pypi: TopHat | Projects | Ecosyste.ms: Papers

10.1093/bib/bbx143

Bioinformatics for precision oncology
Cited by: 49
Author(s): Jochen Singer, Anja Irmisch, Hans‐Joachim Ruscheweyh, Franziska Singer, Nora C. Toussaint, Mitchell P. Levesque, Daniel J. Stekhoven, Niko Beerenwinkel
Software Mentions: 7
Published: almost 9 years ago

10.1534/g3.114.012526

Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing
Cited by: 30
Author(s): Upendra Kumar Devisetty, Michaeal F. Covington, An V. Tat, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 7
Published: almost 12 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

10.1186/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

10.1111/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

10.1371/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

10.1093/dnares/dsaa011

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus
Cited by: 28
Author(s): Shingo Miyauchi, Hayat Hage, Élodie Drula, Laurence Lesage‐Meessen, Jean‐Guy Berrin, David Navarro, Anne Favel, Delphine Chaduli, Sacha Grisel, Mireille Haon, François Piumi, Anthony Levasseur, Anne Lomascolo, Steven Ahrendt, Kerrie Barry, Kurt LaButti, Didier Chevret, Chris Daum, Jérôme Mariette, Christophe Klopp, Daniel Cullen, Ronald P. de Vries, Allen C. Gathman, Matthieu Hainaut, Bernard Henrissat, Kristiina Hildén, Ursula Kües, Walt W. Lilly, Anna Lipzen, Miia Mäkelä, Ángel T. Martı́nez, Mélanie Morel‐Rouhier, Emmanuelle Morin, Jasmyn Pangilinan, Arthur F. J. Ram, Han A. B. Wösten, Francisco J. Ruíz-Dueñas, Robert Riley, Éric Record, Igor V. Grigoriev, Marie‐Noëlle Rosso
Software Mentions: 7
Published: over 6 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pone.0126545

Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability
Cited by: 15
Author(s): Karolis Uziela, Antti Honkela
Software Mentions: 7
Published: over 11 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

10.1136/jitc-2020-000778

M1hottumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer
Cited by: 75
Author(s): Eva M. Garrido-Martín, Toby Mellows, James Clarke, Anusha-Preethi Ganesan, Oliver Wood, Angelica Cazaly, Grégory Seumois, Serena Chee, Aiman Alzetani, Emma V. King, Catherine C. Hedrick, Gareth J. Thomas, Peter S. Friedmann, Christian Ottensmeier, Pandurangan Vijayanand, Tilman Sánchez-Elsner
Software Mentions: 7
Published: over 6 years ago

10.15252/emmm.202013180

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1
Cited by: 21
Author(s): George Sflomos, Laura Battista, Patrick Aouad, Fabio De Martino, Valentina Scabia, Athina Stravodimou, Ayyakkannu Ayyanan, Assia Ifticene‐Treboux, Philipp Bücher, Maryse Fiche, Giovanna Ambrosini, Cathrin Brisken, Rls
Software Mentions: 7
Published: over 5 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

10.1371/journal.pone.0083984

Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes
Cited by: 34
Author(s): Timothy B. Sackton, John H. Werren, Andrew G. Clark
Software Mentions: 7
Published: almost 13 years ago

10.3389/fgene.2019.00185

Myometrial Transcriptional Signatures of Human Parturition
Cited by: 36
Author(s): Zachary Stanfield, Pei F. Lai, Kaiyu Lei, Mark R. Johnson, Andrew M. Blanks, Roberto Romero, Mark R. Chance, Sam Mesiano, Mehmet Koyutürk
Software Mentions: 7
Published: over 7 years ago

10.1371/journal.pone.0187735

Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection
Cited by: 16
Author(s): Maren Pröll, Christiane Neuhoff, K. Schellander, Muhammad Jasim Uddin, Mehmet Ulaş Çınar, Sudeep Sahadevan, Xuecheng Qu, M. S. Islam, Mikhaël Poirier, Marcel A. Müller, Christian Drosten, Dawit Tesfaye, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 7
Published: almost 9 years ago

10.3390/jof7090700

Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi
Cited by: 3
Author(s): Grace N. Ijoma, Sylvie M Heri, Tonderayi Matambo, Memory Tekere
Software Mentions: 7
Published: about 5 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

10.1371/journal.pone.0233899

Recapitulation of prostate tissue cell type-specific transcriptomes by an in vivo primary prostate tissue xenograft model
Cited by: 2
Author(s): Nelson T. Gross, Jianmin Wang, Michael V. Fiandalo, Eduardo Cortes Gomez, Anica Watts, Alejandro Godoy, Gary J. Smith, Yue Wu
Software Mentions: 7
Published: over 6 years ago

10.15252/embr.201642378

Linear ubiquitination by <scp>LUBEL</scp> has a role in Drosophila heat stress response
Cited by: 31
Author(s): Tomoko Asaoka, Jorge Almagro, Christine Ehrhardt, Yi-Chun Isabella Tsai, Alexander Schleiffer, Luiza Deszcz, Sini Junttila, Leonie Ringrose, Karl Mechtler, Anoop Kavirayani, Attila Gyenesei, Kay Hofmann, Peter Duchek, Katrin Rittinger, Fumiyo Ikeda
Software Mentions: 7
Published: about 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: almost 9 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: almost 13 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

10.1371/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: over 11 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

10.1016/j.csbj.2019.04.012

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts
Cited by: 23
Author(s): Isaac A. Babarinde, Yuhao Li, Andrew P. Hutchins
Software Mentions: 6
Published: almost 8 years ago

10.1016/j.csbj.2021.07.010

Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome
Cited by: 3
Author(s): Márton Miskei, Adrienn Horváth, Lívia Viola, L. Varga, Éva Nagy, Orsolya Feró, Zsolt Karányi, Jason Roszik, Csaba Miskey, Zoltán Ivics, Lóránt Székvölgyi
Software Mentions: 6
Published: almost 6 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: over 5 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

10.1186/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.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.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/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

10.3390/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

10.1534/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

10.1371/journal.pone.0175657

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts
Cited by: 28
Author(s): Wolfgang Kaisers, Petra Boukamp, Hans Jürgen Stark, Holger Schwender, Julia Tigges, Jean Krutmann, Heiner Schaal
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0235294

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury
Cited by: 22
Author(s): Elodie Ramond, Jan Paul Dudzic, Bruno Lemaître
Software Mentions: 6
Published: over 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: about 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: over 11 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

10.1371/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: over 12 years ago

10.1371/journal.pone.0152034

System-Wide Associations between DNA-Methylation, Gene Expression, and Humoral Immune Response to Influenza Vaccination
Cited by: 45
Author(s): Michael T. Zimmermann, Ann L. Oberg, Diane E. Grill, Inna G. Ovsyannikova, Iana H. Haralambieva, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 6
Published: over 10 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

10.7554/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: about 10 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: over 9 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: over 10 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: almost 9 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

10.15252/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

10.15252/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: about 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

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

10.1186/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

10.1038/s41598-019-47797-y

Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae
Cited 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: about 7 years ago

10.1038/s41598-019-44302-3

Dose-dependent effects of chronic alcohol drinking on peripheral immune responses
Cited by: 41
Author(s): Suhas Sureshchandra, Anthony M. Raus, Allen Jankeel, Brian Jin Kee Ligh, Nicole A.R. Walter, Natali Newman, Kathleen A. Grant, Ilhem Messaoudi
Software Mentions: 6
Published: over 7 years ago

10.1038/s41598-020-65089-8

Immunorthodontics: in vivo gene expression of orthodontic tooth movement
Cited by: 28
Author(s): Yehuda Klein, Omer Fleissig, David Polak, Yechezkel Barenholz, Ofer Mandelboim, Stella Chaushu
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-018-37397-7

Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
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 9 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 potential
Cited 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: 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

10.1371/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

10.1371/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.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: over 6 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: about 10 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

10.1371/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: about 15 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: almost 7 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

10.7717/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

10.3390/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: over 7 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: over 9 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

10.1186/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

10.1186/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: almost 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: almost 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

10.1002/1878-0261.12435

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

10.1038/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

10.1186/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

10.1038/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

10.1186/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

10.3389/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

10.1016/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: almost 13 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: about 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

10.1186/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

10.3390/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

10.1186/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

10.1111/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

10.18632/oncotarget.22942

S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cells
Cited by: 33
Author(s): Yan Wang, Zhong Sheng Sun, Moshe Szyf
Software Mentions: 6
Published: almost 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.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/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: about 8 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: over 7 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

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