pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0088950

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells
Cited by: 68
Author(s): Jeannine Diesch, Elaine Sanij, Omer Gilan, Christopher G. Love, Hoanh Tran, Nicholas I. Fleming, Jason Ellul, Amalia Marcia, Izhak Haviv, Richard B. Pearson, Eugene Tulchinsky, John M. Mariadason, Oliver M. Sieber, Ross D. Hannan, Amardeep S. Dhillon
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2020.00410

Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria
Cited by: 9
Author(s): Otmane Lamrabet, Astrid Melotti, Frédéric Burdet, Nabil Hanna, Jackie Perrin, Jahn Nitschke, Marco Pagni, Hubert Hilbi, Thierry Soldati, Pierre Cosson
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-015-0834-3

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis
Cited by: 1
Author(s): Sini Rautio, Harri Lähdesmäki
Software Mentions: 4
Published: almost 9 years ago

10.3389/fmicb.2021.644540

Motor Stereotypic Behavior Was Associated With Immune Response in Macaques: Insight From Transcriptome and Gut Microbiota Analysis
Cited by: 3
Author(s): Xuan Pan, Fangyuan Liu, Yang Song, Hongrun Wang, Lingyun Wang, Hong Qiu, Megan Price, Jing Li
Software Mentions: 4
Published: over 3 years ago

10.1002/advs.202000938

Atlas of Musculoskeletal Stem Cells with the Soft and Hard Tissue Differentiation Architecture
Cited by: 7
Author(s): Zi Yin, Junxin Lin, Ruojin Yan, Richun Liu, Mengfei Liu, Bo Zhou, Wenyan Zhou, An Chen, Yangwu Chen, Yin Hu, Chunmei Fan, Kun Zhao, Bowen Wu, Xiaohui Zou, Jin Zhang, Ahmed El-Hashash, Xiao Chen
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2017.00261

Insights into Dynamic Polymicrobial Synergy Revealed by Time-Coursed RNA-Seq
Cited by: 27
Author(s): Erik L. Hendrickson, David A. C. Beck, Daniel P. Miller, Qian Wang, Marvin Whiteley, Richard J. Lamont, Murray Hackett
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2021.736411

Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress
Cited by: 2
Author(s): Dong Han, Qiaojuan Yan, Jun Li, Zhengqiang Jiang, Shanchao Yang
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2018.01551

Concerted Metabolic Shifts Give New Insights Into the Syntrophic Mechanism Between Propionate-Fermenting Pelotomaculum thermopropionicum and Hydrogenotrophic Methanocella conradii
Cited by: 22
Author(s): Pengfei Liu, Yahai Lu
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.11045

Analysis of differences in the transcriptomic profiles of eutopic and ectopic endometriums in women with ovarian endometriosis
Cited by: 5
Author(s): Xiao Feng, Lingbin Qi, Xiaoyu Xu, Yun Feng, Xiaoming Gong, Aixingzi Aili, Yu Chen, Zhigang Xue, Jinfeng Xue, Xiaowen Tong
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2021.664260

Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell
Cited by: 11
Author(s): Michelle M. Halstead, Alma Islas–Trejo, Daniel Estanislao Goszczynski, Juan F. Medrano, Huaijun Zhou, Pablo J. Ross
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-016-2801-4

RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome
Cited by: 8
Author(s): Susan M. Corley, Cesar P Canales, Paulina Carmona-Mora, Veronica Mendoza-Reinosa, Annemiek Beverdam, Edna C. Hardeman, Marc R. Wilkins, Steve Palmer
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-019-5835-6

West Nile virus infection and interferon alpha treatment alter the spectrum and the levels of coding and noncoding host RNAs secreted in extracellular vesicles
Cited by: 20
Author(s): Andrii Slonchak, Brian Clarke, Jason M. Mackenzie, Alberto A. Amarilla, Yin Xiang Setoh, Alexander A. Khromykh
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2694-2

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Cited by: 21
Author(s): Maurizio Pellegrino, Adam Sciambi, Jamie Yates, Joshua D. Mast, Charles Silver, Dennis J. Eastburn
Software Mentions: 4
Published: over 8 years ago

10.3390/pathogens8040183

Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Cited by: 12
Author(s): Soo Jin Oh, Soo Yeon Lim, Mee Hyun Song, Jinhee Ahn, Chan Hee Lee, Ok Sarah Shin
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-016-2925-6

Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi
Cited by: 74
Author(s): S. Matić, Paolo Bagnaresi, Chiara Biselli, Luigi Orrù, Greice Amaral Carneiro, Ilenia Siciliano, Giampiero Valè, M. L. Gullino, D. Spadaro
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-015-1767-y

Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq
Cited by: 132
Author(s): Anto P. Rajkumar, Per Qvist, Ross Lazarus, Francesco Lescai, Jia Ju, Mette Nyegaard, Ole Mors, Anders D. Børglum, Qibin Li, Jane H. Christensen
Software Mentions: 4
Published: over 9 years ago

10.1186/s12989-018-0244-6

Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition
Cited by: 53
Author(s): Deniz Öner, Manosij Ghosh, Hannelore Bové, Matthieu Moisse, Bram Boeckx, Radu Corneliu Duca, Katrien Poels, Katrien Luyts, Eveline Putzeys, Kirsten Van Landuydt, Jeroen Vanoirbeek, Marcel Ameloot, Diether Lambrechts, Lode Godderis, Peter Hoet
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13071-021-04597-6

Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector
Cited by: 5
Author(s): Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-017-3563-3

Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model
Cited by: 30
Author(s): Ying Cai, Rubén Nogales-Cadenas, Quanwei Zhang, Jhih Rong Lin, Wen Zhang, Kelly O’Brien, Cristina Montagna, Zhengdong D. Zhang
Software Mentions: 4
Published: almost 8 years ago

10.3389/fmicb.2019.01975

Functional Genomic Analyses of Exopolysaccharide-Producing Streptococcus thermophilus ASCC 1275 in Response to Milk Fermentation Conditions
Cited by: 8
Author(s): Qinglong Wu, Hung Chu, Aparna Padmanabhan, Nagendra P. Shah
Software Mentions: 4
Published: about 5 years ago

10.1186/s12864-020-6520-5

Identification of eQTLs and sQTLs associated with meat quality in beef
Cited by: 16
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, Raluca G. Mateescu
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-15-845

Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data
Cited by: 66
Author(s): Kunshan Zhang, Kefei Huang, Yuan Luo, Siguang Li
Software Mentions: 4
Published: about 10 years ago

10.1186/1755-8794-7-57

Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model
Cited by: 79
Author(s): Lisette J. A. Kogelman, Susanna Cirera, Daria V. Zhernakova, Merete Fredholm, Lude Franke, Haja N. Kadarmideen
Software Mentions: 4
Published: about 10 years ago

10.3389/fendo.2019.00840

Role of MicroRNAs in the Regulation of Subcutaneous White Adipose Tissue in Individuals With Obesity and Without Type 2 Diabetes
Cited by: 17
Author(s): Olga Brovkina, А Г Никитин, Д. С. Ходырев, Ekaterina A. Shestakova, Igor A. Sklyanik, Anna S. Panevina, Iurii Stafeev, Mikhail Menshikov, Anastasiya A. Kobelyatskaya, Anatoliy Yurasov, V. S. Fedenko, Yu I Yashkov, М. В. Шестакова
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0177739

Transcriptome profiling revealed novel transcriptional regulators in maize responses to Ostrinia furnacalis and jasmonic acid
Cited by: 15
Author(s): Wang Hai, Shengyan Li, Shouzhen Teng, Haisheng Liang, Hongjia Xin, Hongjiang Gao, Dafang Huang, Zhihong Lang
Software Mentions: 4
Published: over 7 years ago

10.1186/s12864-018-5146-3

Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells
Cited by: 18
Author(s): Koryu Kin, Gillian Forbes, Andrew Cassidy, Pauline Schaap
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-020-6613-1

Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals
Cited by: 11
Author(s): Yali Hou, Furong Qi, Xue Bai, Tong Ren, Xu Shen, Qing Chu, Xiquan Zhang, Xuemei Lu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-3345-3

TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq
Cited by: 6
Author(s): Cole M. McQueen, Canaan Whitfield-Cargile, Kranti Konganti, Glenn P. Blodgett, Scott V. Dindot, Noah D. Cohen
Software Mentions: 4
Published: almost 8 years ago

10.3390/v12080817

Host Transcriptional Response to Persistent Infection with a Live-Attenuated Porcine Reproductive and Respiratory Syndrome Virus Strain
Cited by: 6
Author(s): Jayeshbhai Chaudhari, Chia-Sin Liew, Aspen M. Workman, Jean-Jack M. Riethoven, David Steffen, Sarah Sillman, Hiep L.X. Vu
Software Mentions: 4
Published: over 4 years ago

10.18632/aging.103454

Weighted correlation gene network analysis reveals a new stemness index-related survival model for prognostic prediction in hepatocellular carcinoma
Cited by: 14
Author(s): Qiujing Zhang, Jia Wang, Menghan Liu, Qingqing Zhu, Qiang Li, Chao Xie, Congcong Han, Yali Wang, Min Gao, Jie Liu
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-019-6397-3

Host plant adaptation in the polyphagous whitefly, Trialeurodes vaporariorum, is associated with transcriptional plasticity and altered sensitivity to insecticides
Cited by: 25
Author(s): Adam Pym, Kumar Saurabh Singh, A. Nordgren, T.G. Emyr Davies, Christoph Zimmer, Jan Eliáš, Russell Slater, Chris Bass
Software Mentions: 4
Published: almost 5 years ago

10.1111/tpj.15250

The chemical compound ‘Heatin’ stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1‐subfamily of nitrilases
Cited by: 7
Author(s): Lennard van der Woude, Markus Piotrowski, Gruson Klaasse, Judith K Paulus, Daniel Krahn, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser, Ondřej Novák, Karin Ljung, Suzanne Bulder, Marcel van Verk, L. Basten Snoek, Martijn Fiers, Nathaniel I. Martin, R.A.L. van der Hoorn, Stéphanie Robert, Sjef Smeekens, Martijn van Zanten
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: about 4 years ago

10.3389/fnins.2021.671249

Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury
Cited by: 7
Author(s): Victor Gourain, Olivier Armant, Luisa Lübke, Nicolas Diotel, Sepand Rastegar, Uwe Strähle
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-015-2115-y

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars
Cited by: 36
Author(s): Ryan Ghan, Steven C. Van Sluyter, Uri Hochberg, Asfaw Degu, Daniel Hopper, Richard L. Tillet, Karen Schlauch, Paul A. Haynes, Aaron Fait, Grant R. Cramer
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0166944

Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation
Cited by: 23
Author(s): Susan M. Corley, Shan-Yuan Tsai, Marc R. Wilkins, Cynthia Shannon Weickert
Software Mentions: 4
Published: almost 8 years ago

10.1186/1471-2164-15-221

From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
Cited by: 119
Author(s): Inès Zouari, Alessandra Salvioli, Matteo Chialva, Mara Novero, Laura Miozzi, Gian Carlo Tenore, Paolo Bagnaresi, Paola Bonfante
Software Mentions: 4
Published: over 10 years ago

10.31557/APJCP.2020.21.9.2593

Transcriptome Related to Avoiding Immune Destruction in Nasopharyngeal Cancer in Indonesian Patients Using Next-Generation Sequencing
Cited by: 2
Author(s): Risky Hiskia Poluan, Digdo Sudigyo, Gisti Rahmawati, Dicka Wahyu Setiasari, Salsabila Luthfi Sesotyosari, Tirta Wardana, Indwiani Astuti, Didik Setyo Heriyanto, Sagung Rai Indrasari, Cita Herawati, FNU Afiahayati, Sofia Mubarika Haryana
Software Mentions: 4
Published: about 4 years ago

10.3389/fcell.2020.584604

Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage
Cited by: 16
Author(s): Yeliz Demırcı, Gokhan Cucun, Yusuf Kaan Poyraz, Suhaib Mohammed, Guillaume Heger, Irene Papatheodorou, Günes Özhan
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-017-3967-0

Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
Cited by: 15
Author(s): Miriam Payá‐Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart, Margaret Staton
Software Mentions: 4
Published: over 7 years ago

10.3389/fbioe.2020.00155

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis
Cited by: 9
Author(s): Richou Han, Katie Haning, Juan C. Gonzalez-Rivera, Yongqiang Yang, Runxia Li, Seung Hee Cho, Ju Huang, Bobi A. Simonsen, Shihui Yang, Lydia M. Contreras
Software Mentions: 4
Published: over 4 years ago

10.1002/2211-5463.13252

Knockdown of DNA methyltransferase 1 reduces DNA methylation and alters expression patterns of cardiac genes in embryonic cardiomyocytes
Cited by: 4
Author(s): Xiefan Fang, Ryan Poulsen, Lu Zhao, Jingjing Wang, Scott A. Rivkees, Christopher C. Wendler
Software Mentions: 4
Published: over 3 years ago

10.14202/vetworld.2018.1203-1209

An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles
Cited by: 6
Author(s): Kaj Chokeshaiusaha, Thanida Sananmuang, Denis Puthier, Catherine Nguyen
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-016-2618-1

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage
Cited by: 107
Author(s): Irene da Cruz, Rosana Rodríguez-Casuriaga, Federico F. Santiñaque, Joaquina Farías, Gianni Curti, Carlos A. Capoano, Gustavo A. Folle, Ricardo Benavente, José Sotelo‐Silveira, Adriana Geisinger
Software Mentions: 4
Published: over 8 years ago

10.3389/fcimb.2021.723481

Dual RNASeq Reveals NTHi-Macrophage Transcriptomic Changes During Intracellular Persistence
Cited by: 6
Author(s): Jodie Ackland, Ashley Heinson, David W. Cleary, Myron Christodoulides, Tom Wilkinson, Karl J. Staples
Software Mentions: 4
Published: about 3 years ago

10.1155/2020/5974157

Comparative Transcriptome Analysis Reveals the Protective Mechanism of Glycyrrhinic Acid for Deoxynivalenol-Induced Inflammation and Apoptosis in IPEC-J2 Cells
Cited by: 14
Author(s): Xiaoxiang Xu, Guorong Yan, Juan Chang, Ping Wang, Qingqiang Yin, Chaoqi Liu, Qun Zhu, Fushan Lu
Software Mentions: 4
Published: about 4 years ago

10.1186/s13075-015-0677-3

Use of RNA sequencing to evaluate rheumatic disease patients
Cited by: 23
Author(s): Ευγενία Γιαννοπούλου, Olivier Elemento, Lionel B. Ivashkiv
Software Mentions: 4
Published: over 9 years ago

10.1523/ENEURO.0166-18.2018

Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress
Cited by: 45
Author(s): Mikaela Laine, Kalevi Trontti, Zuzanna Misiewicz, Ewa Sokołowska, Natalia Kulesskaya, Aino Heikkinen, Suvi Saarnio, Ingrid Balcells, Pierre Ameslon, Dario Greco, Pirkko Mattila, Pekka Ellonen, Lars Paulín, Petri Auvinen, Eija Jokitalo, Iiris Hovatta
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-016-3306-x

Differences in the skeletal muscle transcriptome profile associated with extreme values of fatty acids content
Cited by: 40
Author(s): Aline Silva Mello Cesar, Luciana Correia de Almeida Regitano, Mirele Daiana Poleti, Sónia C. S. Andrade, P. C. Tizioto, P. S. N. Oliveira, Andrezza Maria Felício, Michele Lopes do Nascimento, Amália Saturnino Chaves, Dante Pazzanese Duarte Lanna, R. R. Túllio, R. T. Nassu, James E. Koltes, Eric R. Fritz-Waters, Gérson Barreto Mourão, Adhemar Zerlotini-Neto, James M. Reecy, Luiz Lehmann Coutinho
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-016-3390-y

LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells
Cited by: 11
Author(s): Alicja Pacholewska, Eliane Marti, Tosso Leeb, Vidhya Jagannathan, Vinzenz Gerber
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12864-019-6204-1

Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment
Cited by: 7
Author(s): Da‐Long Guo, Qiong Li, Xiao-Ru Ji, Zhenguang Wang, Yi‐He Yu
Software Mentions: 4
Published: about 5 years ago

10.1186/s12967-021-02870-x

High copy number variations, particular transcription factors, and low immunity contribute to the stemness of prostate cancer cells
Cited by: 9
Author(s): Zao Dai, Ping Liu
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2016.01661

The Physcomitrella patens Chloroplast Proteome Changes in Response to Protoplastation
Cited by: 13
Author(s): Igor Fesenko, A. V. Seredina, Georgij Arapidi, Vasily V. Ptushenko, Anatoly S. Urban, Ivan Butenko, Sergey I. Kovalchuk, Konstantin Babalyan, Andrey Knyazev, Regina Khazigaleeva, Elena N. Pushkova, Nikolay Anikanov, В. Т. Иванов, Vadim M. Govorun
Software Mentions: 4
Published: about 8 years ago

10.1186/s12859-019-2916-0

A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data
Cited by: 26
Author(s): Anjali Silva, Steven J. Rothstein, Paul D. McNicholas, Sanjeena Subedi
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-018-5265-x

Corn dried distillers grains with solubles (cDDGS) in the diet of pigs change the expression of adipose genes that are potential therapeutic targets in metabolic and cardiovascular diseases
Cited by: 6
Author(s): Maria Oczkowicz, Tomasz Szmatoła, Małgorzata Świątkiewicz, Klaudia Pawlina-Tyszko, Artur Gurgul, Tomasz Ząbek
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-017-4359-1

A next generation sequencing based approach to identify extracellular vesicle mediated mRNA transfers between cells
Cited by: 19
Author(s): Jialiang Yang, Jacob Hagen, Kalyani V. P. Guntur, Kimaada Allette, Sarah Schuyler, Jyoti Ranjan, Francesca Petralia, Stéphane Gesta, Robert Sebra, Milind Mahajan, Bin Zhang, Jun Zhu, Sander M. Houten, Andrew Kasarskis, Vivek K. Vishnudas, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain, Eric E. Schadt, Carmen Argmann, Zhidong Tu
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-017-4411-1

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees
Cited by: 22
Author(s): Ogonna Obudulu, Niklas Mähler, Tomas Skotare, Joakim Bygdell, Ilka Nacif Abreu, Maria Ahnlund, Madhavi Latha Gandla, Anna Petterle, Thomas Moritz, Torgeir R. Hvidsten, Leif J. Jönsson, Gunnar Wingsle, Johan Trygg, Hannele Tuominen
Software Mentions: 4
Published: almost 7 years ago

10.18632/oncotarget.27632

Validated limited gene predictor for cervical cancer lymph node metastases
Cited by: 1
Author(s): Joshua Bloomstein, Rie von Eyben, Avis Chan, Erinn B. Rankin, Daniel R. Fregoso, Jing Wang-Chiang, Lisa Lee, Li Xie, Shannon MacLaughlan David, Henning Stehr, Mohammad Shahrokh Esfahani, Amato J. Giaccia, Elizabeth A. Kidd
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.23638

YAP-associated chromosomal instability and cholangiocarcinoma in mice
Cited by: 41
Author(s): Sumera Rizvi, Samantha R. Fischbach, Steven F. Bronk, Petra Hirsova, Anuradha Krishnan, Renumathy Dhanasekaran, James B. Smadbeck, Rory L. Smoot, George Vasmatzis, Gregory J. Gores
Software Mentions: 4
Published: almost 7 years ago

10.7554/eLife.66014

Competitive binding of STATs to receptor phospho-Tyr motifs accounts for altered cytokine responses
Cited by: 18
Author(s): Stephan Wilmes, Polly-Anne Jeffrey, Jonathan Martínez-Fábregas, Maximillian Hafer, Paul K. Fyfe, Elizabeth Pöhler, Silvia Gaggero, Martín López‐García, Grant Lythe, Charles Taylor, Thomas Guerrier, David Launay, Suman Mitra, Jacob Piehler, Carmen Molina-Parı́s, Ignacio Moraga
Software Mentions: 4
Published: over 3 years ago

10.18632/oncotarget.20977

Selecting lncRNAs in gastric cancer cells for directed therapy with bioactive peptides and chemotherapy drugs
Cited by: 7
Author(s): Wenyan Han, Rui Xiao, Chuanling Zhang, Qimuge Suyila, Xian Li, Xiulan Su
Software Mentions: 4
Published: about 7 years ago

10.1002/1878-0261.12982

CDX2 expression in the hematopoietic lineage promotes leukemogenesis via TGFβ inhibition
Cited by: 6
Author(s): Anne Galland, Victor Gourain, Karima Habbas, Yonca Güler, Elisabeth Martin, Claudine Ebel, Manuela Tavian, Laurent Vallat, Marie‐Pierre Chenard, Laurent Mauvieux, Jean–Noël Freund, Isabelle Duluc, Claire Domon‐Dell
Software Mentions: 4
Published: over 3 years ago

10.1530/ERC-19-0448

Effects of epigenetic pathway inhibitors on corticotroph tumour AtT20 cells
Cited by: 5
Author(s): Kate E Lines, P. Filippakopoulos, Mark Stevenson, Susanne Müller, Helen Lockstone, Benjamin Wright, Stefan Knapp, David Buck, C. Bountra, R V Thakker
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.23280

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts
Cited by: 32
Author(s): Lingjian Yang, Laura Forker, Joely J. Irlam, Nischalan Pillay, Ananya Choudhury, Catharine M L West
Software Mentions: 4
Published: almost 7 years ago

10.1155/2018/3028290

Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-ProducingKlebsiella pneumoniae
Cited by: 4
Author(s): Sheila Adams‐Sapper, Adam Gayoso, Lee W. Riley
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13024-018-0303-3

Inhibition of monocyte-like cell extravasation protects from neurodegeneration in DBA/2J glaucoma
Cited by: 44
Author(s): Pete A. Williams, Catherine E. Braine, Krishnakumar Kizhatil, Nicole E. Foxworth, Nicholas G. Tolman, Jeffrey M. Harder, R. Scott, Gregory L. Sousa, Alyssa Panitch, Gareth R. Howell, Simon W. M. John
Software Mentions: 4
Published: almost 6 years ago

10.1002/ece3.7401

Transcriptome assembly and differential gene expression of the invasive avian malaria parasite Plasmodium relictum in Hawaiʻi
Cited by: 8
Author(s): Elin Videvall, Kristina L. Paxton, Michael G. Campana, Loren Cassin-Sackett, Carter T. Atkinson, Robert C. Fleischer
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.02734

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer
Cited by: 102
Author(s): Sakari Vanharanta, Christina B. Marney, Weiqun Shu, Manuel Valiente, Yilong Zou, Aldo Mele, Robert B. Darnell, Joan Massagué
Software Mentions: 4
Published: over 10 years ago

10.15252/embr.201948882

Mitochondrial protein biogenesis in the synapse is supported by local translation
Cited by: 56
Author(s): Bożena Kuźniewska, Dominik Cysewski, Michał Wasilewski, Paulina Sakowska, Jacek Miłek, Tomasz M. Kuliński, M. Winiarski, Paweł Kozielewicz, Ewelina Knapska, Michał Dadlez, Agnieszka Chacińska, Andrzej Dziembowski, Magdalena Dziembowska
Software Mentions: 4
Published: over 4 years ago

10.1111/mmi.12977

<scp>K</scp>dm<scp>A</scp>, a histone<scp>H</scp>3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in<scp>A</scp>spergillus nidulans
Cited by: 41
Author(s): Agnieszka Gacek‐Matthews, Luke M. Noble, Clemens Gruber, Harald Berger, Michael Sulyok, Ana T. Marcos, Joseph Strauss, Alex Andrianopoulos
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-019-1708-z

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development
Cited by: 30
Author(s): Ming Li, Songtao Yang, Wei Xü, Zhien Pu, Jiayi Feng, Zhangying Wang, Cong Zhang, Peng Ma, Chunguang Du, Feng Lin, Changhe Wei, Shuai Qiao, Hongda Zou, Lei Zhang, Yán Li, Huan Yang, Anzhong Liao, Wei Song, Zhongren Zhang, Ji Li, Kai Wang, Yizheng Zhang, Hao Lin, Jinbo Zhang, Wen-Fang Tan
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.66547

Dual expression of Atoh1 and Ikzf2 promotes transformation of adult cochlear supporting cells into outer hair cells
Cited by: 31
Author(s): Shuangwen Sun, Shuting Li, Zhengnan Luo, Minhui Ren, Shunji He, Guangqin Wang, Zhiyong Liu
Software Mentions: 4
Published: about 3 years ago

10.7554/eLife.16220

Trisomy 21 consistently activates the interferon response
Cited by: 205
Author(s): Kelly D. Sullivan, Hannah C. Lewis, Amanda A. Hill, Ahwan Pandey, Leisa Jackson, Joseph M Cabral, Keith P Smith, L. Alexander Liggett, Eliana B. Gómez, Matthew D. Galbraith, James DeGregori, Joaquín M. Espinosa
Software Mentions: 4
Published: over 8 years ago

10.1186/s10020-019-0102-5

Gut microbiota promote the inflammatory response in the pathogenesis of systemic lupus erythematosus
Cited by: 68
Author(s): Yinglong Ma, Xiaoxue Xu, Mengtao Li, Jun Cai, Qiang Wang, Haitao Niu
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.66522

Ketogenic diet restrains aging-induced exacerbation of coronavirus infection in mice
Cited by: 33
Author(s): Seungjin Ryu, Irina Shchukina, Yun‐Hee Youm, Hua Qing, Brandon Hilliard, Tamara Dlugos, Xinbo Zhang, Yuki Yasumoto, Carmen J. Booth, Carlos Fernández‐Hernando, Yajaira Suárez, Kamal M. Khanna, Tamás L. Horváth, Marcelo O Dietrich, Maxim N. Artyomov, Andrew Wang, Vishwa Deep Dixit
Software Mentions: 4
Published: over 3 years ago

10.1002/ece3.1720

The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development
Cited by: 34
Author(s): Svjetlana Vojvodic, Brian R. Johnson, Brock A. Harpur, Clement F. Kent, Amro Zayed, Kirk E. Anderson, Timothy A. Linksvayer
Software Mentions: 4
Published: about 9 years ago

10.15252/embr.201744059

Transposon‐driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution
Cited by: 33
Author(s): Matthew P Davis, Claudia Carrieri, Harpreet K. Saini, Stijn van Dongen, Tommaso Leonardi, Giovanni Bussotti, Jack Monahan, Tania Auchynnikava, Angelo Bitetti, Juri Rappsilber, Robin C. Allshire, Alena Shkumatava, Dónal O’Carroll, Anton J. Enright
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0141910

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?
Cited by: 25
Author(s): Shanrong Zhao, Li Xi, Baohong Zhang
Software Mentions: 4
Published: about 9 years ago

10.1093/function/zqaa004

The Mechanism of High-Output Cardiac Hypertrophy Arising From Potassium Channel Gain-of-Function in Cantú Syndrome
Cited by: 17
Author(s): Conor McClenaghan, Yan Huang, Scot J. Matkovich, Attila Kovács, Carla J. Weinheimer, Ronald A. Perez, Thomas J. Broekelmann, Theresa Harter, Jin-Moo Lee, Marı́a S. Remedi, Colin G. Nichols
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcimb.2021.698146

L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation
Cited by: 9
Author(s): Erin M. Vasicek, Lindsey O’Neal, Matthew R. Parsek, James Fitch, Peter White, John S. Gunn
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: over 5 years ago

10.1128/JVI.00589-18

Transcriptional and Translational Landscape of Equine Torovirus
Cited by: 22
Author(s): Hazel Stewart, Katherine A. Brown, Adam M. Dinan, Nerea Irigoyen, Eric J. Snijder, Andrew E. Firth
Software Mentions: 4
Published: about 6 years ago

10.3389/fnmol.2018.00178

Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation
Cited by: 21
Author(s): Renjitha Gopurappilly, Bipan Kumar Deb, Pragnya Chakraborty, Gaiti Hasan
Software Mentions: 4
Published: over 6 years ago

10.1038/s41422-018-0066-y

Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta
Cited by: 242
Author(s): Yawei Liu, Xiaoying Fan, Rui Wang, Xiaoyin Lu, Yan-Li Dang, Huiying Wang, Haiyan Lin, Cheng Zhu, Hao Ge, James C. Cross, Hongmei Wang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12918-018-0582-x

A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
Cited by: 6
Author(s): Qingyang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.115.021550

Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response toFusarium graminearum
Cited by: 33
Author(s): Thomas Nußbaumer, Benedikt Warth, Sapna Sharma, Christian Ametz, Christoph Bueschl, Alexandra Parich, Matthias Pfeifer, Gerald Siegwart, Barbara Steiner, Marc Lemmens, Rainer Schuhmacher, Hermann Buerstmayr, Klaus Mayer, Karl G. Kugler, Wolfgang Schweiger
Software Mentions: 4
Published: almost 9 years ago

10.1093/molbev/msw161

Characterization of the Poplar Pan-Genome by Genome-Wide Identification of Structural Variation
Cited by: 82
Author(s): Sara Pinosio, Stefania Giacomello, Patricia Faivre-Rampant, Gail Taylor, Véronique Jorge, Marie Christine Le Paslier, Giusi Zaina, Catherine Bastien, Federica Cattonaro, Fabio Marroni, Michèle Morgante
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-018-4505-4

Transcriptome profiles in peripheral white blood cells at the time of artificial insemination discriminate beef heifers with different fertility potential
Cited by: 28
Author(s): Sarah Dickinson, Brock A. Griffin, Michelle F Elmore, L. A. Kriese-Anderson, J. Bradford Elmore, Paul W. Dyce, Soren P. Rodning, Fernando H. Biase
Software Mentions: 4
Published: almost 7 years ago

10.3390/antiox9050402

Long Non-Coding RNA and mRNA Profiling in Early-Stage Bovine Embryos Treated with Glutathione
Cited by: 1
Author(s): Qihao Guo, Linlin Cui, Weijun Sun, Li Feng, Hao Huang, Xueming Zhao, Huabin Zhu, Weihua Du
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0081809

Next Generation Sequencing Analysis of Human Platelet PolyA+ mRNAs and rRNA-Depleted Total RNA
Cited by: 55
Author(s): Antheia Kissopoulou, Jon Jonasson, Tomas Lindahl, Abdimajid Osman
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12864-017-3675-9

Transcriptome analysis reveals potential mechanisms underlying differential heart development in fast- and slow-growing broilers under heat stress
Cited by: 23
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 7 years ago

10.1016/j.bbr.2017.04.007

Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis
Cited by: 6
Author(s): Hannah Scott, Mark F. Rogers, Helen L. Scott, Colin Campbell, E. Clea Warburton, James B. Uney
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.19406

Modeling susceptibility to drug-induced long QT with a panel of subject-specific induced pluripotent stem cells
Cited by: 79
Author(s): Francesca Stillitano, Jens Hansen, Chi-Wing Kong, Ioannis Karakikes, Christian Funck‐Brentano, Lin Geng, Stuart A. Scott, Stephan Reynier, Wu Ma, Yannick Valogne, Carole Desseaux, Joe‐Elie Salem, Dorota Jeziorowska, Noël Zahr, Ronald Li, Ravi Iyengar, Roger J. Hajjar, Jean‐Sébastien Hulot
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12943-018-0833-x

RNA-Seq profiling of circular RNAs in human laryngeal squamous cell carcinomas
Cited by: 57
Author(s): Cheng Hsien Lu, Xi Su, Amanda Y. Wang, Tao Yuan, Zhenxiao Wang, Chaoping Huang, Yuehua Qiao, Hongyi Hu, Liangfa Liu
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0091918

RNA-Sequence Analysis of Primary Alveolar Macrophages after In Vitro Infection with Porcine Reproductive and Respiratory Syndrome Virus Strains of Differing Virulence
Cited by: 34
Author(s): Bouabid Badaoui, Teresa Rutigliano, Anna Anselmo, Merijn Vanhee, Hans Nauwynck, Elisabetta Giuffra, Sara Botti
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.60987

Adaptive evolution of an essential telomere protein restricts telomeric retrotransposons
Cited by: 9
Author(s): Bastien Saint-Leandre, Courtney J. Christopher, Mia T. Levine
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.21697

Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ
Cited by: 43
Author(s): Lorenzo Rinaldi, Alexandra Avgustinova, Mercé Martı́n, Debayan Datta, Guiomar Solanas, Neus Prats, Salvador Aznar Benitah
Software Mentions: 4
Published: over 7 years ago

10.1016/j.celrep.2020.03.053

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex
Cited by: 82
Author(s): Donna M. Werling, Sirisha Pochareddy, Jinmyung Choi, Joon Yong An, Brooke Sheppard, Minshi Peng, Zhen Li, Claudia Dastmalchi, Gabriel Santpere, André M. M. Sousa, Andrew T.N. Tebbenkamp, Navjot Kaur, Forrest O. Gulden, Michael S. Breen, Lindsay Liang, Michael C. Gilson, Xuefang Zhao, Shan Dong, Lambertus Klei, A. Ercüment Çiçek, Joseph D. Buxbaum, Homa Adle‐Biassette, Jean Léon Thomas, Kimberly A. Aldinger, Diana R. O’Day, Ian A. Glass, Noah Zaitlen, Michael E. Talkowski, Kathryn Roeder, Matthew W. State, Bernie Devlin, Stephan J. Sanders, Nenad Šestan
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.08411

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions
Cited by: 39
Author(s): Anne Plessis, Christoph Hafemeister, Olivia Wilkins, Zennia Jean Gonzaga, Rachel S. Meyer, Inês S. Pires, Christian Müller, Endang M. Septiningsih, Richard Bonneau, Michael D. Purugganan
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12862-021-01762-4

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume
Cited by: 10
Author(s): Man Zhang, Ping Li, Xiao-lan Yan, Jia Wang, Tangren Cheng, Qixiang Zhang
Software Mentions: 4
Published: over 3 years ago

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071