pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1186/s12864-015-2270-1

Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis
Cited by: 66
Author(s): Wenli Li, Amy Turner, Praful Aggarwal, Andrea Matter, Erin Storvick, Donna K. Arnett, Ulrich Broeckel
Software Mentions: 4
Published: almost 11 years ago

10.1186/s12870-018-1602-0

Dual RNA-seq analysis provides new insights into interactions between Norway spruce and necrotrophic pathogen Heterobasidion annosum s.l.
Cited by: 31
Author(s): Andriy Kovalchuk, Zhen Zeng, Rajendra P. Ghimire, Minna Kivimäenpää, Tommaso Raffaello, Mengxia Liu, Mukrimin Mukrimin, Risto Kasanen, Hui Sun, Riitta Julkunen‐Tiitto, Jarmo K. Holopainen, Fred O. Asiegbu
Software Mentions: 4
Published: almost 8 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 9 years ago

10.1186/1471-2164-14-586

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions
Cited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: almost 14 years ago

10.1186/s12870-020-02392-6

Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses
Cited by: 37
Author(s): Colin Kruse, Alexander Meyers, Proma Basu, Sarahann Hutchinson, Darron R. Luesse, Sarah E. Wyatt
Software Mentions: 4
Published: over 6 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 8 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 5 years ago

10.1186/s12870-017-1037-z

Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening
Cited by: 30
Author(s): José A. Freixas Coutin, Seth Munholland, Anjali Silva, Sanjeena Subedi, Lewis Lukens, William L. Crosby, K. Peter Pauls, Gale G. Bozzo
Software Mentions: 4
Published: over 9 years ago

10.1186/s12870-018-1293-6

Integrative genomics approaches validate PpYUC11-like as candidate gene for the stony hard trait in peach (P. persica L. Batsch)
Cited by: 20
Author(s): Marco Cirilli, D. Giovannini, Angelo Ciacciulli, Remo Chiozzotto, Stefano Gattolin, Laura Rossini, A. Liverani, D. Bassi
Software Mentions: 4
Published: over 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 7 years ago

10.1186/s12864-015-2321-7

Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits
Cited by: 16
Author(s): Chiara Biselli, Paolo Bagnaresi, Daniela Cavalluzzo, Simona Urso, Francesca Desiderio, G. Orasen, Alberto Gianinetti, Federico Righettini, M. C. Gennaro, Rosaria Perrini, Manel Ben Hassen, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2020.01628

Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori
Cited by: 9
Author(s): Hirokazu Yano, Zobaidul Alam, Emiko Rimbara, Tomoko Shibata, Masaki Fukuyo, Yoshikazu Furuta, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi
Software Mentions: 4
Published: over 6 years ago

10.1038/s41419-019-2040-0

Severe head dysgenesis resulting from imbalance between anterior and posterior ontogenetic programs
Cited by: 2
Author(s): Emmanuelle Grall, Victor Gourain, Asmaa Naïr, Elisabeth Martin, Marie‐Christine Birling, Jean–Noël Freund, Isabelle Duluc
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-021-07710-2

Whole-genome resequencing provides insights into the population structure and domestication signatures of ducks in eastern China
Cited by: 11
Author(s): Peishi Feng, Tao Zeng, Hua Yang, Guohong Chen, Junzheng Du, Li Chen, Junda Shen, Zhenrong Tao, Ping Wang, Lin Yang, Lizhi Liu
Software Mentions: 4
Published: over 5 years ago

10.1016/j.ajhg.2016.05.030

BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription
Cited by: 116
Author(s): Cristina Dias, Sara Busquets Estruch, Sarah A. Graham, Jeremy F. McRae, Stephen J. Sawiak, Jane A. Hurst, Shelagh Joss, Susan Holder, Jenny Morton, Claire Turner, Julien Thévenon, Kelly Mellul, Gabriela Sánchez-Andrade, Ximena Ibarra-Soria, Pelagia Derizioti, Rui F. Santos, Song-Choon Lee, Laurence Faivre, Tjitske Kleefstra, Pentao Liu, Mathew E. Hurles, Simon E. Fisher, Darren W. Logan
Software Mentions: 4
Published: over 10 years ago

10.1186/s12868-021-00622-7

Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm
Cited by: 7
Author(s): Yutong Pan, Jianing Lu, Biao Yang, Cameron Lenahan, Jianmin Zhang, Anwen Shao
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0163344

Differing Alterations of Two Esca Associated Fungi, Phaeoacremonium aleophilum and Phaeomoniella chlamydospora on Transcriptomic Level, to Co-Cultured Vitis vinifera L. calli
Cited by: 6
Author(s): Jochen Fischer, Stéphane Compant, Romain Pierron, Markus Gorfer, Alban Jacques, Eckhard Thines, Harald Berger
Software Mentions: 4
Published: about 10 years ago

10.1186/s12859-016-1355-4

SPECtre: a spectral coherence-based classifier of actively translated transcripts from ribosome profiling sequence data
Cited by: 40
Author(s): Sang-Young Chun, Caitlin M. Rodriguez, Peter K. Todd, Ryan E. Mills
Software Mentions: 4
Published: almost 10 years ago

10.3389/fimmu.2020.01859

Transcriptional Profiling of CD8+ CMV-Specific T Cell Functional Subsets Obtained Using a Modified Method for Isolating High-Quality RNA From Fixed and Permeabilized Cells
Cited by: 3
Author(s): Zachary R. Healy, Kent J. Weinhold, David M. Murdoch
Software Mentions: 4
Published: about 6 years ago

10.1038/s41421-018-0027-0

Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity
Cited by: 38
Author(s): Chih Chao Hsu, Dan Zhao, Jiejun Shi, Danni Peng, Haipeng Guan, Yuanyuan Li, Yaling Huang, Hong Wen, Wei Li, Haitao Li, Xiaobing Shi
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2021.667177

CXCL8 Associated Dendritic Cell Activation Marker Expression and Recruitment as Indicators of Favorable Outcomes in Colorectal Cancer
Cited by: 20
Author(s): Enhao Li, Xiaobao Yang, Yuzhang Du, Guanzheng Wang, David Chan, Di Wu, Peiqing Xu, Peihong Ni, Dakang Xu, Yiqun Hu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008797

UVR8-mediated inhibition of shade avoidance involves HFR1 stabilization in Arabidopsis
Cited by: 23
Author(s): Eleni Tavridou, Emanuel Schmid‐Siegert, Christian Fankhauser, Roman Ulm
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0191564

Study of formation of green eggshell color in ducks through global gene expression
Cited by: 4
Author(s): Fa Xu, Ang Li, Jing Lan, Yue Ming Wang, Mengmeng Yan, Sen Lian, Xu Wu
Software Mentions: 4
Published: almost 9 years ago

10.18632/aging.102034

A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass
Cited by: 5
Author(s): Xuehui Li, Lei Wei, Qiongye Dong, Liyang Liu, Michael Q. Zhang, Zhen Xie, Xiaowo Wang
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2019.02512

Selective Histone Deacetylase 6 Inhibition Normalizes B Cell Activation and Germinal Center Formation in a Model of Systemic Lupus Erythematosus
Cited by: 26
Author(s): Jingjing Ren, Michelle D. Catalina, Kristin Eden, Xiaofeng Liao, Kaitlin A. Read, Xin Luo, Ryan P. McMillan, Matthew W. Hulver, Matthew Jarpe, Prathyusha Bachali, Amrie C. Grammer, Peter E. Lipsky, Christopher M. Reilly
Software Mentions: 4
Published: about 7 years ago

10.1111/acer.14259

Chronic Voluntary Ethanol Drinking in Cynomolgus Macaques Elicits Gene Expression Changes in Prefrontal Cortical Area 46
Cited by: 4
Author(s): Nicole A.R. Walter, Christina Zheng, Robert P. Searles, Shannon K. McWeeney, Kathleen A. Grant, Robert Hitzemann
Software Mentions: 4
Published: almost 7 years ago

10.3389/fimmu.2018.02533

Adenosinergic Signaling Alters Natural Killer Cell Functional Responses
Cited by: 72
Author(s): Andrea M. Chambers, Jiao Wang, Kyle B. Lupo, Hao Yu, Nadia A. Lanman, Sandro Matosevic
Software Mentions: 4
Published: about 8 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 12 years ago

10.1186/s12859-019-2676-x

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
Cited by: 5
Author(s): Taewoon Joo, Ji-Hye Choi, Jihye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung, Hyun Goo Woo
Software Mentions: 4
Published: over 7 years ago

10.1186/1755-8794-7-32

Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Cited by: 45
Author(s): Zhifu Sun, Liang Wang, Bruce W. Eckloff, Bo Deng, Yi Wang, Jason A. Wampfler, Jiseon Jang, Eric D. Wieben, Jin Jen, Ming You, Ping Yang
Software Mentions: 4
Published: over 12 years ago

10.3389/fimmu.2018.02685

Sepsis Induces a Long-Lasting State of Trained Immunity in Bone Marrow Monocytes
Cited by: 45
Author(s): Katharina Bomans, Judith Schenz, Isabella Sztwiertnia, Dominik Schaack, Markus Weigand, Florian Uhle
Software Mentions: 4
Published: almost 8 years ago

10.1093/molbev/msv016

The Avian Transcriptome Response to Malaria Infection
Cited by: 71
Author(s): Elin Videvall, Charlie K. Cornwallis, Vaidas Palinauskas, Gediminas Valkiūnas, Olof Hellgren
Software Mentions: 4
Published: almost 12 years ago

10.3389/fimmu.2020.577718

Augmenting E Protein Activity Impairs cDC2 Differentiation at the Pre-cDC Stage
Cited by: 0
Author(s): Sandra Bajaña, Kevin L. Thomas, Constantin Georgescu, Ying Zhao, Jonathan D. Wren, Susan Kovats, Xiaohong Sun
Software Mentions: 4
Published: almost 6 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 10 years ago

10.1186/s12864-019-6018-1

Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation
Cited by: 19
Author(s): Izabela Coimbra Ibraim, Mariana Teixeira Dornelles Parise, Doglas Parise, Michelle Zibetti Tadra Sfeir, Thiago Luiz de Paula Castro, Alice R. Wattam, Preetam Ghosh, Debmalya Barh, Emannuel Maltempi Souza, Aristóteles Goés-Neto, Anne Cybelle Pinto Gomide, Vasco Azevedo
Software Mentions: 4
Published: about 7 years ago

10.3389/fimmu.2019.02902

Rainbow Trout IgM+ B Cells Preferentially Respond to Thymus-Independent Antigens but Are Activated by CD40L
Cited by: 14
Author(s): Aitor G. Granja, Pedro Perdiguero, Alba Martín-Martín, Patricia Díaz‐Rosales, Irene Soleto, Carolina Tafalla
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12864-018-4632-y

Gene co-expression networks in liver and muscle transcriptome reveal sex-specific gene expression in lambs fed with a mix of essential oils
Cited by: 18
Author(s): Marcella Sabino, Victor Adriano Okstoft Carmelo, Gianluca Mazzoni, Katia Cappelli, Stefano Capomaccio, Paolo Ajmone‐Marsan, Andrea Verini-Supplizi, Massimo Trabalza‐Marinucci, Haja N. Kadarmideen
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2019.00479

Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC
Cited by: 50
Author(s): Hirotsugu Oda, David B. Beck, Hye Sun Kuehn, Natalia Sampaio Moura, Patrycja Hoffmann, Maria Ibarra, Jennifer Stoddard, Wanxia Li Tsai, Gustavo Gutierrez-Cruz, Massimo Gadina, Sergio D. Rosenzweig, Daniel L. Kastner, Luigi D. Notarangelo, Ivona Aksentijevich
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0192383

Adaptability of the Saccharomyces cerevisiae yeasts to wine fermentation conditions relies on their strong ability to consume nitrogen
Cited by: 40
Author(s): Claire Brice, Francisco A. Cubillos, Sylvie Dequin, Carole Camarasa, Claudio Martı́nez
Software Mentions: 4
Published: over 8 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2019.00308

661W Photoreceptor Cell Line as a Cell Model for Studying Retinal Ciliopathies
Cited by: 37
Author(s): Gabrielle Wheway, Liliya Nazlamova, Dann Turner, Stephen Cross
Software Mentions: 4
Published: over 7 years ago

10.3389/fnins.2021.639527

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders
Cited by: 5
Author(s): Junlin Shen, Bing‐Bing Yang, Zhonghua Xie, Heng Wu, Zhanye Zheng, Jianhua Wang, Ping Wang, Peng Zhang, Wei Li, Zhaoxiang Ye, Chunshui Yu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0210672

Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures
Cited by: 28
Author(s): Tingting Song, Keting Li, Ting Wu, Yi Wang, Xinzhong Zhang, Xuefeng Xu, Yuncong Yao, Zhenhai Han
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0243911

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model
Cited by: 12
Author(s): Linfu Liu, Chuang Liu, Menglong Zhao, Qianru Zhang, Ying Lu, Ping Liu, Hua Yang, Jinliang Yang, Xiaoxin Chen, Yuqin Yao
Software Mentions: 4
Published: almost 6 years ago

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 12 years ago

10.3389/fgene.2021.641117

Gene Expression Analysis Suggests Immunological Changes of Peripheral Blood Monocytes in the Progression of Patients With Coronary Artery Disease
Cited by: 6
Author(s): Chunyue Wang, Chenxi Song, Qianqian Liu, Rui Zhang, Rui Fu, Hao Wang, Yin Ding, Weihua Song, Haitao Zhang, Kefei Dou
Software Mentions: 4
Published: over 5 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 10 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 7 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 6 years ago

10.3389/fgene.2021.650874

Investigating Transcriptional Dynamics Changes and Time-Dependent Marker Gene Expression in the Early Period After Skeletal Muscle Injury in Rats
Cited by: 6
Author(s): Kangning Ren, Liangliang Wang, Liang Wang, Qiu-xiang Du, Jie Cao, Qianqian Jin, Guo-shuai An, Na Li, Li-hong Dang, Yingjie Tian, Ying-Yuan Wang, Jun-hong Sun
Software Mentions: 4
Published: over 5 years ago

10.3389/fgene.2020.608325

Comparative Transcriptome Analysis During the Seven Developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for Terrestrial Adaptation
Cited by: 1
Author(s): Xiaoli Ma, Mei Shang, Baofeng Su, Anne A. Wiley, Max R. Bangs, Veronica Alston, Rhoda Mae C. Simora, Mai Thi Thanh Nguyen, Nathan J. C. Backenstose, Anthony G. Moss, Dương Thúy Yên, Xiaozhu Wang, Rex A. Dunham
Software Mentions: 4
Published: almost 6 years ago

10.3389/fgene.2020.563954

Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer
Cited by: 4
Author(s): Li Weng, Shanshan Shen, Shaoqiu Wu, Xiaoxing Yin, Bingyan Liu, Ming Shang, Xiaoping Zou, Aiwu Mao
Software Mentions: 4
Published: almost 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 10 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 10 years ago

10.15252/embj.2020105784

ALK ligand ALKAL2 potentiates MYCN‐driven neuroblastoma in the absence of ALK mutation
Cited by: 30
Author(s): Marcus Borenäs, Ganesh Umapathy, Wei-Yun Lai, Dan E. Lind, Barbara Witek, Jikui Guan, Patricia Mendoza-García, Tafheem Masudi, A. Claeys, Tzu-Po Chuang, Abeer El Wakil, Badrul Arefin, Susanne Fransson, Jan Koster, Mathias Johansson, Jennie Gaarder, Jimmy Van den Eynden, Bengt Hållberg, Ruth Palmer
Software Mentions: 4
Published: almost 6 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: over 9 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 9 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 10 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: almost 11 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 6 years ago

10.1016/j.ydbio.2016.06.016

Developmentally regulated long non-coding RNAs in Xenopus tropicalis
Cited by: 17
Author(s): Elmira Forouzmand, Nick Owens, Ira L. Blitz, Kitt D. Paraiso, Mustafa K. Khokha, Michael J. Gilchrist, Xiaohui Xie, Ken W.Y. Cho
Software Mentions: 4
Published: over 9 years ago

10.1016/j.devcel.2021.07.018

Reprogrammed lipid metabolism protects inner nuclear membrane against unsaturated fat
Cited by: 28
Author(s): Anete Romanauska, Alwin Köhler
Software Mentions: 4
Published: about 5 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 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 6 years ago

10.1080/21505594.2020.1806665

Tobacco Hornworm (Manduca sexta) caterpillars as a novel host model for the study of fungal virulence and drug efficacy
Cited by: 9
Author(s): Naomi Lyons, Isabel Softley, Andrew Balfour, Carolyn Williamson, Heath O’Brien, Amol Shetty, Vincent M. Bruno, Stephanie Diezmann
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 6 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 8 years ago

10.1038/s42003-021-02203-0

The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function
Cited by: 5
Author(s): Bergithe E. Oftedal, Stefano Maio, Adam E. Handel, White Mpj., Duncan Howie, Simon Davis, Nicolas Prevot, Ioanna A. Rota, Mary E. Deadman, Benedikt M. Kessler, Román Fischer, Nikolaus S. Trede, Erdinç Sezgin, Rick M. Maizels, G A Holländer
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cub.2019.07.083

Genetically Defined Functional Modules for Spatial Orienting in the Mouse Superior Colliculus
Cited by: 60
Author(s): Laura Masullo, Letizia Mariotti, Nicolas Alexandre, Paula Freire-Pritchett, Jérôme Boulanger, Marco Tripodi
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2019.00614

Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines
Cited by: 17
Author(s): Anthony Federico, Tanya T Karagiannis, Kritika Karri, Dileep Kishore, Yusuke Koga, Joshua D. Campbell, Stefano Monti
Software Mentions: 4
Published: over 7 years ago

10.1016/j.devcel.2020.09.025

Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling
Cited by: 27
Author(s): Francisco Bustos, Anna Segarra-Fas, Gino Nardocci, Andrew Cassidy, Odetta Antico, L. S. P. Davidson, Lennart Brandenburg, Thomas Macartney, Rachel Toth, Claire Hastie, Jennifer L. Moran, Robert Gourlay, Joby Varghese, Renata Soares, Martín Montecino, Greg M. Findlay
Software Mentions: 4
Published: almost 6 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 11 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 9 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 10 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 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 6 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 11 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 8 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 9 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 11 years ago

10.1186/s40169-017-0150-9

Single‐cell RNA‐sequencing of the brain
Cited by: 46
Author(s): Raquel Durán, Haichao Wei, Jia Qian Wu
Software Mentions: 4
Published: over 9 years ago

10.1038/s42003-021-02059-4

Three-dimensional tissue-engineered human skeletal muscle model of Pompe disease
Cited by: 13
Author(s): Jason Wang, Chris J. Zhou, Alastair Khodabukus, Sabrina Tran, Sang-oh Han, Aaron L. Carlson, Lauran Madden, Priya S. Kishnani, Dwight D. Koeberl
Software Mentions: 4
Published: over 5 years ago

10.1038/s42003-019-0430-6

Genetic analyses of human fetal retinal pigment epithelium gene expression suggest ocular disease mechanisms
Cited by: 18
Author(s): Boxiang Liu, Melissa A. Calton, Nathan S. Abell, Gillie Benchorin, Michael J. Gloudemans, Ming Chen, Jane Hu, Xin Li, Brunilda Balliu, Dean Bok, Stephen B. Montgomery, Douglas Vollrath
Software Mentions: 4
Published: over 7 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 10 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 5 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 5 years ago

10.15252/embj.2018101430

Cyclin F‐dependent degradation of E2F7 is critical for <scp>DNA</scp> repair and G2‐phase progression
Cited by: 33
Author(s): Ruixue Yuan, Qingwu Liu, Hendrika A. Segeren, Laurensia Yuniati, Daniele Guardavaccaro, Robert Jan Lebbink, Bart Westendorp, Alain de Bruin
Software Mentions: 4
Published: about 7 years ago

10.1242/dmm.042713

Leptin and fractalkine: Novel subcutaneous cytokines in burn injury
Cited by: 4
Author(s): Dominic Friston, Sini Junttila, Júlia Borges Paes Lemes, Helen Laycock, Jose Vicente Torres-Pérez, Elizabeth J. Want, Attila Gyenesei, I. Nagy
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 8 years ago

10.3390/cells9122637

RNA-Seq Analysis of Cisplatin and the Monofunctional Platinum(II) Complex, Phenanthriplatin, in A549 Non-Small Cell Lung Cancer and IMR90 Lung Fibroblast Cell Lines
Cited by: 4
Author(s): Jerry D. Monroe, Satya A. Moolani, Elvin N. Irihamye, Joshua S. Speed, Yann Gibert, Michael E. Smith
Software Mentions: 4
Published: almost 6 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 11 years ago

10.3390/cells9081793

Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis
Cited by: 3
Author(s): Ho‐Su Lee, Maaike Vancamelbeke, Sare Verstockt, Tom Wilms, Bram Verstockt, João Sabino, Marc Ferrante, Séverine Vermeire, Isabelle Cleynen
Software Mentions: 4
Published: over 6 years ago

10.1016/j.molmet.2020.101078

Wnt/β-catenin signaling regulates adipose tissue lipogenesis and adipocyte-specific loss is rigorously defended by neighboring stromal-vascular cells
Cited by: 44
Author(s): Devika P. Bagchi, Akira Nishii, Ziru Li, Jennifer B. DelProposto, Callie A.S. Corsa, Hiroyuki Mori, Julie Hardij, Brian S. Learman, Carey N. Lumeng, Ormond A. MacDougald
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12862-017-1103-z

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: almost 9 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 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: almost 11 years ago

10.3390/cells9122593

Induced Pluripotent Stem Cells to Understand Mucopolysaccharidosis. I: Demonstration of a Migration Defect in Neural Precursors
Cited by: 3
Author(s): Silvin Lito, Adama Sidibé, Sten Ilmjärv, Patricie Burda, Matthias R. Baumgartner, Bernhard Wehrle-Haller, Karl‐Heinz Krause, Antoine Marteyn
Software Mentions: 4
Published: almost 6 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 7 years ago

10.1016/j.dib.2016.05.007

Whole transcriptome data analysis of zebrafish mutants affecting muscle development
Cited by: 7
Author(s): Olivier Armant, Victor Gourain, Christelle Etard, Uwe Strähle
Software Mentions: 4
Published: about 10 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 8 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071