pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.7554/eLife.35551

Ssd1 and Gcn2 suppress global translation efficiency in replicatively aged yeast while their activation extends lifespan
Cited by: 54
Author(s): Zheng Hu, Bo Xia, Spike D. L. Postnikoff, Zih Jie Shen, Alin Tomoiaga, Troy A. A. Harkness, Ja Hwan Seol, Wei Li, Kaifu Chen, Jessica K. Tyler
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9020459

A Mucoralean White Collar-1 Photoreceptor Controls Virulence by Regulating an Intricate Gene Network during Host Interactions
Cited by: 6
Author(s): Carlos Pérez-Arques, María Isabel Navarro-Mendoza, Laura Murcia, Carlos Lax, Marta Silva, Javier Capilla, Eusebio Navarro, Victoriano Garre
Software Mentions: 4
Published: almost 4 years ago

10.1007/s00239-020-09939-z

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila
Cited by: 51
Author(s): Brennen Heames, Julia Schmitz, Erich Bornberg‐Bauer
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0145257

Comparative Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Characterized by Shell Colors: Identification of Genetic Bases Potentially Involved in Pigmentation
Cited by: 73
Author(s): Dandan Feng, Qi Li, Hong Yu, Xuelin Zhao, Lingfeng Kong
Software Mentions: 4
Published: about 9 years ago

10.4049/jimmunol.1900940

Malat1 Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells
Cited by: 45
Author(s): James P. Hewitson, Katie A West, Kylie R. James, Gulab Fatima Rani, Nidhi Sharma Dey, Audrey Romano, Najmeeyah Brown, Sarah A. Teichmann, Paul M. Kaye, Dimitrios Lagos
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-021-97306-3

Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Cited by: 3
Author(s): Ludmila Mudri Hul, A. M. G. Ibelli, Igor Ricardo Savoldi, Débora Ester Petry Marcelino, Lana Teixeira Fernandes, J. O. Peixoto, Maurício Egídio Cantão, R. H. Higa, P. F. Giachetto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-94927-6

Neurotranscriptomic changes associated with chick-directed parental care in adult non-reproductive Japanese quail
Cited by: 6
Author(s): Patrícia C. Lopes, Robert de Bruijn
Software Mentions: 4
Published: over 3 years ago

10.1016/j.ijpara.2018.01.004

Transcriptomic profiling of nematode parasites surviving vaccine exposure
Cited by: 19
Author(s): Guillaume Sallé, Roz Laing, James A. Cotton, Kirsty Maitland, Axel Martinelli, Nancy Holroyd, Alan S. Tracey, Matthew Berriman, William D. Smith, G. F. J. Newlands, Eve Hanks, Eileen Devaney, Collette Britton
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40425-019-0609-x

Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma
Cited by: 22
Author(s): Sehhoon Park, Je‐Gun Joung, Min Ye, Jae‐Yong Nam, Daeun Ryu, Dongryul Oh, Woong-Yang Park, Sehoon Lee, Yoon La Choi, Jin Seok Ahn, Myung‐Ju Ahn, Keunchil Park, Jong‐Mu Sun
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-88363-9

Transcriptional signatures in prefrontal cortex confer vulnerability versus resilience to food and cocaine addiction-like behavior
Cited by: 11
Author(s): Mohit Navandar, Elena Martín‐García, Rafaël Maldonado, Beat Lutz, Susanne Gerber, Iñigo Ruı́z de Azúa
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-021-88709-3

Regulatory role of non-coding RNA in ginseng rusty root symptom tissue
Cited by: 5
Author(s): Xingbo Bian, Pengcheng Yu, Ling Dong, Yan Zhao, Yang He, Yongzhong Han, Lianxue Zhang
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12864-016-3442-3

Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening
Cited by: 65
Author(s): Qianglong Zhu, Shi Liu, Zhu Zhang, Sikandar Amanullah, Angela R. Davis, Feishi Luan
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-021-82729-9

NLRC5/CITA expression correlates with efficient response to checkpoint blockade immunotherapy
Cited by: 14
Author(s): Sayuri Yoshihama, Steven Cho, Jason Yeung, Xuedong Pan, Gregory Lizee, Kranti Konganti, Valen E. Johnson, Koichi S. Kobayashi
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-90653-1

Totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage
Cited by: 17
Author(s): Marino Maemura, Hiroaki Taketsuru, Yuki Nakajima, Ruiqi Shao, Ayaka Kakihara, Jumpei Nogami, Yasuyuki Ohkawa, Yu Ichi Tsukada
Software Mentions: 4
Published: over 3 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 7 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: almost 4 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 3 years ago

10.1038/s41598-020-78364-5

Hdac3 deletion in myeloid progenitor cells enhances bone healing in females and limits osteoclast fusion via Pmepa1
Cited by: 7
Author(s): David H. H. Molstad, Elizabeth L. Zars, Andrew Norton, Kim C. Mansky, Jennifer J. Westendorf, Elizabeth W. Bradley
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-75060-2

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal
Cited by: 1
Author(s): Nathalie Charbonnel, Maxime Galan, Caroline Tatard, Anne Loiseau, Christophe Diagne, Ambroise Dalecky, Hugues Parrinello, Stéphanie Rialle, Dany Séverac, Carine Brouat
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-78366-3

Human kidney clonal proliferation disclose lineage-restricted precursor characteristics
Cited by: 7
Author(s): Osnat Cohen-Zontag, Rotem Gershon, Orit Harari‐Steinberg, Itamar Kanter, Dorit Omer, Oren Pleniceanu, Gal Tam, Sarit Oriel, H Ben-Hur, Guy Katz, Zohar Dotan, Tomer Kalisky, Benjamin Dekel, Naomi Pode‐Shakked
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-020-71889-9

Gene expression is stable in a complete CIB1 knockout keratinocyte model
Cited by: 2
Author(s): Elias Imahorn, Magomet Aushev, Stefan Herms, Per Hoffmann, Sven Cichon, Julia Reichelt, Peter Itin, Bettina Burger
Software Mentions: 4
Published: over 4 years ago

10.3390/metabo11050329

Iron-Bound Lipocalin-2 Protects Renal Cell Carcinoma from Ferroptosis
Cited by: 19
Author(s): Julia K. Meier, Matthias Schnetz, Susanne Beck, Tobias Schmid, Monica Dominguez, Sanela Kalinovic, Andreas Daiber, Bernhard Brüne, Michaela Jung
Software Mentions: 4
Published: over 3 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 5 years ago

10.1038/s41598-020-65916-y

Alterations of transcriptome signatures in head trauma-related neurodegenerative disorders
Cited by: 13
Author(s): Hyesun Cho, Seung Jae Hyeon, Jong-Yeon Shin, Victor E. Alvarez, Thor D. Stein, Jung‐Hee Lee, Neil W. Kowall, Ann C. McKee, Hoon Ryu, Jeong-Sun Seo
Software Mentions: 4
Published: over 4 years ago

10.3390/md17030181

Comparative Transcriptome Analyses Provide Potential Insights into the Molecular Mechanisms of Astaxanthin in the Protection against Alcoholic Liver Disease in Mice
Cited by: 12
Author(s): Huilin Liu, Huimin Liu, Liang Zhu, Ziqi Zhang, Xin Zheng, Jingsheng Liu, Xueqi Fu
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-66630-5

Single-cell RNA sequencing reveals that lung mesenchymal progenitor cells in IPF exhibit pathological features early in their differentiation trajectory
Cited by: 23
Author(s): Daniel Beisang, Karen Smith, Libang Yang, Alexey O. Benyumov, Adam Gilbertsen, Jeremy Herrera, Eric F. Lock, Emilian Racila, Colleen L. Forster, Brian J Sandri, Craig A. Henke, Peter B. Bitterman
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-73146-5

Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development
Cited by: 9
Author(s): David Brena, Joan Bertran, Montserrat Porta-de-la-Riva, Yolanda Guillén, Eric Cornes, Dmytro Kukhtar, Lluís Campos-Vicens, Lierni Fernández, Irene Pecharromán, Albert García-López, Abul B.M.M.K. Islam, Laura Marruecos, Anna Bigas, Julián Cerón, Lluís Espinosa
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-020-79379-8

Upregulation of 5′-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor
Cited by: 2
Author(s): Kyle A. Cottrell, Ryan C. Chiou, Jason D. Weber
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-019-48967-8

Interrogating Mutant Allele Expression via Customized Reference Genomes to Define Influential Cancer Mutations
Cited by: 5
Author(s): Adam Grant, Paris Vail, Megha Padi, Agnieszka K. Witkiewicz, Erik S. Knudsen
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-6564-6

Transcriptome analysis of fungicide-responsive gene expression profiles in two Penicillium italicum strains with different response to the sterol demethylation inhibitor (DMI) fungicide prochloraz
Cited by: 15
Author(s): Tingfu Zhang, Qing Cao, Na Li, De Li Liu, Yongze Yuan
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-50051-0

Genetic lines respond uniquely within the chicken thymic transcriptome to acute heat stress and low dose lipopolysaccharide
Cited by: 14
Author(s): Melissa S. Monson, Angelica G. Van Goor, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 4
Published: over 5 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 4 years ago

10.1038/s41598-019-47454-4

Glial gene networks associated with alcohol dependence
Cited by: 38
Author(s): Emma K. Erickson, Yuri A. Blednov, R. Adron Harris
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-50573-7

Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness
Cited by: 14
Author(s): Gautami Das, Doreen Becker, Vidhya Jagannathan, Orly Goldstein, Evelyn Santana, Kendall Carlin, Raghavi Sudharsan, Tosso Leeb, Yuji Nishizawa, Mineo Kondo, Gustavo D. Aguirre, Keiko Miyadera
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07305-3

Integrated analysis of the methylome and transcriptome of chickens with fatty liver hemorrhagic syndrome
Cited by: 12
Author(s): Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng, Jie Wen
Software Mentions: 4
Published: about 4 years ago

10.26508/lsa.201900303

Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s disease
Cited by: 10
Author(s): Christin Glorioso, Andreas R. Pfenning, Sam S Lee, David A. Bennett, Etienne Sibille, M Kellis, Leonard Guarente
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0117818

mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer
Cited by: 33
Author(s): Silvia von der Heyde, Sven Wagner, Czerny Alexander, M. Nietert, Fabian Ludewig, Gabriela Salinas-Riester, Dorit Arlt, Tim Beißbarth
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-019-42570-7

Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle
Cited by: 22
Author(s): Shino Tanaka, Mehmet Dayı, Y. Maeda, Isheng Jason Tsai, Ryusei Tanaka, Mark W. Bligh, Yuko Takeuchi-Kaneko, Kenji Fukuda, Natsumi Kanzaki, Taisei Kikuchi
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0181061

Comparative transcriptome analysis of flower heterosis in two soybean F1 hybrids by RNA-seq
Cited by: 22
Author(s): Chunbao Zhang, Chunjing Lin, Fuyou Fu, Xiaofang Zhong, Bao Peng, Hao Yan, Jingyong Zhang, Weilong Zhang, Pengnian Wang, Xiaoyang Ding, Wei Zhang, Limei Zhao
Software Mentions: 4
Published: over 7 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: about 4 years ago

10.3390/life11020113

Transcriptomic Analysis of the Anthocyanin Biosynthetic Pathway Reveals the Molecular Mechanism Associated with Purple Color Formation in Dendrobium Nestor
Cited by: 12
Author(s): Xueqiang Cui, Deng Jieling, Chongxing Huang, Xuan Tang, Xianmin Li, Xiuling Li, Lu JiaShi, Zibin Zhang
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-018-37033-4

Transcriptomics analysis of host liver and meta-transcriptome analysis of rumen epimural microbial community in young calves treated with artificial dosing of rumen content from adult donor cow
Cited by: 14
Author(s): Wenli Li, Andrea Edwards, Christina Riehle, Madison S. Cox, Sarah M Raabis, Joseph H. Skarlupka, Andrew J. Steinberger, Jason G. Walling, Derek M. Bickhart, Garret Suen
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-39615-2

Multiple molecular defense strategies in Brachypodium distachyon surmount Hessian fly (Mayetiola destructor) larvae-induced susceptibility for plant survival
Cited by: 9
Author(s): Subhashree Subramanyam, Jill A. Nemacheck, Andrea M. Hargarten, Nagesh Sardesai, Brandon J. Schemerhorn, Christie E. Williams
Software Mentions: 4
Published: almost 6 years ago

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: about 9 years ago

10.1038/s41375-021-01221-5

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia
Cited by: 5
Author(s): Cédric Schleiss, Raphaël Carapito, Luc‐Matthieu Fornecker, Leslie Muller, Nicodème Paul, Ouria Tahar, Angélique Pichot, Manuela Tavian, Alina Nicolae, Laurent Miguet, Laurent Mauvieux, Raoul Herbrecht, Sarah Cianférani, Jean–Noël Freund, Myriam Maumy-Bertrand, Seiamak Bahram, Frédèric Bertrand, Laurent Vallat
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0143742

Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine
Cited by: 11
Author(s): Zhonghua Sheng, Yi Sun, Ruixin Zhu, Na Jiao, Kailin Tang, Zhen Cao, Chao Ma
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-020-57467-z

Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes
Cited by: 17
Author(s): Mitra Etemadikhah, Adnan Niazi, Lennart Wetterberg, Lars Feuk
Software Mentions: 4
Published: about 5 years ago

10.1002/advs.201903366

Transferrin Receptor 1 Regulates Thermogenic Capacity and Cell Fate in Brown/Beige Adipocytes
Cited by: 33
Author(s): Jin Li, Xiaohan Pan, Guihua Pan, Zijun Song, Yao He, Susu Zhang, Xueru Ye, Yang Xiang, Enjun Xie, Xinhui Wang, Xudong Mai, Xing Yin, Biyao Tang, Xuan Shu, Pengyu Chen, Xiaoshuang Dai, Ye Tian, Liheng Yao, Mulan Han, Guohuan Xu, Huijie Zhang, Jia Sun, Hong Chen, Fudi Wang, Junxia Min, Liwei Xie
Software Mentions: 4
Published: almost 5 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 3 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: over 5 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

10.1038/s41598-018-32904-2

Transcriptomics and co-expression networks reveal tissue-specific responses and regulatory hubs under mild and severe drought in papaya (Carica papaya L.)
Cited by: 33
Author(s): Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Jesús Alejandro Zamora‐Briseño, Enrique Castaño, Francisco Espadas-Gil, Jorge Tonatiuh Ayala-Sumuano, Miguel A. Keb-Llanes, Lorenzo Felipe Sánchez Teyer, Luis Carlos Rodríguez-Zapata
Software Mentions: 4
Published: over 6 years ago

10.1016/j.ccell.2019.08.003

Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis
Cited by: 230
Author(s): René Jackstadt, Sander R. van Hooff, Joshua D.G. Leach, Xabier Cortés-Lavaud, Jeroen Lohuis, Rachel A. Ridgway, Valérie M. Wouters, Jatin Roper, Timothy J. Kendall, Campbell S.D. Roxburgh, Paul G. Horgan, Colin Nixon, Craig Nourse, Matthias Gunzer, William Clark, Ann Hedley, Ömer H. Yılmaz, Mamunur Rashid, Peter J. Bailey, Andrew V. Biankin, Andrew D. Campbell, David J. Adams, Simon T. Barry, Colin W. Steele, Jan Paul Medema, Owen J. Sansom
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-35974-4

Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity
Cited by: 29
Author(s): Trine B. Rounge, Sinan Uğur Umu, Andreas Keller, Eckart Meese, Giske Ursin, Steinar Tretli, Robert Lyle, Hilde Langseth
Software Mentions: 4
Published: about 6 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: about 10 years ago

10.1038/s41598-018-25110-7

Transcriptional Profiling of Somatostatin Interneurons in the Spinal Dorsal Horn
Cited by: 43
Author(s): Alexander Chamessian, Michael Young, Yawar J. Qadri, Temugin Berta, Ru-Rong Ji, Thomas Van de Ven
Software Mentions: 4
Published: almost 7 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

10.1371/journal.pntd.0007640

Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice
Cited by: 11
Author(s): Ghalia Boubaker, Sebastian Strempel, Andrew Hemphill, Norbert Müller, Junhua Wang, Bruno Gottstein, Markus Spiliotis
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-25302-1

Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells
Cited by: 8
Author(s): Shuzo Teruya, Tomohisa Okamura, Takashi Komai, Mariko Inoue, Yukiko Iwasaki, Shuji Sumitomo, Hirofumi Shoda, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-24830-0

Novel analysis of the Harderian gland transcriptome response to Newcastle disease virus in two inbred chicken lines
Cited by: 21
Author(s): Melissa S. Deist, Rodrigo A. Gallardo, David Bunn, T. Ross Kelly, Jack C. M. Dekkers, Huaijun Zhou, Susan J. Lamont
Software Mentions: 4
Published: almost 7 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: almost 7 years ago

10.1186/s12864-018-4660-7

Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular
Cited by: 41
Author(s): Osagie Izuogu, Abd A. Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K. Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David Elliott, Mauro Santibanez‐Koref, Michael S. Jackson
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pntd.0001409

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Cited by: 86
Author(s): Young Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline A. McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
Software Mentions: 4
Published: about 13 years ago

10.1016/j.stem.2019.06.011

Outcompeting p53-Mutant Cells in the Normal Esophagus by Redox Manipulation
Cited by: 77
Author(s): David Fernández‐Antorán, Gabriel Piedrafita, Kiyohito Murai, Swee Hoe Ong, Albert Herms, Christian Frezza, Philip H. Jones
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-23207-7

Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation
Cited by: 10
Author(s): Leila Taher, Julia Beck, Wen Li, Catrin Roolf, Jan T. Soller, Barbara C. Rütgen, Sabine E. Hammer, Murali Chodisetti, Sina Sender, Katharina A Sterenczak, Georg Fuellen, Christian Junghanß, Bertram Brenig, Ingo Nolte, Ekkehard Schütz, Hugo Murua Escobar
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-018-29329-2

Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) Infection in retinal pigment epithelium
Cited by: 33
Author(s): Pawan Kumar Singh, Indu Khatri, Alokkumar Jha, Carla D. Pretto, Katherine R. Spindler, Vaithilingaraja Arumugaswami, Shailendra Giri, Ashok Kumar, Manoj Bhasin
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-37284-1

A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status
Cited by: 12
Author(s): Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
Software Mentions: 4
Published: about 6 years ago

10.1093/brain/awaa163

Molecular and cellular correlates of human nerve regeneration: ADCYAP1/PACAP enhance nerve outgrowth
Cited by: 36
Author(s): Georgios Baskozos, Oliver Sandy-Hindmarch, Alex Clark, Katherine Windsor, Páll Karlsson, Greg A. Weir, Lucy A. McDermott, Joanna Burchall, Akira Wiberg, Dominic Furniss, David L.H. Bennett, Annina B. Schmid
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-17337-7

Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes
Cited by: 2
Author(s): Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F. Tsinoremas
Software Mentions: 4
Published: about 7 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: about 7 years ago

10.1371/journal.pone.0232120

Corticosterone and testosterone treatment influence expression of gene pathways linked to meiotic segregation in preovulatory follicles of the domestic hen
Cited by: 2
Author(s): E. Wróbel, Alexandra B. Bentz, W. Walter Lorenz, Steven T. Gardner, Mary T. Mendonça, Kristen J. Navara
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41416-020-01166-z

HOX genes promote cell proliferation and are potential therapeutic targets in adrenocortical tumours
Cited by: 15
Author(s): Jeffrey C. Francis, Jennifer R. Gardiner, Yoan Renaud, Ritika Chauhan, Yacob Weinstein, Celso E. Gómez-Sánchez, Anne‐Marie Lefrançois‐Martinez, Jérôme Bertherat, Pierre Val, Amanda Swain
Software Mentions: 4
Published: about 4 years ago

10.1038/bcj.2017.71

Alternative splicing discriminates molecular subtypes and has prognostic impact in diffuse large B-cell lymphoma
Cited by: 13
Author(s): Suvi‐Katri Leivonen, M.-R. Taskinen, Alejandra Cervera, Marja‐Liisa Karjalainen‐Lindsberg, Jan Delabie, Harald Holte, Rainer Lehtonen, Sampsa Hautaniemi, Sirpa Leppä
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: almost 5 years ago

10.1038/s41598-017-16603-y

RNA-seq of serial kidney biopsies obtained during progression of chronic kidney disease from dogs with X-linked hereditary nephropathy
Cited by: 11
Author(s): Candice P. Chu, Jessica A. Hokamp, Rachel E. Cianciolo, Alan R. Dabney, Candice Brinkmeyer-Langford, George E. Lees, Mary B. Nabity
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-18480-x

RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients
Cited by: 51
Author(s): Jungmok You, Susan M. Corley, Li Wen, Chris Hodge, Roland Hӧllhumer, Michele C. Madigan, Marc R. Wilkins, Gerard Sutton
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-019-5908-6

Grapevine comparative early transcriptomic profiling suggests that Flavescence dorée phytoplasma represses plant responses induced by vector feeding in susceptible varieties
Cited by: 17
Author(s): Nadia Bertazzon, Paolo Bagnaresi, Vally Forte, Elisabetta Mazzucotelli, Luisa Filippin, Davide Guerra, Antonella Zechini, Luigi Cattivelli, Elisa Angelini
Software Mentions: 4
Published: over 5 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

10.1186/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: about 7 years ago

10.1186/s13068-016-0608-9

Time-scale dynamics of proteome and transcriptome of the white-rot fungus Phlebia radiata: growth on spruce wood and decay effect on lignocellulose
Cited by: 91
Author(s): Jaana Kuuskeri, Mari Häkkinen, Pia Laine, Olli‐Pekka Smolander, Fitsum Tamene, Sini Miettinen, Paula Nousiainen, Marianna Kemell, Petri Auvinen, Taina Lundell
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-017-07757-w

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation
Cited by: 63
Author(s): Ann H. Ryu, Walter L. Eckalbar, Anat Kreimer, Nir Yosef, Nadav Ahituv
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-19072-5

Integrative approach using liver and duodenum RNA-Seq data identifies candidate genes and pathways associated with feed efficiency in pigs
Cited by: 45
Author(s): Yuliaxis Ramayo-Caldas, María Ballester, Juan Pablo Sánchez, Olga González‐Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, D. Torrallardona, Raquel Quintanilla
Software Mentions: 4
Published: about 7 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.ppat.1006391

Microbiota-induced peritrophic matrix regulates midgut homeostasis and prevents systemic infection of malaria vector mosquitoes
Cited by: 114
Author(s): Faye H. Rodgers, Mathilde Gendrin, Claudia A. S. Wyer, George K. Christophides
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.ppat.1008066

Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures
Cited by: 25
Author(s): Soo Ching Lee, Mei Tang, Alice V. Easton, Joseph C. Devlin, Ling Ling Chua, Ilseung Cho, Foong Ming Moy, Tsung Fei Khang, Yvonne Ai Lian Lim, P’ng Loke
Software Mentions: 4
Published: about 5 years ago

10.1002/cne.24994

Identification of regenerative processes in neonatal spinal cord injury in the opossum ( <scp> Monodelphis domestica </scp> ): A transcriptomic study
Cited by: 6
Author(s): Benjamin Wheaton, Johnny A. Sena, Anitha Sundararajan, Pooja Umale, Faye Schilkey, Robert D. Miller
Software Mentions: 4
Published: over 4 years ago

10.3390/jcm8081158

Role of MYC-miR-29-B7-H3 in Medulloblastoma Growth and Angiogenesis
Cited by: 29
Author(s): Ian J. Purvis, Avilala Janardhan, Maheedhara R. Guda, Sujatha Venkataraman, Rajeev Vibhakar, Andrew J. Tsung, Kiran Kumar Velpula, Swapna Asuthkar
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.142980

Treating ICB-resistant glioma with anti-CD40 and mitotic spindle checkpoint controller BAL101553 (lisavanbulin)
Cited by: 5
Author(s): Vassilis Genoud, Felipe I Espinoza, Eliana Marinari, Viviane Rochemont, Pierre‐Yves Dietrich, Paul M.J. McSheehy, Felix Bachmann, Heidi A. Lane, Paul R Walker
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-019-6043-0

Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird
Cited by: 12
Author(s): Veronika N. Laine, Irene Verhagen, A. Christa Mateman, Agata Pijl, Tony Williams, Phillip Gienapp, Kees van Oers, Marcel E. Visser
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.138443

Epigenetic regulation of the PGE2 pathway modulates macrophage phenotype in normal and pathologic wound repair
Cited by: 31
Author(s): Frank M. Davis, Lam C. Tsoi, Rachael Wasikowski, Aaron D. denDekker, Amrita Joshi, Carol A. Wilke, Hongping Deng, Sonya Wolf, Andrea Obi, Steven K. Huang, Allison C. Billi, Scott T. Robinson, Jay H Lipinski, William J. Melvin, Christopher O. Audu, Stephan Weidinger, Steven L. Kunkel, Andrew M. Smith, Jóhann E. Guðjónsson, Bethany B. Moore, Katherine A. Gallagher
Software Mentions: 4
Published: over 4 years ago

10.1038/celldisc.2015.45

Mapping gene regulatory circuitry of Pax6 during neurogenesis
Cited by: 56
Author(s): Sudhir Thakurela, Neha Tiwari, Sandra Schick, Angela Garding, Robert Ivánek, Benedikt Berninger, Vijay Tiwari
Software Mentions: 4
Published: about 9 years ago

10.3390/insects11050323

Transcriptome Analysis of the Oriental Fruit Fly Bactrocera dorsalis Early Embryos
Cited by: 2
Author(s): Wei Peng, Shu-Ning Yu, Alfred M. Handler, H. Zhang
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0195747

UXT is required for spermatogenesis in mice
Cited by: 5
Author(s): Eric D. Schafler, Phillip A. Thomas, Susan Ha, Yu Wang, Keria Bermudez-Hernandez, Zuojian Tang, David Fenyö, Margarita Vigodner, Susan K. Logan
Software Mentions: 4
Published: almost 7 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: about 4 years ago

10.1371/journal.ppat.1008633

Dynamic chromatin accessibility profiling reveals changes in host genome organization in response to baculovirus infection
Cited by: 9
Author(s): Xiaodong Kong, Guisheng Wei, Nan Chen, Shudi Zhao, Yongrong Shen, Jianjia Zhang, Li Yang, Xiaoqun Zeng, Xiaoxia Wu
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-018-24227-z

A new way of producing pediocin in Pediococcus acidilactici through intracellular stimulation by internalized inulin nanoparticles
Cited by: 19
Author(s): Whee-Soo Kim, Jun-Yeong Lee, Bijay Singh, Sushila Maharjan, Liang Hong, Sang-Mok Lee, Lianhua Cui, Ki-June Lee, Girak Kim, Cheol‐Heui Yun, Seoung-Hun Kang, Yun‐Jaie Choi, Chong‐Su Cho
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-59934-z

Immunosuppressive effect and global dysregulation of blood transcriptome in response to psychosocial stress in vervet monkeys (Chlorocebus sabaeus)
Cited by: 2
Author(s): Anna J. Jasinska, Ivona Pandrea, Tianyu He, Cassandra Benjamin, Maurice Newton, Jen‐Chieh Lee, Nelson B. Freimer, Giovanni Coppola, J. David Jentsch
Software Mentions: 4
Published: almost 5 years ago

10.1042/BSR20210495

RNA sequencing reveals potential interacting networks between the altered transcriptome and ncRNome in the skeletal muscle of diabetic mice
Cited by: 5
Author(s): Devesh Kesharwani, Amit Kumar, M. Damodara Poojary, Vinod Scaria, Malabika Datta
Software Mentions: 3
Published: over 3 years ago

10.1038/s41438-018-0020-7

Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)
Cited by: 49
Author(s): Jason P. Londo, Alisson P. Kovaleski, Jacquelyn Lillis
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-017-4374-2

A survey on cellular RNA editing activity in response to Candida albicans infections
Cited by: 3
Author(s): Yao‐Wei Huang, Yingying Cao, Jiarui Li, Yuanhua Liu, Zhong Wu, Xuan Li, Chen Chen, Pei Hao
Software Mentions: 3
Published: about 7 years ago

Projects: pypi: HTSeq

Papers Mentioning HTSeq 3,071