Research Papers

25 of 3431 papers

CSV Excel
Quick filters: Open Data Open Code Pre-registered Funding Declared COI Declared Open Access Clear Filters
A comparison of methods for detecting DNA methylation from long-read sequencing of human genomes.
Sigurpalsdottir BD; Stefansson OA; Holley G; Beyter D; Zink F; Hardarson MÞ; Sverrisson SÞ; Kristinsdottir N; Magnusdottir DN; Magnusson OÞ; Gudbjartsson DF; Halldorsson BV; Stefansson K.
Genome Biol (Unknown)
Published: 2024
3/6 Transparent
Data
A comparison of marker gene selection methods for single-cell RNA sequencing data.
Pullin JM; McCarthy DJ.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared
HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells.
Li S; Wang Y; van der Stoel M; Zhou X; Madhusudan S; Kanerva K; Nguyen VD; Eskici N; Olkkonen VM; Zhou Y; Raivio T; Ikonen E.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared
Structured 3' UTRs destabilize mRNAs in plants.
Zhang T; Li C; Zhu J; Li Y; Wang Z; Tong CY; Xi Y; Han Y; Koiwa H; Peng X; Zhang X.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared
DNA satellite and chromatin organization at mouse centromeres and pericentromeres.
Packiaraj J; Thakur J.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared
RUBICON: a framework for designing efficient deep learning-based genomic basecallers.
Singh G; Alser M; Denolf K; Firtina C; Khodamoradi A; Cavlak MB; Corporaal H; Mutlu O.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species h…
Shachar R; Dierks D; Garcia-Campos MA; Uzonyi A; Toth U; Rossmanith W; Schwartz S.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging.
Devos X; Fiche JB; Bardou M; Messina O; Houbron C; Gurgo J; Schaeffer M; Götz M; Walter T; Mueller F; Nollmann M.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites.
Xu S; Wei J; Sun S; Zhang J; Chan TF; Li Y.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Code Funding Declared
Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens.
Alda-Catalinas C; Ibarra-Soria X; Flouri C; Gordillo JE; Cousminer D; Hutchinson A; Sun B; Pembroke W; Ullrich S; Krejci A; Cortes A; Acevedo A; Malla S; Fishwick C; Drewes G; Rapiteanu R.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learn…
Zheng L; Shi S; Lu M; Fang P; Pan Z; Zhang H; Zhou Z; Zhang H; Mou M; Huang S; Tao L; Xia W; Li H; Zeng Z; Zhang S; Chen Y; Li Z; Zhu F.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci.
Fazal S; Danzi MC; Xu I; Kobren SN; Sunyaev S; Reuter C; Marwaha S; Wheeler M; Dolzhenko E; Lucas F; Wuchty S; Tekin M; Züchner S; Aguiar-Pulido V.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease.
Wilson PC; Verma A; Yoshimura Y; Muto Y; Li H; Malvin NP; Dixon EE; Humphreys BD.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells.
Kurosaki T; Rambout X; Maquat LE.
Genome Biol (Unknown)
Published: 2024
3/6 Transparent
Funding Declared
SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-f…
Strober BJ; Tayeb K; Popp J; Qi G; Gordon MG; Perez R; Ye CJ; Battle A.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis.
Fernandes JB; Naish M; Lian Q; Burns R; Tock AJ; Rabanal FA; Wlodzimierz P; Habring A; Nicholas RE; Weigel D; Mercier R; Henderson IR.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environme…
Vochteloo M; Deelen P; Vink B; BIOS Consortium; Tsai EA; Runz H; Andreu-Sánchez S; Fu J; Zhernakova A; Westra HJ; Franke L.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regula…
Tjärnberg A; Beheler-Amass M; Jackson CA; Christiaen LA; Gresham D; Bonneau R.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared
Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult…
Bradfield JP; Kember RL; Ulrich A; Balkiyarova Z; Alyass A; Aris IM; Bell JA; Broadaway KA; Chen Z; Chai JF; Davies NM; Fernandez-Orth D; Bustamante M; Fore R; Ganguli A; Heiskala A; Hottenga JJ; Íñiguez C; Kobes S; Leinonen J; Lowry E; Lyytikainen LP; Mahajan A; Pitkänen N; Schnurr TM; Have CT; Strachan DP; Thiering E; Vogelezang S; Wade KH; Wang CA; Wong A; Holm LA; Chesi A; Choong C; Cruz M; Elliott P; Franks S; Frithioff-Bøjsøe C; Gauderman WJ; Glessner JT; Gilsanz V; Griesman K; Hanson RL; Kaakinen M; Kalkwarf H; Kelly A; Kindler J; Kähönen M; Lanca C; Lappe J; Lee NR; McCormack S; Mentch FD; Mitchell JA; Mononen N; Niinikoski H; Oken E; Pahkala K; Sim X; Teo YY; Baier LJ; van Beijsterveldt T; Adair LS; Boomsma DI; de Geus E; Guxens M; Eriksson JG; Felix JF; Gilliland FD; Biobank PM; Hansen T; Hardy R; Hivert MF; Holm JC; Jaddoe VWV; Järvelin MR; Lehtimäki T; Mackey DA; Meyre D; Mohlke KL; Mykkänen J; Oberfield S; Pennell CE; Perry JRB; Raitakari O; Rivadeneira F; Saw SM; Sebert S; Shepherd JA; Standl M; Sørensen TIA; Timpson NJ; Torrent M; Willemsen G; Hypponen E; Power C; Early Growth Genetics Consortium; McCarthy MI; Freathy RM; Widén E; Hakonarson H; Prokopenko I; Voight BF; Zemel BS; Grant SFA; Cousminer DL.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
Phase separation as a possible mechanism for dosage sensitivity.
Yang L; Lyu J; Li X; Guo G; Zhou X; Chen T; Lin Y; Li T.
Genome Biol (Unknown)
Published: 2024
3/6 Transparent
Funding Declared
Chromatin activity identifies differential gene regulation across human ancestries.
Pettie KP; Mumbach M; Lea AJ; Ayroles J; Chang HY; Kasowski M; Fraser HB.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice a…
Luo H; Lao L; Au KS; Northrup H; He X; Forget D; Gauthier MS; Coulombe B; Bourdeau I; Shi W; Gagliardi L; Fragoso MCBV; Peng J; Wu J.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
ChIPr: accurate prediction of cohesin-mediated 3D genome organization from 2D chromatin features.
Abbas A; Chandratre K; Gao Y; Yuan J; Zhang MQ; Mani RS.
Genome Biol (Unknown)
Published: 2024
5/6 Transparent
Data Code Funding Declared
Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell…
Mason K; Sathe A; Hess PR; Rong J; Wu CY; Furth E; Susztak K; Levinsohn J; Ji HP; Zhang N.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared
RNA-binding protein RBM5 plays an essential role in acute myeloid leukemia by activating the oncogenic protein HOXA9.
Zhang M; Hyle J; Chen X; Xin Y; Jin Y; Zhang J; Yang X; Chen X; Wright S; Liu Z; Rosikiewicz W; Xu B; He L; Liu H; Ping N; Wu D; Wen F; Li C; Xu P.
Genome Biol (Unknown)
Published: 2024
4/6 Transparent
Data Funding Declared