Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

by Barwick, L., Brown, K.K, Castaldi, P.J, Chase, R.P, Cho, M.H, Criner, G., DeMeo, D.L, Flaherty, K., Ghosh, A.J, Hersh, C.P, Hobbs, B.D, Limper, A.H, Martinez, F.J, McGoldrick, D., Moll, M., Morrow, J., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Saferali, A., Sciurba, F., Silverman, E.K, Wise, R., Xu, Z., Yun, J.H, Ziniti, J.
Published 2022

Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles

by Pagnotta, S.M, Risso, D.
Published 2021

GATA2-Mediated Transcriptional Activation of Notch3 Promotes Pancreatic Cancer Liver Metastasis

by Deng, Y., Hu, P., Lin, H., Yang, Z., Zhang, H., Zhang, L.
Published 2022

Transcriptomic Profiling of Peripheral Edge of Lesions to Elucidate the Pathogenesis of Psoriasis Vulgaris

by Boonpethkaew, S., Jumlongpim, O., Komine, M., Meephansan, J., Soonthornchai, W., Tangtanatakul, P., Vipanurat, R., Wongpiyabovorn, J.
Published 2022

Ebola Virus Encodes Two microRNAs in Huh7-Infected Cells

by Diallo, I., Guellal, S., Ho, J., Husseini, Z., Kobinger, G.P, Kozak, R.A, Provost, P., Vion, E.
Published 2022

Species-level resolution of female bladder microbiota from 16s rrna amplicon sequencing

by Fields, I., Gregory, W.T, Hoffman, C., Karstens, L., Mooney, M.A, Siddiqui, N.Y, Simon, H.M, Wolfe, A.J
Published 2021

Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0

by Kariyawasam, H., Law, C.W, Ritchie, M.E, Su, S., Voogd, O.
Published 2021

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

by Aguilar-Ordoñez, I., Barry, B.K, Burke, E.E, Collado-Torres, L., Eagles, N.J, Gutiérrez-Millán, E., Huuki, L., Jaffe, A.E, Leonard, J., Phan, B.D.N, Serrato, V.L, Stolz, J.M
Published 2021

ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring

by Tagashira, M.
Published 2023

Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts

by Cole, J.J, Faydaci, B.A, Goodyear, C.S, Maciewicz, R.A, McGuinness, D., Robertson, N.A, Shaw, R.
Published 2021

The complex transcriptional landscape of magnetosome gene clusters in magnetospirillum gryphiswaldense

by Borgert, L., Busche, T., Dziuba, M., Kalinowski, J., Riese, C.N, Schüler, D., Uebe, R., Wittchen, M.
Published 2021

Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease

by Guennewig, B., Halliday, G.M, Hooshmand, K., Pineda, S.S, Sutherland, G.T
Published 2022

Squalene through Its Post-Squalene Metabolites Is a Modulator of Hepatic Transcriptome in Rabbits

by Abuobeid, R., Arnal, C., Burillo, J.C, Busto, R., Felices, M.J, Lasheras, R., Lasunción, M.A, Martínez-Beamonte, R., Osada, J., Rodríguez-Yoldi, M.J, Sánchez-Marco, J.
Published 2022

Transcriptomic Regulation of Muscle Mitochondria and Calcium Signaling by Insulin/IGF-1 Receptors Depends on FoxO Transcription Factors

by Bhardwaj, G., Dreyfuss, J.M, Kahn, C.R, Klaus, K., Nair, K.S, O’Neill, B.T, Pan, H., Penniman, C.M, Weatherford, E.T
Published 2022

Squalene through Its Post-Squalene Metabolites Is a Modulator of Hepatic Transcriptome in Rabbits

by Abuobeid, R., Arnal, C., Burillo, J.C, Busto, R., Felices, M.J, Lasheras, R., Lasunción, M.A, Martínez-Beamonte, R., Osada, J., Rodríguez-Yoldi, M.J, Sánchez-Marco, J.
Published 2022

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization

by Feng, Y., Li, L.M
Published 2021

Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data

by McNicholas, P.D, Qin, X., Rothstein, S.J, Silva, A., Subedi, S.
Published 2023

Direct RNA sequencing unfolds the complex transcriptome of Vibrio parahaemolyticus

by Al Kadi, M., Iida, T., Ishii, E., Kodama, T., Matsuda, S., Motooka, D., Okuzaki, D., Truong, D.T
Published 2021

MiRge3.0: A comprehensive microRNA and tRF sequencing analysis pipeline

by Halushka, M.K, Patil, A.H
Published 2021

Transcriptome analysis of thymic tissues from Chinese Partridge Shank chickens with or without Newcastle disease virus LaSota vaccine injection via high-throughput RNA sequencing

by Chang, X., Duan, H., Guo, L., Ji, Y., Li, H., Li, M., Nie, F., Zhang, J., Zhou, J.
Published 2022