2024

GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing
Kaur G., Perteghella T., Carbonell-Sala S., Gonzalez-Martinez J., Hunt T., Mądry T., Jungreis I., Arnan C., Lagarde J., Borsari B., Sisu C., Jiang Y., Bennett R., Berry A., Cerdan-Velez D., Cochran K., Vara C., Davidson C., Donaldson S., Dursun C., Gonazlez-Lopez S., Das S. G., Hardy M., Hollis Z., Kay M., Montanes J.C., Ni P., Nurtdinov R., Palumbo E., Pulido-Quetglas C., Suner M.-M., Yu X., Zhang D., Loveland J. E., Alba M. M., Diekhans M., Tanzer A., Mudge J. M., Flicek P., Martin F. J., Gerstein M., Kellis M., Kundaje A., Paten B., Tress M. L., Johnson R., Uszczyńska-Ratajczak B., Frankish A., Guigó R.
bioRxiv (preprint), 2024.10.29.620654 (2024).

CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing
Carbonell-Sala S., Perteghella T., Lagarde J., Nishiyori H., Palumbo E., Arnan C., Takahashi H., Carninci P., Uszczynska-Ratajczak B., Guigó R.
Nature Communications, 15, 5278-5291, (2024).

2023

GENCODE: reference annotation for the human and mouse genomes in 2023
Frankish A., Carbonell-Sala S., Diekhans M., Jungreis I., Loveland J.E., Mudge J.M., Sisu C., Wright J.C., Arnan C., Barnes I., Banerjee A., Bennett R., Berry A., Bignell A., Boix C., Calvet F., Cerdán-Vélez D., Cunningham F., Davidson C., Donaldson S., Dursun C., Fatima R., Giorgetti S., Giron C.G., Gonzalez J.M., Hardy M., Harrison P.W., Hourlier T., Hollis Z., Hunt T., James B., Jiang Y., Johnson R., Kay M., Lagarde J., Martin F.J., Gómez L.M., Nair S., Ni P., Pozo F., Ramalingam V., Ruffier M., Schmitt B.M., Schreiber J.M., Steed E., Suner M.-M., Sumathipala D., Sycheva I., Uszczynska-Ratajczak B., Wass E., Yang Y.T., Yates A., Zafrulla Z., Choudhary J.S., Gerstein M., Guigo R., Hubbard T.J.P., Kellis M., Kundaje A., Paten B., Tress M.L., Flicek P.
Nucleic Acids Research, 51(D1), D942–D949 (2023).

2022

Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish
Uszczynska-Ratajczak B., Sugunan S., Kwiatkowska M., Migdal M., Carbonell-Sala S., Sokol A., Winata C.L., Chacinska A.
Life Science Alliance, 6(1) e202201514 (2022).

2021

Cytosolic aggregation of mitochondrial proteins disrupts cellular homeostasis by stimulating the aggregation of other proteins
Nowicka U., Chroscicki P., Stroobants K., Sladowska M., Turek M., Uszczynska-Ratajczak B., Kundra R., Goral T., Perni M., Dobson C.M., Vendruscolo M., Chacinska A.
eLife, 10, e65484 (2021).

Annotation of Full-length Long Noncoding RNAs with Capture Long-Read Sequencing
Carbonell Sala S., Uszczyńska-Ratajczak B., Lagarde J., Johnson R., Guigó R.
Methods in Molecular Biology, 2254, 133-159 (2021).

GENCODE 2021
Frankish A., Diekhans M., Jungreis I., Lagarde J., Loveland J.E., Mudge J.M., Sisu C., Wright J.C., Armstrong J., Barnes I., Berry A., Bignell A., Boix C., Carbonell Sala S., Cunningham F., Di Domenico T., Donaldson S., Fiddes I.T., García Girón C., Gonzalez J.M., Grego T., Hardy M., Hourlier T., Howe K.L., Hunt T., Izuogu O.G., Johnson R., Martin F.J., Martínez L., Mohanan S., Muir P., Navarro F.C.P., Parker A., Pei B., Pozo F., Riera F.C., Ruffier M., Schmitt B.M., Stapleton E., Suner M.M., Sycheva I., Uszczynska-Ratajczak B., Wolf M.Y., Xu J., Yang Y.T., Yates A., Zerbino D., Zhang Y., Choudhary J.S., Gerstein M., Guigó R., Hubbard T.J.P., Kellis M., Paten B., Tress M.L., Flicek P.
Nucleic Acids Research, 49(D1), D916-D923 (2021).

2020

Deregulation of LINC01087 decodes the heterogeneity of breast cancer segregating luminal from triple-negative patients and predicting their clinical outcome
De Palma F.D.E., Del Monaco V., Pol J.G., Kremer M., D’Argenio V., Stoll G., Montanaro D., Uszczyńska-Ratajczak B., Klein C.C., Vlasova A., Botti G., D’Aiuto M., Baldi A., Guigó R., Kroemer G., Maiuri M.C., Salvatore F.
Pharmacological Research, 161, 105249-105266 (2020).

Expanded encyclopaedias of DNA elements in the human and mouse genomes
ENCODE Project Consortium, Moore J.E., Purcaro M.J., Pratt H.E., Epstein C.B., Shoresh N., Adrian J., Kawli T., Davis C.A., Dobin A., Kaul R., Halow J., Van Nostrand E.L., Freese P., Gorkin D.U., Shen Y., He Y., Mackiewicz M., Pauli-Behn F., Williams B.A., Mortazavi A., Keller C.A., Zhang X.O., Elhajjajy S.I., Huey J., Dickel D.E., Snetkova V., Wei X., Wang X., Rivera-Mulia J.C., Rozowsky J., Zhang J., Chhetri S.B., Zhang J., Victorsen A., White K.P., Visel A., Yeo G.W., Burge C.B., Lécuyer E., Gilbert D.M., Dekker J., Rinn J., Mendenhall E.M., Ecker J.R., Kellis M., Klein R.J., Noble W.S., Kundaje A., Guigó R., Farnham P.J., Cherry J.M., Myers R.M., Ren B., Graveley B.R., Gerstein M.B., Pennacchio L.A., Snyder M.P., Bernstein B.E., Wold B., Hardison R.C., Gingeras T.R., Stamatoyannopoulos J.A., Weng Z.
Nature, 583, 699-710 (2020).

Perspectives on ENCODE
ENCODE Project Consortium, Snyder M.P., Gingeras T.R., Moore J.E., Weng Z., Gerstein M.B., Ren B., Hardison R.C., Stamatoyannopoulos J.A., Graveley B.R., Feingold E.A., Pazin M.J., Pagan M., Gilchrist D.A., Hitz B.C., Cherry J.M., Bernstein B.E., Mendenhall E.M., Zerbino D.R., Frankish A., Flicek P., Myers R.M.
Nature, 583, 693-698 (2020).

2019

Re-annotation of 191 developmental and epileptic encephalopathy associated genes unmasks de novo variants in SCN1A
Steward C.A., Roovers J., Suner M.M., Gonzalez J.M., Uszczynska-Ratajczak B., Pervouchine D., Fitzgerald S., Viola M., Stamberger H., Hamdan F.F., Ceulemans B., Leroy P., Nava C., Lepine A., Tapanari E., Keiller D., Abbs S., Sanchis-Juan A., Grozeva D., Rogers A.S., Diekhans M., Guigó R., Petryszak R., Minassian B.A., Cavalleri G., Vitsios D., Petrovski S., Harrow J., Flicek P., Lucy Raymond F., Lench N.J., Jonghe P., Mudge J.M., Weckhuysen S., Sisodiya S.M., Frankish A.
NPJ Genomic Medicine, 4, 31 (2019).

Mitochondrial stress-dependent regulation of cellular protein synthesis
Topf U., Uszczynska-Ratajczak B., Chacinska A.
Journal of Cell Science, 132, 8 (2019).

Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish
Sokol A.M., Uszczynska-Ratajczak B., Collins M.M., Bazala M., Topf U., Lundegaard P.R., Sugunan S., Guenther S., Kuenne C., Graumann J., Chan S.S.L., Stainier D.Y.R., Chacinska A.
PLoS Genetics, 14, 11, e1007743 (2019).

GENCODE reference annotation for the human and mouse genomes
Frankish A., Diekhans M., Ferreira A.M., Johnson R., Jungreis I., Loveland J., Mudge J.M., Sisu C., Wright J., Armstrong J., Barnes I., Berry A., Bignell A., Carbonell Sala S., Chrast J., Cunningham F., Di Domenico T., Donaldson S., Fiddes I.T., García Girón C., Gonzalez J.M., Grego T., Hardy M., Hourlier T., Hunt T., Izuogu O.G., Lagarde J., Martin F.J., Martínez L., Mohanan S., Muir P., Navarro F.C.P., Parker A., Pei B., Pozo F., Ruffier M., Schmitt B.M., Stapleton E., Suner M.M., Sycheva I., Uszczynska-Ratajczak B., Xu J., Yates A., Zerbino D., Zhang Y., Aken B., Choudhary J.S., Gerstein M., Guigó R., Hubbard T.J.P., Kellis M., Paten B., Reymond A., Tress M.L., Flicek P.
Nucleic Acids Research, 47, D1, D766-D773 (2019).

2018

Towards a complete map of the human long non-coding RNA transcriptome
Uszczynska-Ratajczak B., Lagarde J., Frankish A., Guigó R., Johnson R.
Nature Reviews Genetics, 19, 9, 535-548 (2018).

Gene expression profiling of acute myeloid leukemia samples from adult patients with AML-M1 and -M2 through boutique microarrays, real-time PCR and droplet digital PCR
Handschuh L., Kazmierczak M., Milewski M.C., Góralski M., Luczak M., Wojtaszewska M., Uszczynska-Ratajczak B., Lewandowski K., Komarnicki M., Figlerowicz M.
International Journal of Oncology, 52, 3, 656-678 (2018).

2017

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Lagarde J., Uszczynska-Ratajczak B., Carbonell S., Perez-Lluch S., Abad A., Davis C., Gingeras T., Frankish A., Harrow J., Guigó R., Johnson R.
Nature Genetics, 49, 12, 1731–1740 (2017).

Brain transcriptome sequencing of a natural model of alzheimer’s disease
Altimiras F., Uszczynska-Ratajczak B., Biekofsky R., Vlasova A., Palumbo E., Camara F., Deacon R., Guigó R., Cogram P.
Frontiers in Aging Neuroscience, 9, 64-72 (2017).

2016

Extension of human lncRNA transcripts by RACE coupled with long read high-throughput sequencing (RACE-Seq)
Lagarde J., Uszczynska-Ratajczak B., Santoyo-Lopez J., Manuel Gonzalez J., Tapanari E., Mudge J.M., Steward C., Wilming L., Tanzer A., Howald C., Chrast J., Vela-Boza A., Rueda A., Lopez-Domingo F.J., Dopazo J., Reymond A., Guigó R., Harrow J.
Nature Communications, 17, 7, 12339-12350 (2016).

2015

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
Frankish A., Uszczynska B., Ritchie G.R.S, Gonzalez J.M., Pervouchine D., Petryszak R., Mudge J.M., Fonseca N., Brazma A., Guigo R., Harrow J.
BMC Genomics, 16, Suppl 8:S2 (2015).