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: over 11 years ago
9 downloads last month
Papers Mentioning TopHat 5,017
10.1038/s41598-018-37397-7
Temporal dynamics in meta longitudinal RNA-Seq dataCited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0025279
GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression DifferencesCited 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: over 12 years ago
10.1038/s41598-019-47797-y
Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the PoaceaeCited by: 3
Author(s): John P. Lloyd, Megan J. Bowman, Christina B. Azodi, Rosalie P. Sowers, Gaurav D. Moghe, Kevin L. Childs, Shin-Han Shiu
Software Mentions: 6
Published: over 4 years ago
10.1038/s41598-020-70334-1
Developmental changes in the accessible chromatin, transcriptome and Ascl1-binding correlate with the loss in Müller Glial regenerative potentialCited by: 20
Author(s): Leah S. VandenBosch, Stefanie G. Wohl, Matthew S. Wilken, Marcus Hooper, Connor Finkbeiner, Kristen E. Cox, Laura B. Chipman, Thomas A. Reh
Software Mentions: 6
Published: almost 4 years ago
10.7554/eLife.30860
A high-resolution mRNA expression time course of embryonic development in zebrafishCited 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: over 6 years ago
10.1038/s41598-020-65089-8
Immunorthodontics: in vivo gene expression of orthodontic tooth movementCited by: 28
Author(s): Yehuda Klein, Omer Fleissig, David Polak, Yechezkel Barenholz, Ofer Mandelboim, Stella Chaushu
Software Mentions: 6
Published: about 4 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 StudyCited 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 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 SequencingCited by: 104
Author(s): Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 6
Published: over 12 years ago
10.1016/j.isci.2021.102690
Functional and genomic adaptations of blood monocytes to pregravid obesity during pregnancyCited by: 12
Author(s): Suhas Sureshchandra, Nicole Marshall, Norma Mendoza, Allen Jankeel, Michael Z. Zulu, Ilhem Messaoudi
Software Mentions: 6
Published: almost 3 years ago
10.1038/srep32753
HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell linesCited by: 35
Author(s): Dinar Yunusov, Letícia Anderson, Luis DaSilva, Joanna Wysocka, Toshihiko Ezashi, R. M. Roberts, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: over 7 years ago
10.1186/s12920-020-00819-5
Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastomaCited 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: over 3 years ago
10.1371/journal.pgen.1006563
Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editingCited by: 163
Author(s): Rui Zhang, Patricia Deng, Jacobson Dionna, Jin Billy Li
Software Mentions: 6
Published: over 7 years ago
10.1186/s13072-018-0250-9
Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infectionCited 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 5 years ago
10.1371/journal.pgen.1006840
Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacksCited 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: almost 7 years ago
10.1186/s13024-017-0219-3
Multiscale network modeling of oligodendrocytes reveals molecular components of myelin dysregulation in Alzheimer’s diseaseCited 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: over 6 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 beanCited 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 4 years ago
10.1099/mgen.0.000320
Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomicsCited 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 4 years ago
10.1186/s13059-014-0527-7
The importance of study design for detecting differentially abundant features in high-throughput experimentsCited by: 12
Author(s): Huaien Luo, Juntao Li, Burton Kuan Hui Chia, Paul Robson, Niranjan Nagarajan
Software Mentions: 5
Published: over 9 years ago
10.1186/gb-2014-15-8-r70
DNA copy number evolution in Drosophila cell linesCited by: 94
Author(s): Hangnoh Lee, C. Joel McManus, Dong-Yeon Cho, Matthew L. Eaton, Fioranna Renda, Maria Patrizia Somma, Lucy Cherbas, Gemma E. May, Sara Powell, Dayu Zhang, Lijun Zhan, Alissa Resch, Justen Andrews, S Celniker, Peter Cherbas, Teresa M. Przytycka, Maurizio Gatti, Brian Oliver, Brenton R. Graveley, David M. MacAlpine
Software Mentions: 5
Published: almost 10 years ago
10.1186/s13059-014-0511-2
A genomic and evolutionary approach reveals non-genetic drug resistance in malariaCited by: 34
Author(s): Jonathan D. Herman, Daniel P. Rice, Ulf Ribacke, Jacob Silterra, Amy Deik, Eli L. Moss, Kate M Broadbent, Daniel E. Neafsey, Michael M. Desai, Clary B. Clish, Ralph Mazitschek, Dyann F. Wirth
Software Mentions: 5
Published: over 9 years ago
10.1371/journal.pone.0159093
Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal CortexCited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
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 SetsCited 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 5 years ago
10.1186/s13072-019-0285-6
H3K4me2 functions as a repressive epigenetic mark in plantsCited by: 46
Author(s): Kun Wang, Kunpeng Liu, Liufan Yin, Yu Yu, Ji Qi, Wen‐Hui Shen, Jun Zhu, Yijing Zhang, Dong Ao
Software Mentions: 5
Published: almost 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 MacrophagesCited 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 6 years ago
10.3389/fmicb.2018.02212
A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulansCited by: 29
Author(s): Angelo Pidroni, Birgit Faber, Gerald Brosch, Ingo Bauer, Stefan Graessle
Software Mentions: 5
Published: over 5 years ago
10.26508/lsa.202000946
Prognostic accuracy of MALDI-TOF mass spectrometric analysis of plasma in COVID-19Cited 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: almost 3 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 disorderCited 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 3 years ago
10.18632/oncotarget.16493
ERK signalling modulates epigenome to drive epithelial to mesenchymal transitionCited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: about 7 years ago
10.1186/1471-2164-14-230
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitroCited by: 39
Author(s): Nicolas C. Nalpas, Stephen D. E. Park, David A. Magee, Maria Taraktsoglou, John A. Browne, Kevin M. Conlon, Kévin Rue-Albrecht, Kate E. Killick, Karsten Hokamp, Amanda J. Lohan, Brendan J. Loftus, Eamonn Gormley, Stephen V. Gordon, David E. MacHugh
Software Mentions: 5
Published: about 11 years ago
10.7554/eLife.07103
A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomicsCited 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: almost 9 years ago
10.7554/eLife.37184
An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancerCited 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 6 years ago
10.1371/journal.pgen.1005819
Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor AgeCited 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: about 8 years ago
10.18632/oncotarget.21031
Genome-wide analysis and functional prediction of long non-coding RNAs in mouse uterus during the implantation windowCited 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: over 6 years ago
10.1371/journal.pgen.1004648
Genome-Wide Discovery of Drug-Dependent Human Liver Regulatory ElementsCited 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: over 9 years ago
10.7554/eLife.51373
PHF19 mediated regulation of proliferation and invasiveness in prostate cancer cellsCited by: 18
Author(s): Payal Jain, Cecilia Ballaré, Enrique Blanco, Pedro Vizán, Luciano Di Croce
Software Mentions: 5
Published: about 4 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 cultureCited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: about 9 years ago
10.7554/eLife.07295
Negative regulation of ABA signaling by WRKY33 is critical for Arabidopsis immunity towards Botrytis cinerea 2100Cited by: 179
Author(s): Shouan Liu, Barbara Kracher, J. Ziegler, Rainer P. Birkenbihl, Imre E. Somssich
Software Mentions: 5
Published: almost 9 years ago
10.7554/eLife.27159
Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancerCited 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 7 years ago
10.7554/eLife.49044
NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stressCited 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: over 4 years ago
10.3389/fcell.2020.00557
Comprehensive Analysis of Differentially Expressed lncRNAs in Gastric CancerCited by: 10
Author(s): Nan Xiao, Yang Hu, Liran Juan
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pone.0085568
Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis PipelinesCited 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 10 years ago
10.7554/eLife.15657
An integrative transcriptomic atlas of organogenesis in human embryosCited by: 55
Author(s): Dave T. Gerrard, Andrew Berry, Rachel Jennings, Karen Piper Hanley, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 5
Published: over 7 years ago
10.7554/eLife.64317
Evolutionary shifts in taste coding in the fruit pest Drosophila suzukiiCited by: 33
Author(s): Hany K.M. Dweck, Gaëlle J.S. Talross, Wanyue Wang, John R. Carlson
Software Mentions: 5
Published: about 3 years ago
10.3389/fcvm.2021.683074
A Multi-Omics Approach Using a Mouse Model of Cardiac Malformations for Prioritization of Human Congenital Heart Disease Contributing GenesCited by: 2
Author(s): Adrianna Matos‐Nieves, Sathiyanarayanan Manivannan, Uddalak Majumdar, Kim L. McBride, Peter White, Vidu Garg
Software Mentions: 5
Published: over 2 years ago
10.1186/s12864-020-07002-1
Analysis of the brain transcriptome in lines of laying hens divergently selected for feather peckingCited by: 13
Author(s): Clemens Falker‐Gieske, Andrea Mott, Siegfried Preuß, Sören Franzenburg, W. Bessei, Jörn Bennewitz, Jens Tetens
Software Mentions: 5
Published: over 3 years ago
10.12688/f1000research.6536.1
A reanalysis of mouse ENCODE comparative gene expression dataCited by: 90
Author(s): Yoav Gilad, Orna Mizrahi-Man
Software Mentions: 5
Published: about 9 years ago
10.1371/journal.pgen.1005698
Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegansCited by: 43
Author(s): Maxwell Kramer, Anna Lena Kranz, Amanda Su, Lara Winterkorn, Sarah Elizabeth Albritton, Sevinç Ercan
Software Mentions: 5
Published: over 8 years ago
10.1038/s41598-018-36840-z
Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomasCited by: 28
Author(s): Susan K. Rathe, Flavia E. Popescu, James E. Johnson, Adrienne L. Watson, Tracy A. Marko, Branden S. Moriarity, John R. Ohlfest, David A. Largaespada
Software Mentions: 5
Published: over 5 years ago
10.7554/eLife.44161
Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibitionCited 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: about 5 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 BacteriaCited by: 9
Author(s): Songbao Zou, Qianqian Zhang, Jun Gong
Software Mentions: 5
Published: about 4 years ago
10.1038/srep46203
Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infectionCited by: 25
Author(s): Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Jason R. Grant, R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan, Paul Stothard, Graham Plastow
Software Mentions: 5
Published: about 7 years ago
10.1038/s41598-017-03478-2
Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasisCited by: 5
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zongzhuan Shen
Software Mentions: 5
Published: almost 7 years ago
10.1155/2021/5320445
Predicting Target Genes of San-Huang-Chai-Zhu Formula in Treating ANIT-Induced Acute Intrahepatic Cholestasis Rat Model via Bioinformatics Analysis Combined with Experimental ValidationCited by: 6
Author(s): Jiaming Yao, Junbin Yan, Jinting Wu, Jianshun Yu, Beihui He, Xi Chen
Software Mentions: 5
Published: over 2 years ago
10.3389/fcvm.2020.00052
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic VasculatureCited by: 86
Author(s): Menglan Xiang, Rubén Adrián Grosso, Akiko Takeda, Junliang Pan, Tove Bekkhus, Kevin Brulois, Denis Đermadi, Sofia Nordling, Michael Vanlandewijck, Sirpa Jalkanen, Maria H. Ulvmar, Eugene C. Butcher
Software Mentions: 5
Published: about 4 years ago
10.7554/eLife.21049
Proliferation-independent regulation of organ size by Fgf/Notch signalingCited 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 7 years ago
10.7554/eLife.39054
New insights into the cellular temporal response to proteostatic stressCited 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: over 5 years ago
10.7150/jca.47698
Mass Spectrometry Imaging Differentiates Chromophobe Renal Cell Carcinoma and Renal Oncocytoma with High AccuracyCited 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 4 years ago
10.7150/jca.29958
TGFBI Promotes Tumor Growth and is Associated with Poor Prognosis in Oral Squamous Cell CarcinomaCited 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 5 years ago
10.1371/journal.pone.0235218
Transcriptome profiling of longissimus lumborum in Holstein bulls and steers with different beef qualitiesCited by: 17
Author(s): Yan Li, Meimei Wang, Qiufeng Li, Yanxia Gao, Qian Li, Jianguo Li, Yong Cao
Software Mentions: 5
Published: almost 4 years ago
10.1186/s12879-018-3127-4
“Tuberculosis in advanced HIV infection is associated with increased expression of IFNγ and its downstream targets”Cited by: 18
Author(s): Sheetal Verma, Peicheng Du, Damalie Nakanjako, Sabine Hermans, Jessica Briggs, Lydia Nakiyingi, Jerrold J. Ellner, Yukari C. Manabe, Padmini Salgame
Software Mentions: 5
Published: about 6 years ago
10.1371/journal.pone.0153932
Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. ParatuberculosisCited by: 24
Author(s): Randy J. Hempel, John P. Bannantine, Judith R. Stabel
Software Mentions: 5
Published: about 8 years ago
10.18632/oncotarget.8192
Integrated analysis of long non-coding RNAs in human colorectal cancerCited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: about 8 years ago
10.1186/s12864-018-4926-0
CircMarker: a fast and accurate algorithm for circular RNA detectionCited by: 23
Author(s): Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu, Yufeng Wu
Software Mentions: 5
Published: almost 6 years ago
10.1186/s13041-020-00603-7
Ocular hypertension suppresses homeostatic gene expression in optic nerve head microglia of DBA/2 J miceCited by: 28
Author(s): James R. Tribble, Jeffrey M. Harder, Pete A. Williams, Simon W. M. John
Software Mentions: 5
Published: almost 4 years ago
10.3390/ijms22179146
Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog AnalysesCited by: 5
Author(s): Mirosław Tyrka, Beata Bakera, Magdalena Szeliga, Magdalena Święcicka, Paweł Krajewski, Monika Mokrzycka, Monika Rakoczy-Trojanowska
Software Mentions: 5
Published: over 2 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 1q22Cited by: 11
Author(s): Arttu Autio, Tapio Nevalainen, Binisha H. Mishra, Marja Jylhä, Heini Flinck, Mikko Hurme
Software Mentions: 5
Published: about 4 years ago
10.1210/endocr/bqz044
Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male MiceCited by: 8
Author(s): Poonamjot Deol, Elena Kozlova, Matthew C. Valdez, Catherine Ho, Ei-Wen Yang, H.J. Richardson, Gwendolyn Michelle Gonzalez, Edward Truong, Jack Reid, Joseph M. Valdez, Jonathan Deans, Jose Martinez-Lomeli, Jane R. Evans, Tao Jiang, Frances M. Sladek, Margarita Curras‐Collazo
Software Mentions: 5
Published: over 4 years ago
10.3389/fmicb.2016.01335
Visual Comparative Omics of Fungi for Plant Biomass DeconstructionCited by: 31
Author(s): Shingo Miyauchi, David Navarro, Igor V. Grigoriev, Anna Lipzen, Robert Riley, Didier Chevret, Sacha Grisel, Jean‐Guy Berrin, Bernard Henrissat, Marie‐Noëlle Rosso
Software Mentions: 5
Published: over 7 years ago
10.1093/gigascience/giaa143
High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant <i>Monomorium pharaonis</i>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 3 years ago
10.3389/fphys.2019.01305
The Regulation of Ruminal Short-Chain Fatty Acids on the Functions of Rumen BarriersCited by: 28
Author(s): Hong Shen, Zhihui Xu, Zanming Shen, Zhongyan Lu
Software Mentions: 5
Published: over 4 years ago
10.1186/gb-2014-15-4-r56
Hypermethylation in the ZBTB20 gene is associated with major depressive disorderCited by: 84
Author(s): Matthew N. Davies, Lutz Krause, Jordana T. Bell, Fei Gao, Kirsten Ward, Honglong Wu, Hanlin Lu, Yuan Liu, Pei-Chien Tsai, David A. Collier, Therese M. Murphy, Emma Dempster, Jonathan Mill, Alexis Battle, Sara Mostafavi, Xiaowei Zhu, Anjali K. Henders, Enda M. Byrne, Naomi R. Wray, Nicholas G. Martin, Tim D. Spector, Jun Wang
Software Mentions: 5
Published: over 10 years ago
10.1371/journal.pone.0225180
Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulationCited by: 10
Author(s): Aisling M. Redmond, Soleilmane Omarjee, Igor Chernukhin, Muriel Le Romancer, Jason S. Carroll
Software Mentions: 5
Published: over 4 years ago
10.3390/molecules25214894
Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric ApproachCited by: 8
Author(s): Michał Złoch, Paweł Pomastowski, Ewelina Maślak, Fernanda Monedeiro
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-014-0429-8
Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancerCited by: 177
Author(s): Nicole M. White, Christopher R. Cabanski, Jessica Silva-Fisher, Ha X. Dang, Ramaswamy Govindan, Christopher A. Maher
Software Mentions: 5
Published: almost 10 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) GenomeCited by: 33
Author(s): Ranu Sharma, Vimal Rawat, C.G. Suresh
Software Mentions: 5
Published: over 9 years ago
10.1371/journal.pgen.1008566
The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plantsCited by: 54
Author(s): Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle Henry
Software Mentions: 5
Published: over 4 years ago
10.1111/1755-0998.13257
High quality genome of <i>Erigeron breviscapus</i> provides a reference for herbal plants in AsteraceaeCited 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: over 3 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 treatmentCited 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: almost 6 years ago
10.1371/journal.pone.0151917
Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification PatternsCited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: about 8 years ago
10.7554/eLife.14997
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neuronsCited by: 326
Author(s): Mark S. Cembrowski, Lihua Wang, Ken Sugino, Brenda C. Shields, Nelson Spruston
Software Mentions: 5
Published: about 8 years ago
10.3390/genes10070552
Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic DifferentiationCited by: 14
Author(s): Xitong Zhao, Shaokang Chen, Zhen Tan, Yuan Wang, Fengxia Zhang, Ting Yang, Yibing Liu, Ai Hong, Kai Xing, Chuduan Wang
Software Mentions: 5
Published: almost 5 years ago
10.3389/fonc.2019.01206
Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver RegenerationCited by: 11
Author(s): Pieter Borger, Marcel Schneider, Lukas Frick, Magda Langiewicz, Maksim Sorokin, Anton Buzdin, Ekaterina Kachaylo, Rolf Graf, Bostjan Humar, Pierre‐Alain Clavien
Software Mentions: 5
Published: over 4 years ago
10.1016/j.devcel.2021.07.019
Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competitionCited by: 25
Author(s): Christopher J. Price, Dylan Stavish, Paul J. Gokhale, Ben A. Stevenson, Samantha Sargeant, Joanne Lacey, Tristan A. Rodríguez, Ivana Barbaric
Software Mentions: 5
Published: over 2 years ago
10.1186/1471-2164-15-917
Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgutCited by: 37
Author(s): Matan Shelomi, W. Cameron Jasper, Joel Atallah, Lynn S. Kimsey, Brian R. Johnson
Software Mentions: 5
Published: over 10 years ago
10.7717/peerj.3091
Effect of method of deduplication on estimation of differential gene expression using RNA-seqCited by: 20
Author(s): Anna V. Klepikova, Artem S. Kasianov, Mikhail S. Chesnokov, Н. Л. Лазаревич, Aleksey A. Penin, Maria D. Logacheva
Software Mentions: 5
Published: about 7 years ago
10.1016/j.ccell.2019.02.009
Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic TargetsCited by: 533
Author(s): Luca Cassetta, Stamatina Fragkogianni, Andrew H. Sims, Agnieszka Swierczak, Lesley M. Forrester, Hui Zhang, Daniel Soong, Tiziana Cotechini, Pavana Anur, Elaine Y. Lin, A Fidanza, Martha Lopez‐Yrigoyen, Michael Millar, Alexandra Urman, Zhichao Ai, Paul T. Spellman, E. Shelley Hwang, JM Dixon, Lisa Wiechmann, Lisa M. Coussens, Harriet O. Smith, Jeffrey W. Pollard
Software Mentions: 5
Published: about 5 years ago
10.15252/emmm.202012105
Neuron type‐specific increase in lamin B1 contributes to nuclear dysfunction in Huntington’s diseaseCited by: 23
Author(s): Rafael Alcalá-Vida, Marta Garcia‐Forn, Carla Castany‐Pladevall, Jordi Creus-Muncunill, Yoko Itō, Enrique Blanco, Arantxa Golbano, Kilian Crespí-Vázquez, Aled Parry, Guy Slater, Shamith A. Samarajiwa, Sandra Peiró, Luciano Di Croce, Masashi Narita, Esther Pérez‐Navarro
Software Mentions: 5
Published: over 3 years ago
10.1093/database/bax079
EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus speciesCited 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 7 years ago
10.1038/s42003-018-0037-3
The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organizationCited 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 6 years ago
10.1002/advs.201901672
Comparison of <i>Arachis monticola</i> with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of PeanutCited 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 4 years ago
10.1038/s42003-020-01398-y
Genomic retargeting of p53 and CTCF is associated with transcriptional changes during oncogenic HRas-induced transformationCited 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 3 years ago
10.1186/1471-213X-12-33
Global gene expression of the inner cell mass and trophectoderm of the bovine blastocystCited by: 82
Author(s): Manabu Ozawa, Miki Sakatani, Jiqiang Yao, Savita Shanker, Fahong Yu, Rui Yamashita, Shokichi Wakabayashi, Kenta Nakai, Kyle B. Dobbs, Mateus José Sudano, William G. Farmerie, Peter J. Hansen
Software Mentions: 5
Published: over 11 years ago
10.1038/s42003-021-01716-y
Simple sequence repeats drive genome plasticity and promote adaptive evolution in penaeid shrimpCited 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 3 years ago
10.1038/s42003-020-01620-x
RNA editing enzyme APOBEC3A promotes pro-inflammatory M1 macrophage polarizationCited 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 3 years ago
10.1186/1748-7188-8-25
Data compression for sequencing dataCited by: 84
Author(s): Sebastian Deorowicz, Szymon Grabowski
Software Mentions: 5
Published: over 11 years ago
10.1186/s12859-018-2019-3
Closha: bioinformatics workflow system for the analysis of massive sequencing dataCited 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 6 years ago
10.1523/ENEURO.0288-18.2019
Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative DiseasesCited by: 26
Author(s): Raquel Cuevas-Diaz Duran, Chih Yen Wang, Hui Zheng, Benjamin Deneen, Jia Qian Wu
Software Mentions: 5
Published: about 5 years ago
10.3390/ijms22052353
ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast CancerCited 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: about 3 years ago
10.3390/ijms21051630
Alternatively Constructed Estrogen Receptor Alpha-Driven Super-Enhancers Result in Similar Gene Expression in Breast and Endometrial Cell LinesCited by: 1
Author(s): Dóra Bojcsuk, Gergely Nagy, Bálint László Bálint
Software Mentions: 5
Published: about 4 years ago
10.1038/s41421-017-0003-0
ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cellsCited 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 6 years ago