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

by Pagnotta, S.M, Risso, D.
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

A next generation sequencing-based protocol for screening of variants of concern in autism spectrum disorder

by Budjan, C., Fong, M., Huang, J., Jeong, M.-S, Kong, X.-J, Liu, J., Liu, K., Sherman, H.T, Tian, R., Zhuang, P.
Published 2022

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

Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform

by Cagnin, L., Fleming, R.A, Gerdemann, U., Kaminski, J., Kean, L.S, Keskula, P., Lane, J.F, McGuckin, C., Rui, X., Shalek, A.K, Tkachev, V.
Published 2022

Multi-modality machine learning predicting Parkinson’s disease

by Bandres-Ciga, S., Blauwendraat, C., Bookman, M., Botia, J.A, Campbell, R.H, Carter, J.F, Craig, D.W, Dadu, A., Faghri, F., Hardy, J.A, Hashemi, S.H, Hutchins, E., Iwaki, H., Kim, J.J, Leonard, H.L, Makarious, M.B, Maleknia, M., Morris, H.R, Nalls, M.A, Nojopranoto, W., Saffo, D., Sargent, L., Singleton, A.B, Song, Y., Van Keuren-Jensen, K., Violich, I., Vitale, D.
Published 2022

Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene

by Ashok, T., Barrett, J., Kalkus, A., Morton, B.R
Published 2021

Kmerator Suite: Design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets

by Audoux, J., Bessiere, C., Bouge, A.-L, Boureux, A., Commes, T., Gautheret, D., Gilbert, N., Guibert, B., Riquier, S., Ruffle, F., Xue, H.
Published 2021

Characterization of a novel type III alcohol dehydrogenase from Thermococcus barophilus Ch5

by Dong, K., Jiang, D., Li, Y., Liu, Q., Oger, P., Wu, L., Zhang, L.
Published 2021

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila

by Aguilera, L., González, J., Green, L., Guirao-Rico, S., Horvath, V., Jamilloux, V., Lindstadt, H., Quesneville, H., Radío, S., Rech, G.E
Published 2022

Quantifying the tissue-specific regulatory information within enhancer DNA sequences

by Benner, P., Vingron, M.
Published 2021

Subtype-specific and co-occurring genetic alterations in B-cell non-Hodgkin lymphoma

by Akhter, A., Bhalla, K., Bouska, A., Buckley, S., Carey, C., Chen, B.J, Davidson, M., Davis, R.E, Deng, Q., Fowler, N.H, Gandhi, M., Ghosh, S., Green, M.R, Greiner, T., Hartert, K., Heavican, T., Iqbal, J., Jain, N., Lunning, M.A, Ma, M.C.J, Mansoor, A., Moore, D., Nastoupil, L.J, Neelapu, S., Parekh, S., Perumal, D., Rodig, S.J, Showell, J., Sohani, A.R, Stewart, D., Street, L., Tadros, S., Tobin, J., Vose, J.M, Westin, J.R, Yang, H.
Published 2022

GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs

by Bonnici, V., Garrison, E., Giugno, R., Pinello, L., Tognon, M.
Published 2021

RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes

by Alves-Pereira, C.F, Bortvin, A., Gimelbrant, A.A, Gupta, S., Igarashi, K.J, Lafontaine, D.L, Mendelevich, A., Nag, A., Vigneau, S., Vinogradova, S.
Published 2022

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

by Alexander, R.P, Balaj, L., Chang, J., Kaczor-Urbanowicz, K.E, Kitchen, R.R, LaPlante, E., Losic, B., Mateescu, B., Max, K.E.A, Mestdagh, P., Milosavljevic, A., Roth, M., Rozowsky, J., Spengler, R.M, Stolovitzky, G., Tosar, J.P, Van Nostrand, E.L, White, B.S, Yu, R.
Published 2022

Identification and molecular characterization of the high-affinity copper transporters family in Solanum lycopersicum

by Gabrielli, A., Lafuente, M.T, Perea-García, A., Puig, S., Romero, P., Sampedro, R.
Published 2021

ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

by Arakawa, T., Arner, E., Gao, X., Li, Y., Takizawa, S., Umarov, R.
Published 2021

Transcriptional Correlates of Chronic Alcohol Neuroadaptation in Drosophila Larvae

by Acevedo-Gonzalez, J.P, Anqueira-González, A., Fuenzalida-Uribe, N.L, Ghezzi, A., Irizarry-Hernández, C., Montes-Mercado, A.
Published 2021

Changes in DNA methylation accompany changes in gene expression during chondrocyte hypertrophic differentiation in vitro

by Lessard, S.G, Mukherjee, P., Otero, M., Rourke, B., Singh, P.
Published 2021

Identifying stress responsive genes using overlapping communities in co-expression networks

by Finke, J., Riccio-Rengifo, C., Rocha, C.
Published 2021