Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: TopHat

https://packages.ecosyste.ms/registries/pypi.org/packages/TopHat

TopHat Platform
3 versions
Latest release: about 12 years ago
9 downloads last month

Papers Mentioning TopHat 5,017

Identification of Milk Fat Metabolism-Related Pathways of the Bovine Mammary Gland during Mid and Late Lactation and Functional Verification of the ACSL4 Gene
Cited by: 12
Author(s): Yongliang Fan, Ziyin Han, Xubin Lu, Huimin Zhang, Abdelaziz Adam Idriss Arbab, Juan J. Loor, Yi Yang, Zhangping Yang
Software Mentions: 1
Published: about 4 years ago

10.1186/s13229-015-0017-0

Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders
Cited by: 97
Author(s): Marta Codina‐Solà, Benjamín Rodríguez-Santiago, Aïda Homs, Javier Santoyo, Maria Rigau, Gemma Aznar-Laín, Miguel del Campo, Blanca Gener, Elisabeth Gabau, M.P. Botella, Armand Gutiérrez-Arumí, Guillermo Antiñolo, Luis A. Pérez‐Jurado, Ivon Cuscò
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0137551

Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes
Cited by: 19
Author(s): Yi-Jiang Song, Guiling Li, Jun He, Yao Guo, Yang Li
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0164959

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)
Cited by: 10
Author(s): Lekha T. Pazhamala, Gaurav Agarwal, Prasad Bajaj, Vinay Kumar, Akanksha Kulshreshtha, Rachit K. Saxena, Rajeev K. Varshney
Software Mentions: 1
Published: about 8 years ago

10.7554/eLife.29677

RNG105/caprin1, an RNA granule protein for dendritic mRNA localization, is essential for long-term memory formation
Cited by: 42
Author(s): Kei Ichi Nakayama, Rie Ohashi, Yo Shinoda, Maya Yamazaki, Manabu Abe, Akihiro Fujikawa, Shuji Shigenobu, Akira Futatsugi, Masaharu Noda, Katsuhiko Mikoshiba, Teiichi Furuichi, Kenji Sakimura, Nobuyuki Shiina
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0200914

Studying on the strictly self-compatibility mechanism of ‘Liuyefeitao’ peach (Prunus persica L.)
Cited by: 2
Author(s): Wei Liu, Mao-Song Pei, Anning Zhang
Software Mentions: 1
Published: over 6 years ago

10.3390/genes12040567

Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice
Cited by: 5
Author(s): Shoudong Wang, Shuo Sun, Runze Guo, Wenying Liao, Huixia Shou
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0133923

Calorie Restriction Suppresses Age-Dependent Hippocampal Transcriptional Signatures
Cited by: 53
Author(s): Marissa J. Schafer, Igor Dolgalev, Melissa J. Alldred, Adriana Heguy, Stephen D. Ginsberg
Software Mentions: 1
Published: over 9 years ago

10.3390/genes12050737

Exploration of Alternative Splicing Events in Mesenchymal Stem Cells from Human Induced Pluripotent Stem Cells
Cited by: 4
Author(s): Ji Eun Jeong, Binna Seol, Han-Seop Kim, Jae Yun Kim, Yee Sook Cho
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0117581

Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body
Cited by: 25
Author(s): Masahito Yoshihara, Hiroko Ohmiya, Shotaro Hara, Satoshi Kawasaki, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Motokazu Tsujikawa, Kohji Nishida
Software Mentions: 1
Published: over 9 years ago

10.1186/s13229-017-0174-4

RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome
Cited by: 67
Author(s): Natasha L. Pacheco, Michael R. Heaven, Leanne M. Holt, David K. Crossman, Kristin J. Boggio, Scott A. Shaffer, Daniel Flint, Michelle L. Olsen
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0057563

The Baboon Kidney Transcriptome: Analysis of Transcript Sequence, Splice Variants, and Abundance
Cited by: 22
Author(s): Kimberly D. Spradling, Jeremy P. Glenn, Roy Garcia, Robert E. Shade, Laura A. Cox
Software Mentions: 1
Published: over 11 years ago

10.1186/s12263-017-0557-3

Brain xanthophyll content and exploratory gene expression analysis: subspecies differences in rhesus macaque
Cited by: 5
Author(s): Emily S. Mohn, John W. Erdman, Martha Neuringer, Matthew J. Kuchan, Elizabeth J. Johnson
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.52859

Phrenic-specific transcriptional programs shape respiratory motor output
Cited by: 10
Author(s): Alicia N Vagnozzi, Kiran Garg, Carola Dewitz, Matthew T. Moore, Jared M. Cregg, Lucie Jeannotte, Niccolò Zampieri, Lynn T. Landmesser, Polyxeni Philippidou
Software Mentions: 1
Published: almost 5 years ago

10.1590/1678-4685-GMB-2017-0161

New insights into Phakopsora pachyrhizi infection based on transcriptome analysis in planta
Cited by: 3
Author(s): Michelle Pires Rincão, Mayra Costa da Cruz Gallo de Carvalho, Leandro Costa do Nascimento, Valéria Stefania Lopes-Caitar, Kênia Mara Baiocchi de Carvalho, Luana Mieko Darben, Anderson Hideo Yokoyama, Marcelo Falsarella Carazzolle, R. V. Abdelnoor, Francismar Corrêa Marcelino-Guimarães
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.12805

SIN3A and SIN3B differentially regulate breast cancer metastasis
Cited by: 27
Author(s): Monica J. Lewis, Jianzhong Liu, Emily Falk Libby, Minnkyong Lee, Nigel P.S. Crawford, Douglas R. Hurst
Software Mentions: 1
Published: about 8 years ago