangliang Wu, Yanning Wang, Jingai Tan, Caijing Li, Xiangyu Zhang, Shilei Liu, Shiying Huang, Tao Huang, Mengmeng Yang, Haohua He, Jianmin Bian
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0128916

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples
Cited by: 41
Author(s): Jonathan Scolnick, Michelle Dimon, I‐Ching Wang, Stephanie C. Huelga, Douglas A. Amorese
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0237773

Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development
Cited by: 10
Author(s): José Henrique Ledo, Ran Zhang, Luka Mesin, Diego Mourão-Sá, Estefania P. Azevedo, Olga G. Troyanskaya, Victor Bustos, Paul Greengard
Software Mentions: 2
Published: over 4 years ago

10.1126/sciadv.aba8397

The structures of natively assembled clathrin-coated vesicles
Cited by: 38
Author(s): Mohammadreza Paraan, Joshua H. Mendez, Savanna R. Sharum, Danielle L. Kurtin, Huan He, Scott M. Stagg
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0060019

Coalescent-Based Genome Analyses Resolve the Early Branches of the Euarchontoglires
Cited by: 41
Author(s): Vikas Kumar, Björn M. Hallström, Axel Janke
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0252674

De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome
Cited by: 0
Author(s): Takayuki Hata, Naoto Takada, Chihiro Hayakawa, Mei Kazama, Tomohiro Uchikoba, Makoto Tachikawa, Mitsuhiro Matsuo, Shunji Satoh, Junichi Obokata
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0227496

RNA profiling identifies novel, photoperiod-history dependent markers associated with enhanced saltwater performance in juvenile Atlantic salmon
Cited by: 9
Author(s): Marianne Iversen, Teshome Dagne Mulugeta, Børge Gellein Blikeng, Alexander C. West, Even H. Jørgensen, Simen Rød Sandve, David G. Hazlerigg
Software Mentions: 2
Published: over 4 years ago

10.1002/jev2.12042

Prostate cancer extracellular vesicles mediate intercellular communication with bone marrow cells and promote metastasis in a cholesterol‐dependent manner
Cited by: 35
Author(s): Stephen E. Henrich, Kaylin M. McMahon, Michael P. Plebanek, Andrea E. Calvert, Timothy Joel Feliciano, Samuel K. Parrish, Fabio Tavora, Anthony Mega, André De Souza, Benedito A. Carneiro, C. Shad Thaxton
Software Mentions: 2
Published: almost 4 years ago

10.1126/sciadv.abe4577

Vitamin D deficiency exacerbates UV/endorphin and opioid addiction
Cited by: 14
Author(s): Lajos Kemény, Kathleen C. Robinson, Andrea L. Hermann, Deena M. Walker, Susan Regan, Yik Weng Yew, Yi Chun Lai, Nicholas Theodosakis, Phillip D. Rivera, Weihua Ding, Liuyue Yang, Tobias A. Beyer, Yong-Hwee Eddie Loh, Jennifer A. Lo, Anita A. J. van der Sande, William Sarnie, David Kotler, Jennifer J. Hsiao, Mack Y. Su, Shinichiro Kato, Joseph Kotler, Staci D. Bilbo, Vanita Chopra, Matthew P. Salomon, Shiqian Shen, Dave S. B. Hoon, Maryam M. Asgari, Sarah E. Wakeman, Eric J. Nestler, David E. Fisher
Software Mentions: 2
Published: over 3 years ago

10.3390/plants10020304

Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions
Cited by: 5
Author(s): Yan Chen, Min Liu, Zhicheng Dong
Software Mentions: 2
Published: almost 4 years ago

10.3390/plants9060674

Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis
Cited by: 3
Author(s): Tomoko Yamaguchi, Y. Kurihara, Yuko Makita, Emiko Okubo-Kurihara, Ami Kageyama, Emi Osada, Setsuko Shimada, Hiroko Tsuchida, Hiroaki Shimada, Minami Matsui
Software Mentions: 2
Published: over 4 years ago

10.3390/plants9111548

RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile
Cited by: 6
Author(s): Boas Pucker, Anna Schwandner, Sarah Becker, Ludger Hausmann, Prisca Viehöver, Reinhard Töpfer, Bernd Weißhaar, Daniela Holtgräwe
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pbio.1002435

How Many Parameters Does It Take to Describe Disease Tolerance?
Cited by: 72
Author(s): Alan K. Louie, Kyung Han Song, Alejandra Guzmán Hotson, Ann T. Tate, David Schneider
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pbio.3000582

Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize
Cited by: 57
Author(s): Yalin Liu, Handong Su, Jing Zhang, Yang Liu, Chao Feng, Fangpu Han
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pbio.1002379

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
Cited by: 335
Author(s): James B. Pease, David C. Haak, Matthew W. Hahn, Leonie C. Moyle
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pbio.3000498

Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids
Cited by: 116
Author(s): Sapna Chhabra, Lizhong Liu, Ryan Goh, Xiangyu Kong, Aryeh Warmflash
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pbio.3000324

DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program
Cited by: 71
Author(s): Yao-Long Yan, Chao Zhang, Jun Hao, Xuelian Wang, Ming Jia, Mi Li, Jie Na, Xinli Hu, Yangming Wang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.2005903

Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast
Cited by: 27
Author(s): Yinuo J. Wang, Pavanapuresan P. Vaidyanathan, María F. Rojas-Durán, Namrata D. Udeshi, Kristen M. Bartoli, Steven A. Carr, Wendy V. Gilbert
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pbio.3000087

Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome
Cited by: 19
Author(s): María de los Ángeles Serrano, Bradley L. Demarest, Tarlynn Tone-Pah-Hote, Martin Tristani‐Firouzi, H. Joseph Yost
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pbio.3001385

The induction of preterm labor in rhesus macaques is determined by the strength of immune response to intrauterine infection
Cited by: 11
Author(s): Monica Cappelletti, Pietro Presicce, Feiyang Ma, Paranthaman Senthamaraikannan, Lisa Miller, Matteo Pellegrini, Myung Shin Sim, Alan H. Jobe, Senad Divanovic, Sing Sing Way, Claire Chougnet, Suhas G. Kallapur
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pbio.3000245

Simple nutrients bypass the requirement for HLH-30 in coupling lysosomal nutrient sensing to survival
Cited by: 15
Author(s): John T. Murphy, Haiyan Liu, Xiucui Ma, Alexander Shaver, Brian M. Egan, Clara Oh, Alexander Boyko, Travis Mazer, Samuel Ang, Rohan Khopkar, Ali Javaheri, Sandeep Kumar, Xuntian Jiang, Daniel S. Ory, Kartik Mani, Scot J. Matkovich, Kerry Kornfeld, Abhinav Diwan
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pcbi.1008173

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data
Cited by: 53
Author(s): Hyeon Jin Kim, Galip Gürkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pcbi.1007278

Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer
Cited by: 22
Author(s): Morgan Craig, Kamran Kaveh, Alec N. Woosley, Andrew S. Brown, David Goldman, Elliot O. Eton, Ravindra Mehta, Andrew Dhawan, Kazuya Arai, Mahbuba Rahman, Sidi Chen, Martin A. Nowak, Aaron Goldman
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1005766

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis
Cited by: 41
Author(s): Kaido Lepik, Tarmo Annilo, Viktorija Kukuškina, Kai Kisand, Zoltán Kutalik, Pärt Peterson, Hedi Peterson
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pcbi.1007925

Detecting differential alternative splicing events in scRNA-seq with or without Unique Molecular Identifiers
Cited by: 19
Author(s): Yu Hu, Kai Wang, Mingyao Li
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1006635

Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS
Cited by: 146
Author(s): Lisa Krug, Nabanita Chatterjee, Rebeca Borges-Monroy, Stephen Hearn, Wen‐Wei Liao, Kathleen M. Morrill, Lisa Prazak, Nikolay V. Rozhkov, Delphine Theodorou, Molly Gale Hammell, Josh Dubnau
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1007932

Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation
Cited by: 34
Author(s): Mary Leatham-Jensen, Christopher M. Uyehara, Brian D. Strahl, A. Gregory Matera, Robert J. Duronio, Daniel J. McKay
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1008916

Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity
Cited by: 17
Author(s): Zhengzheng S. Liang, Irène Cimino, Binnaz Yalcin, Narayanan Raghupathy, Valerie E. Vancollie, Ximena Ibarra-Soria, Helen V. Firth, Debra Rimmington, I. Sadaf Farooqi, Christopher J. Lelliott, Steven C. Munger, Stephen O’Rahilly, Anne C. Ferguson‐Smith, Anthony P. Coll, Darren W. Logan
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pgen.1009642

Repeated evolution of circadian clock dysregulation in cavefish populations
Cited by: 22
Author(s): Katya L. Mack, James B. Jaggard, Jenna Persons, Emma Y. Roback, Courtney N. Passow, Bethany A. Stanhope, Estephany Ferrufino, Dai Tsuchiya, Sarah E. Smith, Brian D. Slaughter, Johanna E. Kowalko, Nicolas Rohner, Alex C. Keene, Suzanne E. McGaugh
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1009284

A rare coding mutation in the MAST2 gene causes venous thrombosis in a French family with unexplained thrombophilia: The Breizh MAST2 Arg89Gln variant
Cited by: 4
Author(s): Pierre‐Emmanuel Morange, Franck Peiretti, Lénaïck Gourhant, Carole Proust, Omar Soukarieh, Anne-Sophie Pulcrano-Nicolas, Ganapathi-Varma Saripella, Luca Stefanucci, Romaric Lacroix, Manal Ibrahim‐Kosta, Catherine A. Lemarié, Mattia Frontini, Marie‐Christine Alessi, David‐Alexandre Trégouët, Francis Couturaud
Software Mentions: 2
Published: almost 4 years ago

Projects: cran: STAR

Papers Mentioning STAR 5,759