pypi: TopHat | Projects | Ecosyste.ms: Papers

10.7554/eLife.56689

Genome streamlining in a minute herbivore that manipulates its host plant
Cited by: 30
Author(s): Robert Greenhalgh, Wannes Dermauw, Joris J. Glas, Stéphane Rombauts, Nicky Wybouw, Jainy Thomas, Juan M. Alba, Ellen J. Pritham, Saioa Legarrea, René Feyereisen, Yves Van de Peer, Thomas Van Leeuwen, Richard M. Clark, Merijn R. Kant
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.ppat.1005438

Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression
Cited by: 42
Author(s): Jason Lamontagne, Joshua Chang Mell, Michael J. Bouchard
Software Mentions: 7
Published: over 10 years ago

10.1186/1471-2164-15-702

Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves
Cited by: 58
Author(s): Adrienne N. Moran Lauter, Gregory A. Peiffer, Tao Yin, Steven A. Whitham, Dianne Cook, Randy C. Shoemaker, Michelle A. Graham
Software Mentions: 7
Published: about 12 years ago

10.1038/s41598-018-24863-5

Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC induction
Cited by: 15
Author(s): Zhong Liu, Haiyuan Mu, Bingqiang Wen, Wei Zhang, Qingqing Wei, Ge Gao, Jianyong Han, Suying Cao
Software Mentions: 7
Published: over 8 years ago

10.1186/1471-2164-14-204

RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome
Cited by: 63
Author(s): Yvan Wenger, Brigitte Galliot
Software Mentions: 7
Published: over 13 years ago

10.1186/s13059-017-1286-z

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Cited by: 68
Author(s): Matthias Heinig, Michiel E. Adriaens, Sebastian Schäfer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, András Varró, Nanette H. Bishopric, Alfred L. George, Cristobal dos Remedios, Aida Moreno‐Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J.R. Barton, Stuart A. Cook, Yigal M. Pinto, Connie R. Bezzina, Norbert Hübner
Software Mentions: 7
Published: almost 9 years ago

10.1093/gigascience/giy093

Leveraging multiple transcriptome assembly methods for improved gene structure annotation
Cited by: 110
Author(s): Luca Venturini, Shabhonam Caim, Gemy Kaithakottil, Daniel Mapleson, David Swarbreck
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pgen.1005930

Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Cited by: 36
Author(s): Erica Hildebrand, Sue Biggins
Software Mentions: 7
Published: over 10 years ago

10.1186/s13073-020-00788-5

Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation
Cited by: 10
Author(s): Shi Yang Liu, Nathan Harmston, Trudy Lee Glaser, Yunka Wong, Zheng Zhong, Babita Madan, David M. Virshup, Enrico Petretto
Software Mentions: 7
Published: almost 6 years ago

10.1186/1471-2229-13-213

Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17
Cited by: 12
Author(s): Claude Urbany, Andreas Benke, Johanna Marsian, Bruno Huettel, Richard Reinhardt, Benjamin Stich
Software Mentions: 7
Published: almost 13 years ago

10.1371/journal.pbio.3000988

The molecular and metabolic program by which white adipocytes adapt to cool physiologic temperatures
Cited by: 9
Author(s): Hiroyuki Mori, Colleen E. Dugan, Akira Nishii, Ameena Benchamana, Ziru Li, Thomas S. Cadenhead, Arun K. Das, Charles R. Evans, Katherine A. Overmyer, Steven M. Romanelli, Sydney K. Peterson, Devika P. Bagchi, Callie A.S. Corsa, Julie Hardij, Brian S. Learman, Mahmoud El Azzouny, Joshua J. Coon, Ken Inoki, Ormond A. MacDougald
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-020-01992-7

TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription
Cited by: 5
Author(s): Guangyu Wang, Qingshu Meng, Bo Xia, Shuo Zhang, Jie Lv, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao, Kaifu Chen
Software Mentions: 7
Published: over 6 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 10 years ago

10.1038/srep41531

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence
Cited by: 23
Author(s): Matthew J. Neave, Agus Sunarto, Kenneth A. McColl
Software Mentions: 7
Published: over 9 years ago

10.1038/s41598-020-73391-8

Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
Cited by: 36
Author(s): Meaghan L. Pimsler, Kennan Oyen, James D. Herndon, Jason M. Jackson, James P. Strange, Michael E. Dillon, Jeffrey D. Lozier
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.60176

Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus
Cited by: 21
Author(s): Taro Maeda, Shunichi Takahashi, Takao Yoshida, Shigeru Shimamura, Yoshihiro Takaki, Yukiko Nagai, Atsushi Toyoda, Yutaka Suzuki, Asuka Arimoto, Hisaki Ishii, Nori Satoh, Tomoaki Nishiyama, Mitsuyasu Hasebe, Tadashi Maruyama, Jun Minagawa, Junichi Obokata, Shuji Shigenobu
Software Mentions: 7
Published: over 5 years ago

10.12688/f1000research.17145.2

False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors
Cited by: 35
Author(s): Ashis Saha, Alexis Battle
Software Mentions: 7
Published: over 7 years ago

10.1111/pbi.13205

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass
Cited by: 45
Author(s): Linkai Huang, Guangyan Feng, Haidong Yan, Zhongren Zhang, B. Shaun Bushman, Jianping Wang, Aureliano Bombarely, Mingzhou Li, Zhongfu Yang, Gang Nie, Wengang Xie, Lei Xu, Peilin Chen, Xinxin Zhao, Wenkai Jiang, Xinquan Zhang
Software Mentions: 7
Published: about 7 years ago

10.1186/s13059-017-1197-z

H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity
Cited by: 66
Author(s): Yue Zhou, Francisco J. Romero–Campero, Ángeles Gómez-Zambrano, Franziska Turck, Myriam Calonje
Software Mentions: 7
Published: over 9 years ago

10.1186/s12864-018-4934-0

Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola
Cited by: 30
Author(s): Xiaofei Liang, Shengping Shang, Qiuyue Dong, Bo Wang, Rong Zhang, Mark L. Gleason, Guangyu Sun
Software Mentions: 7
Published: about 8 years ago

10.1186/s12915-020-0752-3

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells
Cited by: 33
Author(s): Donnchadh S. Dunican, Heidi K. Mjoseng, Leanne Duthie, Ilya M. Flyamer, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0029685

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Cited by: 104
Author(s): Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 6
Published: over 14 years ago

10.1371/journal.pone.0147426

Transcriptomic Profile of Whole Blood Cells from Elderly Subjects Fed Probiotic Bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a Phase I Open Label Study
Cited by: 16
Author(s): Gloria Solano‐Aguilar, Aleksey Molokin, Christine Botelho, Anne‐Maria Fiorino, Bryan T. Vinyard, Robert Li, Celine Chen, Joseph F. Urban, Harry Dawson, Irina Andreyeva, Miriam Haverkamp, Patricia L. Hibberd
Software Mentions: 6
Published: over 10 years ago

10.1186/s12859-019-3121-x

A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
Cited by: 2
Author(s): Stanislav Listopad, Trina M. Norden-Krichmar
Software Mentions: 6
Published: almost 7 years ago

10.3390/genes10070514

Transcriptional Analysis of the Early Ripening of ‘Kyoho’ Grape in Response to the Treatment of Riboflavin
Cited by: 9
Author(s): Zhenguang Wang, Lili Guo, Xiao-Ru Ji, Yi‐He Yu, Guohai Zhang, Da‐Long Guo
Software Mentions: 6
Published: about 7 years ago

10.3390/pathogens8040195

An Acute Stress Model in New Zealand White Rabbits Exhibits Altered Immune Response to Infection with West Nile Virus
Cited by: 5
Author(s): Willy W. Suen, Mitchell Imoda, Albert W Thomas, Nur N B M Nasir, Nawaporn Tearnsing, Wenqi Wang, Helle Bielefeldt‐Ohmann
Software Mentions: 6
Published: almost 7 years ago

10.7717/peerj.8371

The effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells
Cited by: 4
Author(s): Monika Ruszkowska, Agnieszka Sadowska, Anna Nynca, Karina Orlowska, Sylwia Świgońska, Tomasz Molcan, Łukasz Paukszto, J Jastrzebski, Renata E. Ciereszko
Software Mentions: 6
Published: over 6 years ago

10.3389/fpls.2017.01926

A Pectin Methylesterase ZmPme3 Is Expressed in Gametophyte factor1-s (Ga1-s) Silks and Maps to that Locus in Maize (Zea mays L.)
Cited by: 28
Author(s): Adrienne N. Moran Lauter, Michael G. Muszynski, Ryan D. Huffman, M. Paul Scott
Software Mentions: 6
Published: almost 9 years ago

10.1186/1471-2105-15-167

PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis
Cited by: 4
Author(s): Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta, Zhumur Ghosh
Software Mentions: 6
Published: over 12 years ago

10.1186/1471-2105-15-S3-A7

Oqtans: a multifunctional workbench for RNA-seq data analysis
Cited by: 0
Author(s): Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Kaushik Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch
Software Mentions: 6
Published: over 12 years ago

10.1111/acel.12740

Comparative transcriptomics across 14Drosophilaspecies reveals signatures of longevity
Cited by: 33
Author(s): Siming Ma, Andrei Avanesov, Emily Porter, Byeong Cheol Lee, Marco Mariotti, Nadezhda Zemskaya, Roderic Guigó, Alexey Moskalev, Vadim N. Gladyshev
Software Mentions: 6
Published: over 8 years ago

10.3389/fphys.2019.01370

A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart
Cited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: almost 7 years ago

10.1002/1878-0261.12435

Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA‐seq and VirTect
Cited by: 7
Author(s): Atlas Khan, Qian Liu, Xuelian Chen, Andres Stucky, Parish P. Sedghizadeh, Daniel Adelpour, Xi Zhang, Kai Wang, Jiang Zhong
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2019.02491

Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection
Cited by: 30
Author(s): Liming Gu, Huixiong Deng, Zhihui Ren, Ying Zhao, Shun Yu, Yingzhu Guo, Jianping Dai, Xiaoxuan Chen, Kangsheng Li, Rui Li, Gefei Wang
Software Mentions: 6
Published: almost 7 years ago

10.1002/1878-0261.12829

Identification of RUNX1T1 as a potential epigenetic modifier in small‐cell lung cancer
Cited by: 10
Author(s): He Tian, Gary Wildey, Karen McColl, Alyssa Savadelis, Kyle B. Spainhower, Cassidy McColl, Adam Kresak, Aik Choon Tan, Michael Yang, Ata Abbas, Afshin Dowlati
Software Mentions: 6
Published: almost 6 years ago

10.1099/mgen.0.000320

Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics
Cited by: 0
Author(s): Amol C. Shetty, John Mattick, Matthew Chung, Carrie McCracken, Anup Mahurkar, Scott G. Filler, Claire M. Fraser, David A. Rasko, Vincent M. Bruno, Julie C. Dunning Hotopp
Software Mentions: 6
Published: over 6 years ago

10.3389/fpls.2018.01212

A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant–Microbe Interactions
Cited by: 12
Author(s): Silvia Zanini, Ena Šečić, Lukas Jelonek, Karl-Heinz Kögel
Software Mentions: 6
Published: about 8 years ago

10.3390/v10090512

Robust Innate Immunity of Young Rabbits Mediates Resistance to Rabbit Hemorrhagic Disease Caused by Lagovirus Europaeus GI.1 But Not GI.2
Cited by: 28
Author(s): Matthew J. Neave, Robyn N. Hall, Nina Huang, Kenneth A. McColl, Peter J. Kerr, Marion Hoehn, Jennifer Taylor, Tanja Strive
Software Mentions: 6
Published: almost 8 years ago

10.1111/acel.13153

Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease
Cited by: 44
Author(s): Min Young Lee, Jung‐Hee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong Yeon Shin, Ann C. McKee, Neil W. Kowall, Jong‐Il Kim, Thor D. Stein, Daehee Hwang, Hoon Ryu
Software Mentions: 6
Published: over 6 years ago

10.1186/s13072-018-0250-9

Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection
Cited by: 29
Author(s): José Luis Ruiz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Jean-Bosco Ouédraogo, Victor G. Corcés, Elena Gómez-Díaz
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2019.01408

Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6A
Cited by: 19
Author(s): Anthony J. Saviola, Cosima Zimmermann, Michael Mariani, Sylvia Signorelli, Diana L. Gerrard, Joseph R. Boyd, Darren J. Wight, Guillaume Morissette, Annie Gravel, Isabelle Dubuc, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 6
Published: about 7 years ago

10.1038/s42003-020-01364-8

Embryonic liver developmental trajectory revealed by single-cell RNA sequencing in the Foxa2eGFP mouse
Cited by: 22
Author(s): Tingzhen Mu, Liqin Xu, Yu Zhong, Xinyu Liu, Zhikun Zhao, Changyuan Huang, Xiaofeng Lan, Chengchen Lufei, Yi Zhou, Yixun Su, Luang Xu, Miaomiao Jiang, Hong Zhou, Xinxin Lin, Liang Wu, Siqi Peng, Shiping Liu, Susanne Brix, Michael Dean, N. Ray Dunn, Kenneth S. Zaret, Xin-Yuan Fu, Yong Hou
Software Mentions: 6
Published: almost 6 years ago

10.3390/jpm9020021

The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis
Cited by: 6
Author(s): Marín de Evsikova C, Isaac Raplee, John H. Lockhart, G Jaimes, Evsikov Av
Software Mentions: 6
Published: over 7 years ago

10.1186/s13148-018-0582-0

Differential open chromatin profile and transcriptomic signature define depot-specific human subcutaneous preadipocytes: primary outcomes
Cited by: 20
Author(s): Adeline Divoux, Katalin Sandor, Dóra Bojcsuk, Amlan Talukder, Xiaoman Li, Bálint László Bálint, Timothy F. Osborne, Steven R. Smith
Software Mentions: 6
Published: almost 8 years ago

10.1038/s41422-020-0300-2

Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses
Cited by: 80
Author(s): Siyuan Hou, Zongcheng Li, Xiaona Zheng, Yun Gao, Ji Dong, Yanli Ni, Xiaobo Wang, Yunqiao Li, Xiaochen Ding, Zhilin Chang, Shuaili Li, Yuqiong Hu, Xiaoying Fan, Yu Hou, Lu Wen, Bing Liu, Fuchou Tang, Yu Lan
Software Mentions: 6
Published: over 6 years ago

10.1155/2018/8354350

Systematic Analysis of RNA Regulatory Network in Rat Brain after Ischemic Stroke
Cited by: 11
Author(s): Liu Juan, Kunshan Zhang, Bin Hu, Siguang Li, Qing Li, Yuan Luo, Yang Wang, Zhifeng Deng
Software Mentions: 6
Published: over 8 years ago

10.1038/s41419-018-0600-3

Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes
Cited by: 5
Author(s): Zhen Li, Shuiping Li, Ruoyan Li, Haitao Zhu, Xia Liu, Xingxing Guo, Lili Mu, Jie-Jing Cai, Fan Bai, Guoqiang Chen, Dengli Hong
Software Mentions: 6
Published: over 8 years ago

10.1590/1678-4685-GMB-2018-0259

Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean
Cited by: 16
Author(s): Wendell Jacinto Pereira, Arthur Tavares de Oliveira Melo, Alexandre Siqueira Guedes Coelho, Fabiana Aparecida Rodrigues, Sujan Mamidi, Sérgio Amorim de Alencar, Anna Cristina Lanna, P. A. M. R. Valdisser, C. Brondani, Ivanildo Ramalho do Nascimento-Júnior, T. C. de O. Borba, R. P. Vianello
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0025279

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Cited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: almost 15 years ago

10.7554/eLife.30860

A high-resolution mRNA expression time course of embryonic development in zebrafish
Cited by: 218
Author(s): Richard White, John Collins, Ian Sealy, Neha Wali, Christopher M. Dooley, Zsofia Digby, Derek L. Stemple, Daniel N. Murphy, Konstantinos Billis, Thibaut Hourlier, Anja Füllgrabe, Matthew P Davis, Anton J. Enright, Elisabeth M Busch-Nentwich
Software Mentions: 6
Published: almost 9 years ago

10.1016/j.stemcr.2017.09.018

Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos
Cited by: 33
Author(s): Rachel Jennings, Andrew Berry, Dave T. Gerrard, Stephen J. Wearne, James Strutt, Sarah Withey, Mariya Chhatriwala, Karen Piper Hanley, Ludovic Vallier, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 6
Published: almost 9 years ago

10.1038/s41598-021-90093-x

Prematurity alters the progenitor cell program of the upper respiratory tract of neonates
Cited by: 6
Author(s): Jessica E. Shui, Wei Wang, Helu Liu, Анна Степанова, Grace Liao, Jun Qian, Xingbin Ai, Vadim S. Ten, Jining Lü, Wellington V. Cardoso
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-017-3860-x

Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction
Cited by: 29
Author(s): Hideaki Hiraki, Hiroshi Kagoshima, Christopher Kraus, Philipp H. Schiffer, Yumiko Ueta, Michael Kroiher, Einhard Schierenberg, Yuji Kohara
Software Mentions: 6
Published: about 9 years ago

10.1186/s12864-019-6061-y

Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks
Cited by: 12
Author(s): Jim A. Mossman, Leann M. Biancani, David M. Rand
Software Mentions: 6
Published: about 7 years ago

10.1371/journal.pone.0053822

Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Cited by: 31
Author(s): Helena Storvall, Daniel Ramsköld, Rickard Sandberg
Software Mentions: 6
Published: over 13 years ago

10.1016/j.cell.2013.11.043

The Architecture of Parent-of-Origin Effects in Mice
Cited by: 79
Author(s): Richard Mott, Yuan Wei, Pamela J. Kaisaki, Xiangchao Gan, James Cleak, Andrew Edwards, Amelie Baud, Jonathan Flint
Software Mentions: 6
Published: over 12 years ago

10.1038/s41598-020-74567-y

Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction
Cited by: 11
Author(s): Tong Li, Po-Yen Wu, John H. Phan, Hamid R Hassazadeh, Weida Tong, May D. Wang
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12920-016-0164-y

Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease
Cited by: 84
Author(s): Alexandra Dumitriu, Javad Golji, Adam Labadorf, Benbo Gao, Thomas G. Beach, Richard H. Myers, Kenneth A. Longo, Jeanne C. Latourelle
Software Mentions: 6
Published: almost 11 years ago

10.1186/s12920-020-00819-5

Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastoma
Cited by: 6
Author(s): Eun-Jin Lee, Ji Won Lee, Boram Lee, Kyunghee Park, Joon Ho Shim, Keon Hee Yoo, Hong Hoe Koo, Ki Woong Sung, Woong-Yang Park
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-017-16685-8

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
Cited by: 7
Author(s): Nadia Boufaied, Christopher Nash, Annie Rochette, Anthony K. Smith, Brigid Orr, O. Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.ppat.1008754

JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Cited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: about 6 years ago

10.1038/srep32753

HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell lines
Cited by: 35
Author(s): Dinar Yunusov, Letícia Anderson, Luis DaSilva, Joanna Wysocka, Toshihiko Ezashi, R. M. Roberts, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: about 10 years ago

10.1038/s41598-018-21161-y

Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
Cited by: 16
Author(s): Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masamitsu Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pgen.1006563

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
Cited by: 163
Author(s): Rui Zhang, Patricia Deng, Jacobson Dionna, Jin Billy Li
Software Mentions: 6
Published: over 9 years ago

10.1186/s13073-015-0237-0

Identification of global regulators of T-helper cell lineage specification
Cited by: 36
Author(s): Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerström, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lähdesmäki, Riitta Lahesmaa
Software Mentions: 6
Published: almost 11 years ago

10.1371/journal.pgen.1006840

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Cited by: 54
Author(s): Syed Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles K. Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-017-1594-z

Identification of long non-coding transcripts with feature selection: a comparative study
Cited by: 20
Author(s): Giovanna Maria Ventola, Teresa Maria Rosaria Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pcbi.1003731

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Cited by: 654
Author(s): Rekin’s Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval-Sánchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean‐Christophe Marine, Stein Aerts
Software Mentions: 6
Published: about 12 years ago

10.1186/s12864-018-5066-2

A comparative analysis of library prep approaches for sequencing low input translatome samples
Cited by: 52
Author(s): Yang Song, Béatrice Milon, Sandra Ott, Xüna Zhao, Lisa Sadzewicz, Amol C. Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar, Ronna Hertzano
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pcbi.1003671

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Cited by: 41
Author(s): Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng
Software Mentions: 6
Published: about 12 years ago

10.1371/journal.pcbi.1004393

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
Cited by: 73
Author(s): Malachi Griffith, Jason Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith
Software Mentions: 6
Published: about 11 years ago

10.1371/journal.pcbi.1005420

A comprehensive overview and evaluation of circular RNA detection tools
Cited by: 285
Author(s): Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou
Software Mentions: 6
Published: over 9 years ago

10.3390/ani11030625

RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats
Cited by: 6
Author(s): Dongdong Bo, Xunping Jiang, Guiqiong Liu, Ronggui Hu, Yuqing Chong
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-016-2746-7

Transcriptome analysis of human brain tissue identifies reduced expression of complement complex C1Q Genes in Rett syndrome
Cited by: 34
Author(s): Peijie Lin, Laura Nicholls, Hassan Assareh, Zhiming Fang, Timothy G. Amos, Richard J. Edwards, Amelia A. Assareh, Irina Voineagu
Software Mentions: 6
Published: over 10 years ago

10.1186/s13059-020-02190-1

DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis
Cited by: 12
Author(s): Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed, Olivier Mathieu
Software Mentions: 6
Published: almost 6 years ago

10.1186/s13059-017-1321-0

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading
Cited by: 55
Author(s): Roberta Tarallo, Giorgio Giurato, Giuseppina Bruno, Maria Ravo, Francesca Rizzo, Annamaria Salvati, Luca Ricciardi, Giovanna Marchese, Angela Cordella, Teresa Rocco, Valerio Gigantino, Biancamaria Pierri, Giovanni Cimmino, Luciano Milanesi, Concetta Ambrosino, Tuula A. Nyman, Giovanni Nassa, Alessandro Weisz
Software Mentions: 6
Published: almost 9 years ago

10.1186/s12864-019-6076-4

Transcriptome analysis of the effect of C-C chemokine receptor 5 deficiency on cell response to Toxoplasma gondii in brain cells
Cited by: 7
Author(s): Kaoru Kobayashi, Kousuke Umeda, Fumie Ihara, Sadao Tanaka, Junya Yamagishi, Yutaka Suzuki, Yoshifumi Nishikawa
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pcbi.1004274

Genome Modeling System: A Knowledge Management Platform for Genomics
Cited by: 77
Author(s): Malachi Griffith, Scott M. Smith, Avinash Ramu, Matthew B. Callaway, Anthony M. Brummett, Michael J. Kiwala, Adam Coffman, Allison Regier, Benjamin J. Oberkfell, Gabriel E. Sanderson, Thomas P. Mooney, Nathaniel G. Nutter, Edward A. Belter, Feiyu Du, R.L. Long, Travis E. Abbott, Ian T. Ferguson, David Morton, Mark M. Burnett, James V. Weible, Joshua B. Peck, Adam F. Dukes, Joshua F. McMichael, Justin T. Lolofie, Brian R. Derickson, Jasreet Hundal, Zachary L. Skidmore, Benjamin J. Ainscough, Nathan D. Dees, William Schierding, Cyriac Kandoth, Kyung H. Kim, Charles Lu, Christopher Harris, Nicole Maher, Christopher A. Maher, Vincent Magrini, Benjamin Abbott, Ken Chen, Eric M. Clark, Indraniel Das, Xian Fan, Amy E. Hawkins, Todd G. Hepler, Todd Wylie, Shawn Leonard, W.E. Schroeder, Xiaoqi Shi, Lynn K. Carmichael, Matthew R. Weil, Richard W. Wohlstadter, Gary Stiehr, Michael D. McLellan, Craig Pohl, Christopher A. Miller, Daniel C. Koboldt, Jason Walker, James M. Eldred, David E. Larson, David J. Dooling, Ding Li, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 6
Published: about 11 years ago

10.1186/s12864-021-07812-x

Stage-specific transcriptomic changes in pancreatic α-cells after massive β-cell loss
Cited by: 9
Author(s): Daniel Oropeza, Valentina Cigliola, Agustín Romero, Simona Chera, Santiago A. Rodríguez-Seguí, Pedro Luis Herrera
Software Mentions: 6
Published: about 5 years ago

10.1186/1471-2105-14-320

Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
Cited by: 40
Author(s): David Sturgill, John H. Malone, Xia Sun, Harold E. Smith, Léonard Rabinow, Marie-Laure Samson, Brian Oliver
Software Mentions: 6
Published: almost 13 years ago

10.1186/s12859-016-1195-2

A fuzzy method for RNA-Seq differential expression analysis in presence of multireads
Cited by: 16
Author(s): Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni
Software Mentions: 6
Published: almost 10 years ago

10.1186/s12864-017-4386-y

Global accumulation of circRNAs during aging in Caenorhabditis elegans
Cited by: 127
Author(s): Mariela Cortés-López, Matthew Gruner, Daphne A. Cooper, Hannah N. Gruner, Alexandru-Ioan Voda, Alexander M. van der Linden, Pedro Miura
Software Mentions: 6
Published: over 8 years ago

10.1186/s12864-015-2346-y

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis
Cited by: 12
Author(s): Dmitry Velmeshev, Patrick Lally, Marco Magistri, Mohammad Ali Faghihi
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.ppat.1008589

High-throughput sequencing analysis of a “hit and run” cell and animal model of KSHV tumorigenesis
Cited by: 12
Author(s): Julián Naipauer, Daria Salyakina, Guy Journo, Santas Rosario, Siôn L. Williams, Martı́n C. Abba, Meir Shamay, Enrique A. Mesri
Software Mentions: 6
Published: about 6 years ago

10.1186/s13059-017-1284-1

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Cited by: 75
Author(s): N. Davidson, Anthony D. K. Hawkins, Alicia Oshlack
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-016-1104-8

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Cited by: 75
Author(s): Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach, Hubert Rehrauer
Software Mentions: 6
Published: over 10 years ago

10.1186/s13059-016-0969-1

Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling
Cited by: 136
Author(s): Steven Flygare, Keith E. Simmon, Chase Miller, Yi Qiao, Brett Kennedy, Tonya Di Sera, Erin H. Graf, Keith D. Tardif, Aurélie Kapusta, Shawn Rynearson, Chris Stockmann, Krista Queen, Suxiang Tong, Karl V. Voelkerding, Anne J. Blaschke, Carrie L. Byington, Seema Jain, Andrew T. Pavia, Kwabena Krow Ampofo, Karen Eilbeck, Gábor Marth, Mark Yandell, Robert Salais
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pcbi.1009095

Identifying the combinatorial control of signal-dependent transcription factors
Cited by: 15
Author(s): Ning Wang, Diane Lefaudeux, Anup Mazumder, Jingyi Jessica Li, Alexander Hoffmann
Software Mentions: 6
Published: about 5 years ago

10.1186/gm549

A genome scale overexpression screen to reveal drug activity in human cells
Cited by: 30
Author(s): Anthony Arnoldo, Saranya Kittanakom, Lawrence E. Heisler, Anthony B. Mak, Andrey I. Shukalyuk, Dax Torti, Jason Moffat, Guri Giaever, Corey Nislow
Software Mentions: 6
Published: over 12 years ago

10.1186/s13024-017-0219-3

Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s disease
Cited by: 92
Author(s): Andrew McKenzie, Sarah Moyon, Minghui Wang, Igor Katsyv, Won Min Song, Xianxiao Zhou, Eric B. Dammer, Duc M. Duong, Joshua D. Aaker, Yang Zhao, Noam D. Beckmann, Pei Wang, Jun Zhu, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Brian Popko, Patrizia Casaccia, Bin Zhang
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.pone.0207051

A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles
Cited by: 4
Author(s): Leonardo Abdala Elias, Denise Brentan Silva, Ricardo Silva, Yan‐Qiong Peng, Da‐Rong Yang, Norberto P. Lopes, Rodrigo Augusto Santinelo Pereira
Software Mentions: 6
Published: almost 8 years ago

10.7554/eLife.19127

Regulation of X-linked gene expression during early mouse development by Rlim
Cited by: 36
Author(s): Feng Wang, Jongdae Shin, Jeremy Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K. Shalek, Aviv Regev, Jeanne B. Lawrence, Eduardo M. Torres, Lihua Julie Zhu, Oliver J. Rando, Ingolf Bach
Software Mentions: 6
Published: almost 10 years ago

10.1093/database/bay014

TransAtlasDB: an integrated database connecting expression data, metadata and variants
Cited by: 2
Author(s): Modupeore O. Adetunji, Susan J. Lamont, Carl J. Schmidt
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0123380

Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)
Cited by: 41
Author(s): Christopher Terranova, Sridhar T. Narla, Yu Wei Lee, Jonathan Bard, Abhirath Parikh, Ewa K. Stachowiak, Emmanuel S. Tzanakakis, Michael Buck, Barbara Birkaya, Michal K. Stachowiak
Software Mentions: 6
Published: over 11 years ago

10.3389/fimmu.2021.724015

Transcriptional, Epigenetic, and Functional Reprogramming of Monocytes From Non-Human Primates Following Chronic Alcohol Drinking
Cited by: 11
Author(s): Sloan A. Lewis, Suhas Sureshchandra, Brianna Doratt, Vanessa Jiménez, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: about 5 years ago

10.15252/embj.2021108345

Piwi–piRNA complexes induce stepwise changes in nuclear architecture at target loci
Cited by: 4
Author(s): Yuka W. Iwasaki, Sira Sriswasdi, Yasuha Kinugasa, Jun Adachi, Yasunori Horikoshi, Aoi Shibuya, Wataru Iwasaki, Satoshi Tashiro, Takeshi Tomonaga, Haruhiko Siomi
Software Mentions: 6
Published: about 5 years ago

10.1534/g3.118.200865

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi)
Cited by: 16
Author(s): Karen M. Kapheim, Hailin Pan, Cai Li, Charles Blatti, Brock A. Harpur, Panagiotis Ioannidis, Beryl M. Jones, Clement F. Kent, Livio Ruzzante, Laura Sloofman, Eckart Stolle, Robert M. Waterhouse, Amro Zayed, Guojie Zhang, William T. Wcislo
Software Mentions: 6
Published: over 7 years ago

10.1534/g3.113.006742

The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector
Cited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: about 13 years ago

10.15252/emmm.201708587

Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator
Cited by: 54
Author(s): Snehajyoti Chatterjee, Raphaelle Cassel, Anne Schneider‐Anthony, Karine Mérienne, Brigitte Cosquer, Laura Tzeplaeff, Sarmistha Sinha, Manoj Kumar, Piyush Chaturbedy, M. Eswaramoorthy, Stéphanie Le Gras, Céline Keime, Olivier Bousiges, P. Dutar, Petnoï Petsophonsakul, Claire Rampon, Jean‐Christophe Cassel, Luc Buée, David Blum, Tapas K. Kundu, Anne‐Laurence Boutillier
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0071745

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol
Cited by: 20
Author(s): Zhifu Sun, Yan W. Asmann, Asha Nair, Yuji Zhang, Liguo Wang, Krishna R. Kalari, Aditya Bhagwate, Tiffany R. Baker, Jennifer M. Carr, Jean Pierre A. Kocher, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 6
Published: about 13 years ago

Projects: pypi: TopHat

Science Score: 90/100

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Papers Mentioning TopHat 5,017