pypi: TopHat | Projects | Ecosyste.ms: Papers

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: over 4 years ago

10.1038/sdata.2017.51

Transcriptomic analysis of gene signatures associated with sickle pain
Cited by: 8
Author(s): Jinny Paul, Anupam Aich, Juan E. Abrahante, Ying Wang, Rebecca S. LaRue, Susan K. Rathe, Krystina R. Kalland, Aditya Mittal, Ritu Jha, Fei Peng, David A. Largaespada, Anindya Bagchi, Kalpna Gupta
Software Mentions: 6
Published: about 8 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 13 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 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 14 years ago

10.1186/s12284-016-0098-1

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress
Cited by: 32
Author(s): Elena Baldoni, Paolo Bagnaresi, Franca Locatelli, Monica Mattana, Annamaria Genga
Software Mentions: 6
Published: about 9 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: almost 12 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 7 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: almost 4 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: about 7 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 9 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 9 years ago

10.1534/g3.114.016196

A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti
Cited by: 53
Author(s): Benjamin R. Evans, Andrea Gloria‐Soria, Lin Hou, Carolyn S. McBride, Mariangela Bonizzoni, Hongyu Zhao, Jeffrey R. Powell
Software Mentions: 6
Published: about 10 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 8 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: over 7 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 8 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 5 years ago

10.1371/journal.pgen.1004648

Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory Elements
Cited by: 36
Author(s): Robin P. Smith, Walter L. Eckalbar, Kari M. Morrissey, Marcelo R. Luizon, Thomas J. Hoffmann, Xinwei Sun, Stacy L. Jones, Shelley Force Aldred, Anuradha Ramamoorthy, Zeruesenay Desta, Yunlong Liu, Todd C. Skaar, Nathan D. Trinklein, Kathleen M. Giacomini, Nadav Ahituv
Software Mentions: 5
Published: almost 11 years ago

10.1038/s42003-021-01716-y

Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimp
Cited by: 28
Author(s): Jianbo Yuan, Xiaojun Zhang, Min Wang, Yamin Sun, Xianhui Qin, Shihao Li, Yang Yu, Yi Gao, Fei Liu, Jie Kong, Guangyi Fan, Chengsong Zhang, Lu Feng, Jianhai Xiang, Fuhua Li
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-020-01398-y

Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformation
Cited by: 2
Author(s): Michal Schwartz, Avital Sarusi Portugez, Bracha Zukerman Attia, Miriam Tannenbaum, Leslie E. Cohen, Olga Loza, Emily Chase, Yousef Turman, Tommy Kaplan, Zaidoun Salah, Ofir Hakim
Software Mentions: 5
Published: over 4 years ago

10.1111/1755-0998.13257

High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae
Cited by: 19
Author(s): Simei He, Dong Xiao, Guanghui Zhang, Wei Fan, Shengchang Duan, Hong Shi, Dawei Li, Rui Li, Cuizhi Geng, Guangqiang Long, Yan Zhao, Mo Chen, Mi Yan, Jianli Yang, Yingchun Lu, Yanli Zhou, Wei Chen, Yang Dong, Shengchao Yang
Software Mentions: 5
Published: almost 5 years ago

10.1093/gigascience/giaa143

High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis
Cited by: 7
Author(s): Qionghua Gao, Zijun Xiong, Rasmus Stenbak Larsen, Long Zhang, Jie Zhao, Guo Ding, Ruoping Zhao, Chengyuan Liu, Ran Hao, Guojie Zhang
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.591806

Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves
Cited by: 11
Author(s): Xuedong Yang, Yahui Liu, Hui Zhang, Jinyu Wang, Gaurav Zinta, Shangbo Xie, Weimin Zhu, Wen-Feng Nie
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2019.01347

Emerging Roles of Heat-Induced circRNAs Related to Lactogenesis in Lactating Sows
Cited by: 11
Author(s): Jiajie Sun, Haojie Zhang, Bao-Yu Hu, Yueqin Xie, Dongyang Wang, Jinzhi Zhang, Ting Chen, Junyi Luo, Songbo Wang, Qinyan Jiang, Qianyun Xi, Zujing Chen, Yongliang Zhang
Software Mentions: 5
Published: over 5 years ago

10.1002/1878-0261.12314

Induced <scp>PTF</scp> 1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment
Cited by: 17
Author(s): Brad L. Jakubison, Patrick G. Schweickert, Sarah E. Moser, Yi Yang, Hongyu Gao, Kathleen M. Scully, Pamela Itkin-Ansari, Yunlong Liu, Stephen F. Konieczny
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pgen.1005698

Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans
Cited by: 43
Author(s): Maxwell Kramer, Anna Lena Kranz, Amanda Su, Lara Winterkorn, Sarah Elizabeth Albritton, Sevinç Ercan
Software Mentions: 5
Published: over 9 years ago

10.3389/fgene.2016.00080

Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks
Cited by: 12
Author(s): Bahareh Rahmani, Michael T. Zimmermann, Diane E. Grill, Richard B. Kennedy, Ann L. Oberg, Bill C. White, Gregory A. Poland, Brett A. McKinney
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-018-20262-y

Comparative analyses of co-evolving host-parasite associations reveal unique gene expression patterns underlying slavemaker raiding and host defensive phenotypes
Cited by: 15
Author(s): Austin Alleman, Barbara Feldmeyer, Susanne Foitzik
Software Mentions: 5
Published: over 7 years ago

10.3390/molecules25214894

Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach
Cited by: 8
Author(s): Michał Złoch, Paweł Pomastowski, Ewelina Maślak, Fernanda Monedeiro
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0085568

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines
Cited by: 58
Author(s): Oliver Rupp, J. Ole Becker, Karina Brinkrolf, Christina Timmermann, Nicole Borth, Alfred Pühler, Thomas Noll, Alexander Goesmann
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0153932

Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis
Cited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0235218

Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualities
Cited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: about 5 years ago

10.1016/j.immuni.2017.12.010

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages
Cited by: 153
Author(s): Zsolt Czimmerer, Bence Dániel, Attila Horváth, Dominik Rückerl, Gergely Nagy, Máté Kiss, Matthew Peloquin, Marietta Margit Budai, Ixchelt Cuaranta-Monroy, Zoltán Simándi, László Steiner, Béla Nagy, Szilárd Póliska, Csaba Bankó, Zsolt Bacsó, Ira G. Schulman, Sascha Sauer, Jean Deleuze, Judith E. Allen, Szilvia Benkő, László Nagy
Software Mentions: 5
Published: over 7 years ago

10.1186/s12934-015-0226-4

An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture
Cited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: over 10 years ago

10.1038/onc.2016.382

Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer
Cited by: 125
Author(s): Alison Harrod, Janet S. Fulton, Van Nguyen, Manikandan Periyasamy, L Ramos-Garcia, C-F Lai, Gergana Metodieva, Alex de Giorgio, Richard Williams, Delfran Batista dos Santos, Pablo Gómez, M-L Lin, Metodi V. Metodiev, Justin Stebbing, Leandro Castellano, Luca Magnani, R. Charles Coombes, Laki Buluwela, Simak Ali
Software Mentions: 5
Published: almost 9 years ago

10.3389/fgene.2018.00491

Dynamic Changes in the Global MicroRNAome and Transcriptome Identify Key Nodes Associated With Ovarian Development in Chickens
Cited by: 12
Author(s): Wenwen Wang, Keliang Wu, Meiting Jia, Siyuan Sun, Kang Li, Qin Zhang, Hui Tang
Software Mentions: 5
Published: almost 7 years ago

10.1186/s12983-015-0109-x

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex
Cited by: 33
Author(s): Andrey Rozenberg, Mrutyunjaya Parida, Florian Leese, Linda C. Weiss, Ralph Tollrian, J. Robert Manak
Software Mentions: 5
Published: about 10 years ago

10.3390/ijms21031067

Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress
Cited by: 32
Author(s): Zhaoyang Hu, Yufei Zhang, Yue Ping He, Qingqing Cao, Ting Zhang, Laiqing Lou, Qingqing Cai
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms19020593

Luminal lncRNAs Regulation by ERα-Controlled Enhancers in a Ligand-Independent Manner in Breast Cancer Cells
Cited by: 13
Author(s): Valentina Miano, Giulio Ferrero, Valentina Rosti, Eleonora Manitta, Jamal Elhasnaoui, Giulia Basile, Michele De Bortoli
Software Mentions: 5
Published: over 7 years ago

10.1038/s41421-017-0003-0

ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
Cited by: 46
Author(s): Si Wang, Boqiang Hu, Zicheng Ding, Yujiao Dang, Jun Wu, Di Li, Xiaoling Liu, Bailong Xiao, Weiqi Zhang, Rui Ren, Jinghui Lei, Huifang Hu, Chang Chen, Piu Chan, Dong Liu, Jing Qu, Fuchou Tang, Guang Hui Liu
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.31683

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm
Cited by: 36
Author(s): Xinan Yang, Rangarajan D. Nadadur, Catharina R.E. Hilvering, Valerio Bianchi, Michael S. Werner, Stefan R. Mazurek, Margaret Gadek, Karen Shen, Joseph D. Goldman, Leonid Tyan, Jenna C. Bekeny, Johnathon M Hall, Nutishia Lee, Carlos Perez-Cervantes, Ozanna Burnicka-Turek, Kenneth D. Poss, Christopher R. Weber, Wouter de Laat, Alexander J. Ruthenburg, Ivan P. Moskowitz
Software Mentions: 5
Published: over 7 years ago

10.1038/s41420-019-0184-4

A six-inhibitor culture medium for improving naïve-type pluripotency of porcine pluripotent stem cells
Cited by: 15
Author(s): Ye Yuan, Jin‐Kyu Park, Yuchen Tian, Jungmin Choi, Rolando Pasquariello, Andrei P. Alexenko, Aihua Dai, Susanta K. Behura, R. Michael Roberts, Toshihiko Ezashi
Software Mentions: 5
Published: about 6 years ago

10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome
Cited by: 20
Author(s): Jie Du, Lin Zhang
Software Mentions: 5
Published: about 10 years ago

10.26508/lsa.202000946

Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19
Cited by: 23
Author(s): Lucas Cardoso Lázari, Fábio Ghilardi, Lívia Rosa-Fernandes, Diego M. Assis, José Carlos Nicolau, Verônica Feijoli Santiago, Talia Falcão Dalçóquio, Cláudia Blanes Angeli, Adriádne Justi Bertolin, Cláudio Romero Farias Marinho, Carsten Wrenger, Edison Luiz Durigon, Rinaldo Focaccia Siciliano, Giuseppe Palmisano
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.25762

Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution
Cited by: 102
Author(s): Yuh Chwen G Lee, Gary H. Karpen
Software Mentions: 5
Published: about 8 years ago

10.3390/ijms22052353

ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer
Cited by: 3
Author(s): Leqin Yan, Sally Gaddis, Luis Della Coletta, John Repass, Katherine Powell, Melissa S. Simper, Yueping Chen, Michelle Byrom, Yi Zhong, Kevin Lin, Bin Liu, Yao Lu, Jianjun Shen, Michael C. MacLeod
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1008566

The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants
Cited by: 54
Author(s): Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle Henry
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.584116

Rheumatoid Arthritis Synovial Fluid Neutrophils Drive Inflammation Through Production of Chemokines, Reactive Oxygen Species, and Neutrophil Extracellular Traps
Cited by: 62
Author(s): Helen L. Wright, Max Lyon, Elinor A Chapman, Robert J. Moots, Steven W. Edwards
Software Mentions: 5
Published: over 4 years ago

10.1534/g3.115.019166

Genome-Wide Analysis ofDrosophilaRBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis
Cited by: 15
Author(s): Yiliang Wei, Shamba S. Mondal, Rima Mouawad, Bartek Wilczyński, R. William Henry, David N. Arnosti
Software Mentions: 5
Published: about 10 years ago

10.1155/2017/6218353

Circular RNAs: Biogenesis, Function, and a Role as Possible Cancer Biomarkers
Cited by: 105
Author(s): Luka Bolha, Metka Ravnik‐Glavač, Damjan Glavač
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0225180

Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation
Cited by: 10
Author(s): Aisling M. Redmond, Soleilmane Omarjee, Igor Chernukhin, Muriel Le Romancer, Jason S. Carroll
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.00425

Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka (Oryzias latipes)
Cited by: 18
Author(s): Yo Okamura, Natsuki Morimoto, Daisuke Ikeda, Naoki Mizusawa, Shugo Watabe, Hiroshi Miyanishi, Yuichi Saeki, Haruko Takeyama, Takashi Aoki, Masato Kinoshita, Tomoya Kono, Masahiro Sakai, Jun ichi Hikima
Software Mentions: 5
Published: over 5 years ago

10.1186/s13041-020-00603-7

Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J mice
Cited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-018-33718-y

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat
Cited by: 40
Author(s): Yongpeng Li, Xing Fu, Meicheng Zhao, Wei Zhang, Bo Li, Diaoguo An, Junming Li, Aimin Zhang, Renyi Liu, Xigang Liu
Software Mentions: 5
Published: almost 7 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: almost 12 years ago

10.7554/eLife.50541

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Cited by: 62
Author(s): Rita A Batista, Jordi Moreno‐Romero, Yue Qiu, Joram van Boven, Juan Santos‐González, Duarte D. Figueiredo, Claudia Köhler
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2019.00766

Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data
Cited by: 30
Author(s): Sharmin Akter, Dong Xu, Susan C. Nagel, John J. Bromfield, Katherine E. Pelch, Gilbert B Wilshire, Trupti Joshi
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes5040957

High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
Cited by: 57
Author(s): Vahan Simonyan, Raja Mazumder
Software Mentions: 5
Published: almost 11 years ago

10.1128/mBio.01496-21

The Interspecific Fungal Hybrid Verticillium longisporum Displays Subgenome-Specific Gene Expression
Cited by: 6
Author(s): Jasper R L Depotter, Fabian van Beveren, Luis Rodríguez‐Moreno, Holger Kramer, Edgar A. Chavarro Carrero, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Thomas A. Wood, Bart P.H.J. Thomma, Michael Seidl
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2018.00441

Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle
Cited by: 30
Author(s): Tassia M. Goncalves, Luciana Correia de Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sónia Cristina da Silva Andrade, Gérson Barreto Mourão, G. Gasparin, Gabriel Costa Monteiro Moreira, Eric R. Fritz-Waters, James M. Reecy
Software Mentions: 5
Published: almost 7 years ago

10.1038/s41598-017-11036-z

SRSF1 suppresses selection of intron-distal 5′ splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein
Cited by: 3
Author(s): Khalid Ahsan, Akio Matsubara, Mohammad Alinoor Rahman, Jun‐ichi Takeda, Mohammad Nazim, Bisei Ohkawara, Mikako Ito, Kinji Ohno
Software Mentions: 5
Published: almost 8 years ago

10.1074/mcp.RA118.000832

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets
Cited by: 17
Author(s): Zhe Ren, Da Qi, Nina Pugh, Kai Li, Bo Wen, Ruo Zhou, Shaohang Xu, Siqi Liu, Andrew R. Jones
Software Mentions: 5
Published: over 6 years ago

10.3390/microorganisms8040559

Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria
Cited by: 9
Author(s): Songbao Zou, Qianqian Zhang, Jun Gong
Software Mentions: 5
Published: over 5 years ago

10.1186/s12979-020-00182-0

Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22
Cited by: 11
Author(s): Arttu Autio, Tapio Nevalainen, Binisha H. Mishra, Marja Jylhä, Heini Flinck, Mikko Hurme
Software Mentions: 5
Published: about 5 years ago

10.1084/jem.20191257

Combined deletion of Bap1, Nf2, and Cdkn2ab causes rapid onset of malignant mesothelioma in mice
Cited by: 28
Author(s): Jitendra Badhai, Gaurav Kumar Pandey, Ji‐Ying Song, Oscar Krijgsman, Rajith Bhaskaran, G. Chandrasekaran, Min-Chul Kwon, Lorenzo Bombardelli, Kim Monkhorst, Cristoforo Grasso, John Zevenhoven, Jan van der Vliet, Miranda Cozijnsen, Paul Krimpenfort, Daniel S. Peeper, Maarten van Lohuizen, Anton Berns
Software Mentions: 5
Published: over 5 years ago

10.7150/jca.29958

TGFBI Promotes Tumor Growth and is Associated with Poor Prognosis in Oral Squamous Cell Carcinoma
Cited by: 16
Author(s): Bingjie Wang, Kun-Ping Chi, Ruling Shen, Saiwei Zheng, Yang Guo, Jianfeng Li, Jian Fei, Yuan He
Software Mentions: 5
Published: over 6 years ago

10.7150/jca.47698

Mass Spectrometry Imaging Differentiates Chromophobe Renal Cell Carcinoma and Renal Oncocytoma with High Accuracy
Cited by: 7
Author(s): Mark Kriegsmann, Rita Casadonte, Nadine Maurer, Christine Stoehr, Franziska Erlmeier, Holger Moch, Kerstin Junker, Christiane Zgorzelski, Wilko Weichert, Kristina Schwamborn, Sören‐Oliver Deininger, Matthias M. Gaida, Gunhild Mechtersheimer, Albrecht Stenzinger, Peter Schirmacher, Arndt Hartmann, Joerg Kriegsmann, Katharina Kriegsmann
Software Mentions: 5
Published: over 5 years ago

10.1038/sdata.2015.51

De novo transcriptome profiling of highly purified human lymphocytes primary cells
Cited by: 34
Author(s): Raoul Jean Pierre Bonnal, Valeria Ranzani, Alberto Arrigoni, Serena Maria Curti, Ilaria Panzeri, Paola Gruarin, Sergio Abrignani, Grazisa Rossetti, Massimiliano Pagani
Software Mentions: 5
Published: almost 10 years ago

10.1534/g3.116.030783

ChloroSeq, an Optimized Chloroplast RNA-Seq Bioinformatic Pipeline, Reveals Remodeling of the Organellar Transcriptome Under Heat Stress
Cited by: 47
Author(s): Benoît Castandet, Amber M. Hotto, Susan R. Strickler, David B. Stern
Software Mentions: 5
Published: almost 9 years ago

10.3390/ijms21051630

Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell Lines
Cited by: 1
Author(s): Dóra Bojcsuk, Gergely Nagy, Bálint László Bálint
Software Mentions: 5
Published: over 5 years ago

10.1111/pbi.12852

The transcriptome, extracellular proteome and active secretome of agroinfiltratedNicotiana benthamianauncover a large, diverse protease repertoire
Cited by: 52
Author(s): Friederike Grosse‐Holz, Steven L. Kelly, Svenja Blaskowski, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 5
Published: over 7 years ago

10.1186/s12859-018-2019-3

Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: over 7 years ago

10.1186/s12967-020-02695-0

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2
Cited by: 39
Author(s): Abul B.M.M.K. Islam, A. A. Khan, Rasel Ahmed, Md. Sabbir Hossain, Shah Md. Tamim Kabir, Md Shahidul Islam, Amam Zonaed Siddiki
Software Mentions: 5
Published: over 4 years ago

10.1038/s42003-018-0037-3

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization
Cited by: 18
Author(s): Lisa Lindström, Tongbin Li, Darina Malycheva, Arun Kancharla, Helén Nilsson, Neelanjan Vishnu, Hindrik Mulder, Martin Johansson, Catalina Ana Rosselló, María Alvarado-Kristensson
Software Mentions: 5
Published: about 7 years ago

10.1523/ENEURO.0288-18.2019

Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative Diseases
Cited by: 26
Author(s): Raquel Cuevas-Diaz Duran, Chih Yen Wang, Hui Zheng, Benjamin Deneen, Jia Qian Wu
Software Mentions: 5
Published: over 6 years ago

10.1093/database/bax079

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species
Cited by: 9
Author(s): Leandro Costa do Nascimento, Marcela Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas S. Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle
Software Mentions: 5
Published: over 8 years ago

10.1038/s42003-020-01620-x

RNA editing enzyme APOBEC3A promotes pro-inflammatory M1 macrophage polarization
Cited by: 20
Author(s): Emad Alqassim, Shraddha Sharma, Aalia Khan, Tiffany R. Emmons, Eduardo Cortes Gomez, Abdulrahman A. Alahmari, Kelly L. Singel, Jaron Mark, Bruce A. Davidson, AJ Robert McGray, Qian Liu, Brian D. Lichty, Kirsten B. Moysich, Jianmin Wang, Kunle Odunsi, Brahm H. Segal, Bora E. Baysal
Software Mentions: 5
Published: over 4 years ago

10.1002/pld3.239

N6‐methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis
Cited by: 35
Author(s): Marianne C. Kramer, Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. García, Eric Lyons, Mark A. Beilstein, Brian D. Gregory
Software Mentions: 5
Published: about 5 years ago

10.18632/oncotarget.8192

Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: over 9 years ago

10.1186/s12974-021-02154-7

Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder
Cited by: 11
Author(s): Fumie Horiuchi, Yuta Yoshino, Hiroshi Kumon, Rie Hosokawa, Kiwamu Nakachi, Kentaro Kawabe, Jun‐ichi Iga, Shu‐ichi Ueno
Software Mentions: 5
Published: about 4 years ago

10.18632/oncotarget.16493

ERK signalling modulates epigenome to drive epithelial to mesenchymal transition
Cited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: over 8 years ago

10.1186/s12870-020-02702-y

Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development
Cited by: 3
Author(s): Xiaobo Zhao, Chunjuan Li, Hao Zhang, Yan Cheng, Quanxi Sun, Juan Wang, Cuiling Yuan, Shiguang Shan
Software Mentions: 5
Published: almost 5 years ago

10.18632/oncotarget.21031

Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation window
Cited by: 22
Author(s): Qi Wang, Nan Wang, Rui Cai, Fan Zhao, Yi Xiong, Xiao Li, Aihua Wang, Peng Lin, Yaping Jin
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.37184

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer
Cited by: 68
Author(s): Ji Li, Peter S. Choi, Christine L. Chaffer, Katherine Labella, Justin Hwang, Andrew O. Giacomelli, Jong Wook Kim, Nina Ilić, John G. Doench, Seav Huong Ly, Chao Dai, Kimberly R. Hagel, Andrew L. Hong, Ole Gjoerup, Shom Goel, Jennifer Y Ge, David E. Root, Jean J. Zhao, Angela N. Brooks, Robert A. Weinberg, William C. Hahn
Software Mentions: 5
Published: almost 7 years ago

10.1002/advs.201901672

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut
Cited by: 38
Author(s): Dongmei Yin, Changmian Ji, Qingxin Song, Wan–Ke Zhang, Xingguo Zhang, Kunkun Zhao, Charles Y. Chen, Chuan Tang Wang, He Guo, Zhe Liang, Xingli Ma, Zhongfeng Li, Yueyi Tang, Yuejun Wang, Ké Li, Longlong Ning, Hui Zhang, Kai Zhao, Xuming Li, Haiyan Yu, Lei Yan, Mingcheng Wang, Liming Ma, Hongkun Zheng, Yijing Zhang, Jinsong Zhang, Wei Hu, Z Jeffrey Chen
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0151917

Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns
Cited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: over 9 years ago

10.7554/eLife.44161

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition
Cited by: 30
Author(s): Andrew L. Hong, Yuen-Yi Tseng, Jeremiah A. Wala, Won-Jun Kim, Bryan D. Kynnap, Mihir B. Doshi, Guillaume Kugener, Gabriel J. Sandoval, Thomas P. Howard, Ji Li, Xiaoping Yang, Michelle Tillgren, Mahmhoud Ghandi, Abeer Sayeed, Rebecca Deasy, Abigail Ward, Brian McSteen, Katherine Labella, Paula Keskula, Adam Tracy, Cora Connor, Catherine Clinton, Alanna J. Church, Brian D. Crompton, Katherine A. Janeway, Barbara Van Hare, David Sandak, Ole Gjoerup, Pratiti Bandopadhayay, Paul A. Clemons, Stuart L. Schreiber, David E. Root, Prafulla C. Gokhale, N. Susan, Elizabeth Mullen, Charles W.M. Roberts, Cigall Kadoch, Rameen Beroukhim, Keith L. Ligon, Jesse S. Boehm, William C. Hahn
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0109715

Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in Cicer arietinum (Chickpea) Genome
Cited by: 33
Author(s): Ranu Sharma, Vimal Rawat, C.G. Suresh
Software Mentions: 5
Published: almost 11 years ago

10.1186/1748-7188-8-25

Data compression for sequencing data
Cited by: 84
Author(s): Sebastian Deorowicz, Szymon Grabowski
Software Mentions: 5
Published: over 12 years ago

10.7554/eLife.64317

Evolutionary shifts in taste coding in the fruit pest Drosophila suzukii
Cited by: 33
Author(s): Hany K.M. Dweck, Gaëlle J.S. Talross, Wanyue Wang, John R. Carlson
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.21049

Proliferation-independent regulation of organ size by Fgf/Notch signaling
Cited by: 36
Author(s): Agnė Kozlovskaja-Gumbrienė, Yi Ren, Alexander Richard, Andy Aman, Ryan Jiskra, Danielle Nagelberg, Holger Knaut, Melainia McClain, Tatjana Piotrowski
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.07103

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics
Cited by: 103
Author(s): Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L Kagan, Jonathan E. Burnett, Constance H Huang, Amy Mitrano, Claudia Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana M. Parast, Tomàs Marquès‐Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad
Software Mentions: 5
Published: about 10 years ago

10.7554/eLife.51373

PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cells
Cited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.07295

Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100
Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: about 10 years ago

10.7554/eLife.49044

NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress
Cited by: 22
Author(s): Dongdong Han, Lars Schomacher, Katrin M. Schüle, Medhavi Mallick, Michael U. Musheev, Emil Karaulanov, Laura Krebs, Annika von Seggern, Christof Niehrs
Software Mentions: 5
Published: almost 6 years ago

10.7554/eLife.15657

An integrative transcriptomic atlas of organogenesis in human embryos
Cited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: almost 9 years ago

10.7554/eLife.39054

New insights into the cellular temporal response to proteostatic stress
Cited by: 40
Author(s): Justin Rendleman, Zhe Cheng, Shuvadeep Maity, Nicolai Kastelic, Mathias Munschauer, Kristina Allgoewer, Guoshou Teo, Yun Bin Matteo Zhang, Amy Lei, Brian J. Parker, Markus Landthaler, Lindsay Freeberg, Scott Kuersten, Hyungwon Choi, Christine Vogel
Software Mentions: 5
Published: almost 7 years ago

10.7554/eLife.27159

Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer
Cited by: 29
Author(s): Laura Cato, Antje Neeb, Adam Sharp, Víctor Buzón, Scott B. Ficarro, Linxiao Yang, Claudia Muhle‐Goll, Nane C. Kuznik, Ruth Riisnaes, Daniel Nava Rodrigues, Olivier Armant, Victor Gourain, Guillaume Adelmant, Emmanuel Amankwah Ntim, Thomas Westerling, David Dolling, Pasquale Rescigno, Ines Figueiredo, Friedrich Fauser, Jiansheng Wu, Jaice T. Rottenberg, L. Shatkina, Claudia Ester, Burkhard Luy, Holger Puchta, Jakob Troppmair, Nicole Jung, Stefan Bräse, Uwe Strähle, Jarrod A. Marto, G. Ulrich Nienhaus, Bissan Al‐Lazikani, Xavier Salvatella, Johann S. de Bono, Andrew C. B. Cato, Myles Brown
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.14997

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons
Cited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: over 9 years ago

Projects: pypi: TopHat

Science Score: 90/100

Bonuses:

Penalties:

Papers Mentioning TopHat 5,017