cran: STAR | Projects | Ecosyste.ms: Papers

10.1186/1471-2105-8-382

XSTREAM: A practical algorithm for identification and architecture modeling of tandem repeats in protein sequences
Cited by: 139
Author(s): Aaron M. Newman, J. B. Cooper
Software Mentions: 1
Published: about 17 years ago

10.1107/S2059798319016577

Amyloid structure determination in RELION-3.1
Cited by: 136
Author(s): S.H.W. Scheres
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms19113618

Cytotoxicity and Transcriptomic Analysis of Silver Nanoparticles in Mouse Embryonic Fibroblast Cells
Cited by: 63
Author(s): Sangiliyandi Gurunathan, Muhammad Qasim, Chanhyeok Park, Hyunjin Yoo, Dong Yoon Choi, Hyuk Song, Chankyu Park, Jin‐Hoi Kim, Kwonho Hong
Software Mentions: 1
Published: about 6 years ago

10.1093/gigascience/giy092

Hot-starting software containers for STAR aligner
Cited by: 8
Author(s): Pai Zhang, Ling‐Hong Hung, Wes Lloyd, Ka Yee Yeung
Software Mentions: 1
Published: over 6 years ago

10.1177/1759091415593066

Combined HDAC1 and HDAC2 Depletion Promotes Retinal Ganglion Cell Survival After Injury Through Reduction of p53 Target Gene Expression
Cited by: 42
Author(s): Frédéric Lebrun-Julien, Ueli Suter
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-07613-2

Resilience, plasticity and robustness in gene expression during aging in the brain of outbred deer mice
Cited by: 2
Author(s): Elham Soltanmohammadi, Youwen Zhang, Ioulia Chatzistamou, Hippokratis Kiaris
Software Mentions: 1
Published: over 3 years ago

10.3390/ijms20030750

Development of SNP, KASP, and SSR Markers by BSR-Seq Technology for Saturation of Genetic Linkage Map and Efficient Detection of Wheat Powdery Mildew Resistance Gene Pm61
Cited by: 14
Author(s): Jinghuang Hu, Jingting Li, Peipei Wu, Yahui Li, Dan Qiu, Yunfeng Qu, Jingzhong Xie, Hongjun Zhang, Li Yang, Tiantian Fu, Yan Yu, Mengjuan Li, Hongwei Liu, Tong Zhu, Yang Zhou, Zhiyong Liu, Hongjie Li
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12859-015-0654-5

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale
Cited by: 122
Author(s): Hani Z. Girgis
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0186888

TrpA1 activation in peripheral sensory neurons underlies the ionic basis of pain hypersensitivity in response to vinca alkaloids
Cited by: 19
Author(s): Nina Boiko, Geraldo Medrano, Elizabeth Montano, Nan Jiang, Claire Williams, Ngonidzashe B Madungwe, Jean C. Bopassa, Charles C. Kim, Jay Z. Parrish, Kenneth M. Hargreaves, James D. Stockand, Benjamin A. Eaton
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-76904-7

Transcriptomic analysis of micropapillary high grade T1 urothelial bladder cancer
Cited by: 3
Author(s): Michaela Bowden, Rosa Nadal, Chensheng W. Zhou, Lillian Werner, Justine A. Barletta, Núria Juanpere, Josep Lloreta, Silvia Hernández‐Llodrà, Juan Moróte, Inés de Torres, Anna Orsola, Paloma Cejas, Henry W. Long, Joaquim Bellmunt
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-020-76870-0

Inactivation of mediator complex protein 22 in podocytes results in intracellular vacuole formation, podocyte loss and premature death
Cited by: 1
Author(s): Patricia Q. Rodriguez, David Unnersjö‐Jess, Sonia Zambrano, Jing Guo, Katja Möller-Hackbarth, Hans Blom, Timo Jahnukainen, Lwaki Ebarasi, Jaakko Patrakka
Software Mentions: 1
Published: about 4 years ago

10.1093/gigascience/giz019

De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis)
Cited by: 25
Author(s): Kui Wang, Pengpeng Li, Yongyang Gao, Chunqin Liu, Qinglei Wang, Jing Yin, Jie Zhang, Geng Li, Changlong Shu
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20051137

CD99 Expression in Glioblastoma Molecular Subtypes and Role in Migration and Invasion
Cited by: 14
Author(s): Laís Cavalca Cardoso, Roseli da Silva Soares, Talita de Sousa Laurentino, Antônio Marcondes Lerário, Suely Kazue Nagahashi Marie, Sueli Mieko Oba-Shinjo
Software Mentions: 1
Published: over 5 years ago

10.3390/cancers13092250

IGF2 Mediates Resistance to Isoform-Selective-Inhibitors of the PI3K in HPV Positive Head and Neck Cancer
Cited by: 6
Author(s): Mai Badarni, Manu Prasad, Artemiy Golden, Baisali Bhattacharya, Liron Levin, Ksenia M. Yegodayev, Orr Dimitstein, Ben‐Zion Joshua, Limor Cohen, Ekaterina Khrameeva, Dexin Kong, Angel Porgador, Alex Braiman, Jennifer R. Grandis, Barak Rotblat, Moshe Elkabets
Software Mentions: 1
Published: over 3 years ago

10.1186/s12864-021-07748-2

Transcriptomic analysis of caecal tissue in inbred chicken lines that exhibit heritable differences in resistance to Campylobacter jejuni
Cited by: 6
Author(s): Kay Russell, Jacqueline Smith, Abi Bremner, Cosmin Chintoan-Uta, Lonneke Vervelde, Androniki Psifidi, Mark P. Stevens
Software Mentions: 1
Published: over 3 years ago

10.9734/INDJ/2016/26203

Examining the Impact of Patient-Reported Hope for Improvement and Patient Satisfaction with Clinician/Treatment on the Outcome of Major Depressive Disorder Treatment
Cited by: 1
Author(s): Waguih William IsHak, Jennice Vilhauer, Richard Kwock, Fan Wu, Sherif H. Gohar, Katherine L. Collison, Sasha Thomas, Lancer Naghdechi, David Elashoff
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-020-76621-1

Phylogenetic analysis of cell-cycle regulatory proteins within the Symbiodiniaceae
Cited by: 1
Author(s): Lucy M. Gorman, Shaun P. Wilkinson, Sheila A. Kitchen, Clinton A. Oakley, Arthur R. Grossman, Virginia M. Weis, Simon K. Davy
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-77638-2

Identifying chromatin features that regulate gene expression distribution
Cited by: 3
Author(s): Thanutra Zhang, Robert T. Foreman, Roy Wollman
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-77694-8

Application of multi-omics technology for the elucidation of anti-pneumococcal activity of 3-acyl-2-phenylamino-1,4-dihydroquinolin-4-one (APDQ) derivative against Streptococcus pneumoniae
Cited by: 0
Author(s): Sangyeop Lee, Hayoung Lee, Sung Ho Yun, Sangmi Jun, Yujeong Lee, Wooyoung Kim, Edmond Changkyun Park, Joonyoung Baek, Yoonna Kwak, Soojin Noh, Gon Seo, Soojin Jang, Chul Min Park, Kyung Sik Kim
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-021-07757-1

SnoRNA copy regulation affects family size, genomic location and family abundance levels
Cited by: 11
Author(s): David Μ. Bergeron, Cédric Laforest, Stacey Carpentier, Annabelle Calvé, Étienne Fafard-Couture, Gabrielle Deschamps-Francoeur, Michelle S. Scott
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-020-77816-2

Transcriptomic analysis of tobacco-flavored E-cigarette and menthol-flavored E-cigarette exposure in the human middle ear
Cited by: 2
Author(s): Jae‐Jun Song, Yoon Young Go, Jong Kyou Lee, Bum Sang Lee, Su Kyoung Park, Harry Jung, Jun Ho Lee, Jiwon Chang
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-020-77840-2

Wide-ranging transcriptomic analysis of Poncirus trifoliata, Citrus sunki, Citrus sinensis and contrasting hybrids reveals HLB tolerance mechanisms
Cited by: 17
Author(s): Maiara Curtolo, Inaiara de Souza Pacheco, Leonardo Pires Boava, Marco Aurélio Takita, Laís Moreira Granato, Diogo Manzano Galdeano, Alessandra Alves de Souza, Mariângela Cristofani–Yaly, Marcos Antônio Machado
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-016-3098-z

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction
Cited by: 24
Author(s): Erfan Sayyari, Siavash Mirarab
Software Mentions: 1
Published: about 8 years ago

10.1590/S1980-57642009DN30300008

The ex-illiterate brain: The critical period, cognitive reserve and HAROLD model
Cited by: 11
Author(s): Maria Vãnia Nunes, Alexandre Castro-Caldas, Dolores Del Rio, F Maestú, Tomás Ortiz
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2164-15-1089

RETRACTED ARTICLE: Species-specific chemosensory gene expression in the olfactory organs of the malaria vector Anopheles gambiae
Cited by: 15
Author(s): Theresa K Hodges, Luciano V. Cosme, Giridhar Athrey, Sharmila Pathikonda, Willem Takken, Michel A. Slotman
Software Mentions: 1
Published: almost 10 years ago

10.3390/cells9030783

A Wnt-BMP4 Signaling Axis Induces MSX and NOTCH Proteins and Promotes Growth Suppression and Differentiation in Neuroblastoma
Cited by: 8
Author(s): Marianna Szemes, Zsombor Melegh, Jacob Bellamy, Alexander Greenhough, Madhu Kollareddy, Daniel Catchpoole, Karim Malik
Software Mentions: 1
Published: over 4 years ago

10.3390/cells9071683

Inter-Tumor Heterogeneity—Melanomas Respond Differently to GM-CSF-Mediated Activation
Cited by: 10
Author(s): Adi Moshe, Sivan Izraely, Orit Sagi‐Assif, Sapir Malka, Shlomit Ben‐Menachem, Tsipi Meshel, Metsada Pasmanik‐Chor, Dave S. B. Hoon
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1006407

Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns
Cited by: 32
Author(s): T. Cohen, Liron Levin, Dan Mo
Software Mentions: 1
Published: about 8 years ago

10.3390/cells10092313

The Endothelial Landscape and Its Role in Von Hippel–Lindau Disease
Cited by: 5
Author(s): Isabel de Rojas-P, Virginia Albiñana, Lyudmyla Taranets, Lucía Recio-Poveda, Ángel M. Cuesta, Nikita Popov, Thales Kronenberger, Luisa María Botella
Software Mentions: 1
Published: about 3 years ago

10.1186/s12859-018-2436-3

ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Cited by: 25
Author(s): Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-015-2349-8

FRAMA: from RNA-seq data to annotated mRNA assemblies
Cited by: 31
Author(s): Martin Bens, Arne Sahm, Marco Groth, Niels Jahn, Michaela Morhart, Susanne Holtze, Thomas B. Hildebrandt, Matthias Platzer, Karol Szafranski
Software Mentions: 1
Published: almost 9 years ago

10.1002/glia.23516

The miRNA biogenesis pathway prevents inappropriate expression of injury response genes in developing and adult Schwann cells
Cited by: 8
Author(s): Deniz Gökbuget, Jorge A. Pereira, Lennart Opitz, Dominik Christe, Tobias Keßler, Antonin Marchais, Ueli Suter
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.34985

Reduced expression of C/EBPβ-LIP extends health and lifespan in mice
Cited by: 19
Author(s): Christine Müller, Laura M Zidek, Tobias Ackermann, Tristan de Jong, Peng Liu, Verena Kliche, Mohamad Amr Zaini, Gertrud Kortman, Liesbeth Harkema, Dineke S. Verbeek, Jan Tuckermann, Julia von Maltzahn, Alain de Bruin, Victor Guryev, Zhaoqi Wang, Cornelis F. Calkhoven
Software Mentions: 1
Published: over 6 years ago

10.1080/16549716.2019.1664103

The logic model for Uganda’s health sector preparedness for public health threats and emergencies
Cited by: 12
Author(s): Alex Riolexus Ario, Issa Makumbi, Lilian Bulage, Simon Kyazze, Joshua Kayiwa, Milton Wetaka, Juliet N. Kasule, Felix Ocom
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0149229

Major Transcriptome Changes Accompany the Growth of Pseudomonas aeruginosa in Blood from Patients with Severe Thermal Injuries
Cited by: 30
Author(s): Cassandra Kruczek, Kameswara Rao Kottapalli, Sharmila Dissanaike, Nyaradzo Dzvova, John Griswold, Jane A. Colmer-Hamood, Abdul N. Hamood
Software Mentions: 1
Published: over 8 years ago

10.3390/cancers12030620

RNA Immune Signatures from Pan-Cancer Analysis Are Prognostic for High-Grade Serous Ovarian Cancer and Other Female Cancers
Cited by: 12
Author(s): Wendell Jones, Chad M. Michener, Charles V. Biscotti, Elena Ioana Braicu, Jalid Sehouli, Mahrukh K. Ganapathi, Ram Ganapathi
Software Mentions: 1
Published: over 4 years ago

10.3390/ijms20071689

A Transcriptomic Insight into the Impact of Colon Cancer Cells on Mast Cells
Cited by: 10
Author(s): Yingxin Yu, Bart R. Blokhuis, Johan Garssen, Frank A. Redegeld
Software Mentions: 1
Published: over 5 years ago

10.1186/s12955-018-0858-2

Assessing the reliability of the short form 12 (SF-12) health survey in adults with mental health conditions: a report from the wellness incentive and navigation (WIN) study
Cited by: 138
Author(s): Tianyao Huo, Yi Guo, Elizabeth Shenkman, Keith E. Muller
Software Mentions: 1
Published: almost 7 years ago

10.1186/1477-7525-8-82

Validation study of a web-based assessment of functional recovery after radical prostatectomy
Cited by: 57
Author(s): Andrew J. Vickers, Caroline Savage, Marwan Shouery, James A. Eastham, Peter T. Scardino, Ethan Basch
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-020-03593-4

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
Cited by: 5
Author(s): Stefan Niebler, André C. Müller, Thomas Hankeln, Bertil Schmidt
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1007443

Convergent evolution of gene expression in two high-toothed stickleback populations
Cited by: 27
Author(s): James C. Hart, Nicholas Ellis, Michael B. Eisen, Craig T. Miller
Software Mentions: 1
Published: over 6 years ago

10.1016/j.heliyon.2020.e05850

Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2
Cited by: 49
Author(s): Kun Sun, Liuqi Gu, Li Ma, Yugang Duan
Software Mentions: 1
Published: almost 4 years ago

10.1007/s11886-017-0886-2

Ablative Radiotherapy as a Noninvasive Alternative to Catheter Ablation for Cardiac Arrhythmias
Cited by: 38
Author(s): Paul C. Zei, Scott G. Soltys
Software Mentions: 1
Published: over 7 years ago

10.3390/cells9081806

In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences
Cited by: 16
Author(s): Annie Robic, Julie Demars, Christa Kühn
Software Mentions: 1
Published: over 4 years ago

10.1038/s41437-021-00434-9

On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae)
Cited by: 7
Author(s): Jörg A. Bachmann, Andrew Tedder, Marco Fracassetti, Kim A. Steige, Clément Lafon‐Placette, Claudia Köhler, Tanja Slotte
Software Mentions: 1
Published: over 3 years ago

10.1186/s40478-020-00951-4

Fusions involving BCOR and CREBBP are rare events in infiltrating glioma
Cited by: 11
Author(s): David Pisapia, Kentaro Ohara, Rohan Bareja, David Wilkes, Erika Hissong, Jaclyn A. Croyle, Joon‐Hyung Kim, Jad Saab, Theresa Y. MacDonald, Shaham Beg, Catherine O’Reilly, Sarah Kudman, Mark A. Rubin, Olivier Elemento, Andrea Sboner, Jeffrey P. Greenfield, Juan Miguel Mosquera
Software Mentions: 1
Published: over 4 years ago

10.1016/j.yjmcc.2019.02.002

Stromal cell-derived factor-1α signals via the endothelium to protect the heart against ischaemia-reperfusion injury
Cited by: 15
Author(s): Daniel I Bromage, Staša Taferner, Zhenhe He, Oliver J. Ziff, Derek M. Yellon, Sean M. Davidson
Software Mentions: 1
Published: over 5 years ago

10.1186/s13073-018-0567-9

Single-cell transcriptome analysis of lineage diversity in high-grade glioma
Cited by: 157
Author(s): Jinzhou Yuan, Hanna Mendes Levitin, Véronique Frattini, Erin C. Bush, Deborah Boyett, Jorge Samanamud, Michele Ceccarelli, Athanassios Dovas, George Zanazzi, Peter Canoll, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter A. Sims
Software Mentions: 1
Published: over 6 years ago

10.1038/s41375-021-01376-1

CXCR4 hyperactivation cooperates with TCL1 in CLL development and aggressiveness
Cited by: 4
Author(s): Richard T. Lewis, H. Carlo Maurer, Nikita Singh, Irene González-Menéndez, Matthias Wirth, Markus Schick, Zhang Le, Konstandina Isaakidis, Anna Katharina Scherger, Veronika Schulze, Junyan Lu, Thorsten Zenz, Katja Steiger, Roland Rad, Leticia Quintanilla-Martı́nez, Marion Espéli, Karl Balabanian, Ulrich Keller, Stefan Habringer
Software Mentions: 1
Published: over 3 years ago

10.1038/s41375-018-0108-y

Kinase domain activation through gene rearrangement in multiple myeloma
Cited by: 26
Author(s): Gareth J. Morgan, Jie He, Ruslana G. Tytarenko, Purvi Patel, Owen Stephens, Shan Zhong, Shayu Deshpande, Michael Bauer, Niels Weinhold, Carolina Schinke, Leo Rasche, Mark Bailey, Siraj M. Ali, Jeff Ross, Vincent A. Miller, P. J. Stephens, Sharmilan Thanendrarajan, Maurizio Zangari, Frits van Rhee, Tariq I. Mughal, Faith E. Davies, Brian A. Walker
Software Mentions: 1
Published: over 6 years ago

10.1007/s00109-020-01937-4

Molecular karyotyping and gene expression analysis in childhood cancer patients
Cited by: 4
Author(s): Danuta Galetzka, Tobias Müller, Marcus Dittrich, Miriam Endres, Nergiz Kartal, Olesja Sinizyn, Steffen Rapp, Tanja Zeller, Christian Müller, Thomas Hankeln, Peter Scholz-Kreisel, Heather Chorzempa, Johanna Mirsch, Alicia Schulze, Heidi Rossmann, Claudia Sissi, T. Haaf, Dirk Prawitt, Manuela Marron, Heinz Schmidberger
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1009320

Lhx6 regulates canonical Wnt signaling to control the fate of mesenchymal progenitor cells during mouse molar root patterning
Cited by: 8
Author(s): Jinzhi He, Junjun Jing, Jifan Feng, Xia Han, Yuan Yuan, Tingwei Guo, Fei Pei, Yuanyuan Ma, Courtney Cho, Thach-Vu Ho, Yang Chai
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pgen.1003714

A Shift to Organismal Stress Resistance in Programmed Cell Death Mutants
Cited by: 36
Author(s): Meredith E. Judy, Ayumi Nakamura, Anne Huang, Harli Grant, Helen McCurdy, Kurt F. Weiberth, Fuying Gao, Giovanni Coppola, Cynthia Kenyon, Aimee W. Kao
Software Mentions: 1
Published: about 11 years ago

10.1186/s13073-015-0152-4

Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
Cited by: 71
Author(s): Patrick Deelen, Daria V. Zhernakova, Mark de Haan, Marijke van der Sijde, Marc Jan Bonder, Juha Karjalainen, K. Joeri van der Velde, Kristin M. Abbott, Jingyuan Fu, Cisca Wijmenga, Richard J. Sinke, Morris A. Swertz, Lude Franke
Software Mentions: 1
Published: over 9 years ago

10.1093/gbe/evab178

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae
Cited by: 5
Author(s): Chris J. Hulatt, René H. Wijffels, Matthew C. Posewitz
Software Mentions: 1
Published: over 3 years ago

10.1093/gbe/evaa235

A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis
Cited by: 27
Author(s): Eiichi Shoguchi, Girish Beedessee, Kanako Hisata, Isao Tada, Haruhi Narisoko, Noriyuki Satoh, Masanobu Kawachi, Chuya Shinzato
Software Mentions: 1
Published: about 4 years ago

10.1093/gbe/evaa195

Comprehensive Transcriptome of the Maize Stalk Borer,Busseola fusca, from Multiple Tissue Types, Developmental Stages, and Parasitoid Wasp Exposures
Cited by: 1
Author(s):
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pgen.1006453

Investigating Conservation of the Cell-Cycle-Regulated Transcriptional Program in the Fungal Pathogen, Cryptococcus neoformans
Cited by: 38
Author(s): Christina M. Kelliher, Adam R. Leman, Crystal S Sierra, Steven B. Haase
Software Mentions: 1
Published: almost 8 years ago

10.1093/gbe/evz176

Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly
Cited by: 4
Author(s): Lars Höök, Luis Leal, Venkat Talla, Niclas Backström
Software Mentions: 1
Published: over 5 years ago

10.1093/gbe/evz141

The Genome Sequence of the Anthelmintic-Susceptible New Zealand Haemonchus contortus
Cited by: 25
Author(s): Nikola Palevich, Paul Maclean, Abdul Baten, Richard W. Scott, David M Leathwick
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1008744

Coordinate genomic association of transcription factors controlled by an imported quorum sensing peptide in Cryptococcus neoformans
Cited by: 9
Author(s): Diana Summers, Daniela S. Perry, Beiduo Rao, Hiten D. Madhani
Software Mentions: 1
Published: about 4 years ago

10.1186/s13059-021-02434-8

Specific splice junction detection in single cells with SICILIAN
Cited by: 12
Author(s): Roozbeh Dehghannasiri, Julia Eve Olivieri, Ana Damljanovic, Julia Salzman
Software Mentions: 1
Published: over 3 years ago

10.1186/s13059-021-02399-8

LIQA: long-read isoform quantification and analysis
Cited by: 37
Author(s): Yu Hu, Fang Li, Xuelian Chen, Jiang Zhong, Mingyao Li, Kai Wang
Software Mentions: 1
Published: over 3 years ago

10.1186/s13059-021-02350-x

Intergenic RNA mainly derives from nascent transcripts of known genes
Cited by: 13
Author(s): Antonella Federico, Julian A. Zagalak, Jan Attig, Jernej Ule, Nicholas M. Luscombe
Software Mentions: 1
Published: over 3 years ago

10.1186/s13059-020-02180-3

Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
Cited by: 89
Author(s): Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jèssica Gómez‐Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo‐Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, André Corvelo, Leonor Frías, Marta Gut, Toni Gabaldón, Alberto Pallavicini, Carlos Canchaya, Beatriz Novoa, Tyler Alioto, David Posada, António Figueras
Software Mentions: 1
Published: about 4 years ago

10.1186/s13059-020-02094-0

Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
Cited by: 52
Author(s): Qingxin Song, Atsumi Ando, Ning Jiang, Yoko Ikeda, Z Jeffrey Chen
Software Mentions: 1
Published: over 4 years ago

10.1186/s13100-016-0085-5

Chicken (Gallus gallus) endogenous retrovirus generates genomic variations in the chicken genome
Cited by: 18
Author(s): Jinmin Lee, Seyoung Mun, Dong Hee Kim, Chun-Sung Cho, Do Hoon Oh, Kyudong Han
Software Mentions: 1
Published: almost 8 years ago

10.1016/j.midw.2019.08.002

“Nobody knows, or seems to know how rheumatology and breastfeeding works”: Women's experiences of breastfeeding whilst managing a long-term limiting condition – A qualitative visual methods study
Cited by: 13
Author(s): Denitza Williams, Jessica Webber, Bethan Pell, Aimee Grant, Julia Sanders, Ernest Choy, Adrian Edwards, Ann M. Taylor, Meng‐Chieh Wu, Rhiannon Phillips
Software Mentions: 1
Published: about 5 years ago

10.3390/microorganisms9010144

HbxB Is a Key Regulator for Stress Response and β-Glucan Biogenesis in Aspergillus nidulans
Cited by: 3
Author(s): Sung-Hun Son, Mi-Kyung Lee, Ye-Eun Son, Hee-Soo Park
Software Mentions: 1
Published: almost 4 years ago

10.3389/fonc.2020.00982

RNA-Seq Profiling of Serum Exosomal Circular RNAs Reveals Circ-PNN as a Potential Biomarker for Human Colorectal Cancer
Cited by: 67
Author(s): Yan Xie, Juan Li, Peilong Li, Ning Li, Ying Zhang, Helen Binang, Yinghui Zhao, Weili Duan, Yingjie Chen, Yunshan Wang, Du Li, Chuanxin Wang
Software Mentions: 1
Published: over 4 years ago

10.3390/microorganisms8091319

Genome Wide Analysis Reveals the Role of VadA in Stress Response, Germination, and Sterigmatocystin Production in Aspergillus nidulans Conidia
Cited by: 8
Author(s): Ye-Eun Son, Hee-Soo Park
Software Mentions: 1
Published: about 4 years ago

10.3389/fonc.2020.632187

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects
Cited by: 14
Author(s): Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Software Mentions: 1
Published: almost 4 years ago

10.3389/fonc.2021.612354

Inhibition of HSP90 as a Strategy to Radiosensitize Glioblastoma: Targeting the DNA Damage Response and Beyond
Cited by: 10
Author(s): Michael Orth, Valérie Albrecht, Karin Seidl, Linda Kinzel, Kristian Unger, Julia Heß, Lisa Kreutzer, Na Sun, Benjamin Stegen, Alexander Nieto, Jessica Maas, Nicolas Winssinger, Anna A. Friedl, Axel Walch, Claus Belka, Horst Zitzelsberger, Maximilian Niyazi, Kirsten Lauber
Software Mentions: 1
Published: over 3 years ago

10.18632/oncotarget.26673

The X-linked tumor suppressor TSPX downregulates cancer-drivers/oncogenes in prostate cancer in a C-terminal acidic domain dependent manner
Cited by: 5
Author(s): Tatsuo Kido, Yunmin Li, Yuichiro Tanaka, Rajvir Dahiya, Yun‐Fai Chris Lau
Software Mentions: 1
Published: almost 6 years ago

10.3389/fonc.2021.622244

Patient-Derived Nasopharyngeal Cancer Organoids for Disease Modeling and Radiation Dose Optimization
Cited by: 11
Author(s): Sasidharan Swarnalatha Lucky, Martin Law, Man Tin Lui, Jamie Mong, Jin Shi, Sidney Yu, Do Kun Yoon, Shih Kien Djeng, Ji‐Guang Wang, Chwee Ming Lim, Min Tan
Software Mentions: 1
Published: almost 4 years ago

10.3389/fonc.2019.01120

Epstein-Barr Virus BART Long Non-coding RNAs Function as Epigenetic Modulators in Nasopharyngeal Carcinoma
Cited by: 43
Author(s): Rob J. A. Verhoeven, S. Y. Tong, Bobo Wing-Yee Mok, Jiayan Liu, Songtao He, Jingfeng Zong, Yixin Chen, Sai‐Wah Tsao, Maria Li Lung, Honglin Chen
Software Mentions: 1
Published: about 5 years ago

10.18632/oncotarget.26797

Clinical validation of the tempus xT next-generation targeted oncology sequencing assay
Cited by: 101
Author(s): Nike Beaubier, Robert Tell, Denise Lau, Jerod Parsons, Stephen J. Bush, Jason Perera, Shelly Sorrells, Timothy Baker, Alan L. Chang, Jackson Michuda, Catherine Iguartua, Shelley M. MacNeil, Kaanan P. Shah, Philip Ellis, Kimberly Yeatts, Brett Mahon, Timothy J. Taxter, Martin Bontrager, Aly A. Khan, Robert Huether, Eric Lefkofsky, Kevin P. White
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2020.01498

Immune-Related Gene Expression and Cytokine Secretion Is Reduced Among African American Colon Cancer Patients
Cited by: 26
Author(s): Jenny Paredes, Jovanny Zabaleta, Jone Garai, Ping Ji, Sayed Imtiaz, Marzia Spagnardi, Joussette I. Alvarado, Li Li, Mubarak Akadri, Kaylene Barrera, María Muñoz-Sagastibelza, Raavi Gupta, Mohamed Alshal, Maksim Agaronov, Henry Talus, Xuefeng Wang, John M. Carethers, Jennie L. Williams, Laura Martello
Software Mentions: 1
Published: about 4 years ago

10.3389/fonc.2015.00016

Therapeutic Re-Activation of Protein Phosphatase 2A in Acute Myeloid Leukemia
Cited by: 23
Author(s): Kavitha Ramaswamy, Barbara Spitzer, Alex Kentsis
Software Mentions: 1
Published: almost 10 years ago

10.3389/fonc.2020.611467

Identification of STRBP as a Novel JAK2 Fusion Partner Gene in a Young Adult With Philadelphia Chromosome-Like B-Lymphoblastic Leukemia
Cited by: 4
Author(s): Xinyue Zhang, Haiping Dai, Zheng Li, Jia Yin, Xingping Lang, Chen Yang, Sheng Xiao, Mingqing Zhu, Dandan Liu, Hong Liu, Hongjie Shen, Depei Wu, Xiaowen Tang
Software Mentions: 1
Published: almost 4 years ago

10.3389/fonc.2020.01203

A Greedy Algorithm-Based Stem Cell LncRNA Signature Identifies a Novel Subgroup of Lung Adenocarcinoma Patients With Poor Prognosis
Cited by: 3
Author(s): Seema Khadirnaikar, Annesha Chatterjee, Pranjal Kumar, Sudhanshu Shukla
Software Mentions: 1
Published: over 4 years ago

10.3389/fonc.2019.01279

Fry Is Required for Mammary Gland Development During Pregnant Periods and Affects the Morphology and Growth of Breast Cancer Cells
Cited by: 6
Author(s): Yan Liu, Xushen Chen, Zhihong Gong, Hao Zhang, Fudong Fan, Xiaojiang Tang, Jie Wang, Peng Xu, Helmut Zarbl, Xuefeng Ren
Software Mentions: 1
Published: about 5 years ago

10.3389/fonc.2021.732644

RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples
Cited by: 4
Author(s): Maxim Sorokin, Alexander Gorelyshev, Victor Efimov, Evgenia Zotova, Marianna Zolotovskaia, Elizaveta Rabushko, Denis Kuzmin, Alexander Seryakov, Dmitri Kamashev, Xinmin Li, Elena Poddubskaya, Maria Suntsova, Anton Buzdin
Software Mentions: 1
Published: about 3 years ago

10.3389/fonc.2021.620912

Loss of TARBP2 Drives the Progression of Hepatocellular Carcinoma via miR-145-SERPINE1 Axis
Cited by: 6
Author(s): Li Man Li, Chang Chen, Ruo Xi Ran, Jing Huang, Hui Sun, Chang Zeng, Zhou Zhang, Wei Zhang, Song Mei Liu
Software Mentions: 1
Published: over 3 years ago

10.18632/oncotarget.26808

Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer
Cited by: 9
Author(s): Jessica Kaufmann, Nicolas Wentzensen, Titus J. Brinker, Niels Grabe
Software Mentions: 1
Published: over 5 years ago

10.3389/fonc.2018.00140

Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants
Cited by: 6
Author(s): Vanessa Lattimore, John Pearson, Margaret J. Currie, Amanda B. Spurdle, kConFab Investigators, Bridget A. Robinson, Logan C. Walker
Software Mentions: 1
Published: over 6 years ago

10.3389/fnins.2019.01453

Physical Activity Induces Nucleus Accumbens Genes Expression Changes Preventing Chronic Pain Susceptibility Promoted by High-Fat Diet and Sedentary Behavior in Mice
Cited by: 9
Author(s): Arthur Freitas Brandao, Ivan José Magayewski Bonet, Marco Pagliusi, Gabriel Gerardini Zanetti, Nam Pho, Cláudia Herrera Tambeli, Carlos Amílcar Parada, André Schwambach Vieira, César Renato Sartori
Software Mentions: 1
Published: almost 5 years ago

10.3389/fnins.2020.00508

Inferior Colliculus Transcriptome After Status Epilepticus in the Genetically Audiogenic Seizure-Prone Hamster GASH/Sal
Cited by: 6
Author(s): Sandra M. Díaz-Rodríguez, Daniel López-López, M.J. Herrero-Turrión, Ricardo Gómez-Nieto, Ángel Canal-Alonso, Dolores E. López
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.01367-19

Complete Genome Sequences for Two Talaromyces marneffei Clinical Isolates from Northern and Southern Vietnam
Cited by: 5
Author(s): Christina A. Cuomo, Terrance Shea, Thu Nguyen, Philip Ashton, John R. Perfect, Thuy Le
Software Mentions: 1
Published: almost 5 years ago

10.7554/eLife.66808

Expansion of CD10neg neutrophils and CD14+HLA-DRneg/low monocytes driving proinflammatory responses in patients with acute myocardial infarction
Cited by: 18
Author(s): Daniela Fraccarollo, Jonas Neuser, Julian Möller, Christian Riehle, Paolo Galuppo, Johann Bauersachs
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00294-21

Transcriptome RNA Sequencing Data Set of Differential Gene Expression in Escherichia coli BW25113 Wild-Type and slyA Mutant Strains
Cited by: 1
Author(s): Olabisi Ojo, Derrick Scott, BA Iwalokun, Babatunde Odetoyin, Anne Grove
Software Mentions: 1
Published: over 3 years ago

10.3389/fneur.2020.540878

Involvement of CXCL1/CXCR2 During Microglia Activation Following Inflammation-Sensitized Hypoxic-Ischemic Brain Injury in Neonatal Rats
Cited by: 30
Author(s): Meray Serdar, Karina Kempe, Ralf Herrmann, Daniel Picard, Marc Remke, Josephine Herz, Ivo Bendix, Ursula Felderhoff-Müser, Hemmen Sabir
Software Mentions: 1
Published: about 4 years ago

10.3389/fneur.2019.00647

STIR-Net: Deep Spatial-Temporal Image Restoration Net for Radiation Reduction in CT Perfusion
Cited by: 17
Author(s): Yao Xiao, Peng Liu, Yun Liang, Skylar E. Stolte, Pina C. Sanelli, Ajay Gupta, Jana Ivanidze, Ruogu Fang
Software Mentions: 1
Published: over 5 years ago

10.3389/fneur.2020.00033

Top Common Differentially Expressed Genes in the Epileptogenic Nucleus of Two Strains of Rodents Susceptible to Audiogenic Seizures: WAR and GASH/Sal
Cited by: 9
Author(s): Samara Damasceno, Ricardo Gómez-Nieto, Norberto García-Cairasco, M.J. Herrero-Turrión, Faustino Marı́n, Dolores E. López
Software Mentions: 1
Published: almost 5 years ago

10.3389/fnmol.2019.00037

Transcriptome Analysis of the Human Tibial Nerve Identifies Sexually Dimorphic Expression of Genes Involved in Pain, Inflammation, and Neuro-Immunity
Cited by: 36
Author(s): Pradipta Ray, Junaid Sarfraz Khan, Andi Wangzhou, Diana Tavares‐Ferreira, Armen N. Akopian, Gregory Dussor, Theodore J. Price
Software Mentions: 1
Published: over 5 years ago

10.3389/fnmol.2020.00043

Interference With Complex IV as a Model of Age-Related Decline in Synaptic Connectivity
Cited by: 10
Author(s): Martin Kriebel, Julia Ebel, Florian Battke, Stefan Griesbach, Hansjürgen Volkmer
Software Mentions: 1
Published: over 4 years ago

10.3389/fnmol.2020.00154

Gene Expression Profile at the Motor Endplate of the Neuromuscular Junction of Fast-Twitch Muscle
Cited by: 11
Author(s): Kun Huang, Jin Li, Mikako Ito, Jun‐ichi Takeda, Bisei Ohkawara, Tomoo Ogi, Akio Matsubara, Kinji Ohno
Software Mentions: 1
Published: about 4 years ago

10.3389/fnmol.2018.00463

Transcriptomic Analysis of Zebrafish TDP-43 Transgenic Lines
Cited by: 17
Author(s): Alexandra Lissouba, Meijiang Liao, Edor Kabashi, Pierre Drapeau
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41375-021-01263-9

Gene expression derived from alternative promoters improves prognostic stratification in multiple myeloma
Cited by: 7
Author(s): Luis Vítores Valcárcel, Ane Amundarain, Marta Kulis, Stella Charalampopoulou, Ari Melnick, Jesús F. San Miguel, José I. Martín‐Subero, Francisco J Planes, Xabier Agirre, Felipe Prósper
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00012-19

Near-Complete Genome Sequences of Vesicular Stomatitis Virus Indiana Laboratory Strains HR and T1026R1 and Plaque Isolates 22-20 and 22-25
Cited by: 4
Author(s): Thomas M. Russell, Evan E. Santo, Lisa Golebiewski, Nathan Haseley, Maureen C. Ferran
Software Mentions: 1
Published: over 5 years ago

Projects: cran: STAR

Papers Mentioning STAR 5,759