Research Papers

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A genome catalog of the early-life human skin microbiome.
Shen Z; Robert L; Stolpman M; Che Y; Allen KJ; Saffery R; Walsh A; Young A; Eckert J; Deming C; Chen Q; Conlan S; Laky K; Li JM; Chatman L; Kashaf SS; NISC Comparative Sequencing Program; VITALITY team; Kong HH; Frischmeyer-Guerrerio PA; Perrett KP; Segre JA.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
The chromatin landscape of the euryarchaeon Haloferax volcanii.
Marinov GK; Bagdatli ST; Wu T; He C; Kundaje A; Greenleaf WJ.
Genome Biol (Unknown)
Published: 2023
4/6 Transparent
Data Funding Declared
Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.
Manzano-Morales S; Liu Y; González-Bodí S; Huerta-Cepas J; Iranzo J.
Genome Biol (Unknown)
Published: 2023
4/6 Transparent
Data Funding Declared
The Quartet Data Portal: integration of community-wide resources for multiomics quality control.
Yang J; Liu Y; Shang J; Chen Q; Chen Q; Ren L; Zhang N; Yu Y; Li Z; Song Y; Yang S; Scherer A; Tong W; Hong H; Xiao W; Shi L; Zheng Y.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data.
Lee MYY; Kaestner KH; Li M.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Utilizing AAV-mediated LEAPER 2.0 for programmable RNA editing in non-human primates and nonsense mutation correction i…
Yi Z; Zhao Y; Yi Z; Zhang Y; Tang G; Zhang X; Tang H; Zhang W; Zhao Y; Xu H; Nie Y; Sun X; Xing L; Dai L; Yuan P; Wei W.
Genome Biol (Unknown)
Published: 2023
4/6 Transparent
Data Funding Declared
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.
Pochon Z; Bergfeldt N; Kırdök E; Vicente M; Naidoo T; van der Valk T; Altınışık NE; Krzewińska M; Dalén L; Götherström A; Mirabello C; Unneberg P; Oskolkov N.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental f…
Hippen AA; Omran DK; Weber LM; Jung E; Drapkin R; Doherty JA; Hicks SC; Greene CS.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
SPIRAL: integrating and aligning spatially resolved transcriptomics data across different experiments, conditions, and …
Guo T; Yuan Z; Pan Y; Wang J; Chen F; Zhang MQ; Li X.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applicatio…
Zheng H; Vijg J; Fard AT; Mar JC.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of memb…
Carbonetto P; Luo K; Sarkar A; Hung A; Tayeb K; Pott S; Stephens M.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Single-cell metabolic profiling reveals subgroups of primary human hepatocytes with heterogeneous responses to drug cha…
Sanchez-Quant E; Richter ML; Colomé-Tatché M; Martinez-Jimenez CP.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types hi…
Huuki-Myers LA; Montgomery KD; Kwon SH; Page SC; Hicks SC; Maynard KR; Collado-Torres L.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasit…
Wang C; Dong Y; Li C; Oberstaller J; Zhang M; Gibbons J; Pires CV; Xiao M; Zhu L; Jiang RHY; Kim K; Miao J; Otto TD; Cui L; Adams JH; Liu X.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal d…
Zhang P; Wang X; Li S; Cao X; Zou J; Fang Y; Shi Y; Xiang F; Shen B; Li Y; Fang B; Zhang Y; Guo R; Lv Q; Zhang L; Lu Y; Wang Y; Yu J; Xie Y; Wang R; Chen X; Yu J; Zhang Z; He J; Zhan J; Lv W; Nie Y; Cai J; Xu X; Hu J; Zhang Q; Gao T; Jiang X; Tan X; Xue N; Wang Y; Ren Y; Wang L; Zhang H; Ning Y; Chen J; Zhang L; Jin S; Ren F; Ehrlich SD; Zhao L; Ding X.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Robust, scalable, and informative clustering for diverse biological networks.
Gaiteri C; Connell DR; Sultan FA; Iatrou A; Ng B; Szymanski BK; Zhang A; Tasaki S.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Genomic variant benchmark: if you cannot measure it, you cannot improve it.
Majidian S; Agustinho DP; Chin CS; Sedlazeck FJ; Mahmoud M.
Genome Biol (Unknown)
Published: 2023
3/6 Transparent
Funding Declared
GenArk: towards a million UCSC genome browsers.
Clawson H; Lee BT; Raney BJ; Barber GP; Casper J; Diekhans M; Fischer C; Gonzalez JN; Hinrichs AS; Lee CM; Nassar LR; Perez G; Wick B; Schmelter D; Speir ML; Armstrong J; Zweig AS; Kuhn RM; Kirilenko BM; Hiller M; Haussler D; Kent WJ; Haeussler M.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.
Cui L; Yang B; Xiao S; Gao J; Baud A; Graham D; McBride M; Dominiczak A; Schafer S; Aumatell RL; Mont C; Teruel AF; Hübner N; Flint J; Mott R; Huang L.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Dosage compensation of Z sex chromosome genes in avian fibroblast cells.
Deviatiiarov R; Nagai H; Ismagulov G; Stupina A; Wada K; Ide S; Toji N; Zhang H; Sukparangsi W; Intarapat S; Gusev O; Sheng G.
Genome Biol (Unknown)
Published: 2023
4/6 Transparent
Data Funding Declared
DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection.
Hausmann F; Ergen C; Khatri R; Marouf M; Hänzelmann S; Gagliani N; Huber S; Machart P; Bonn S.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Disparities in spatially variable gene calling highlight the need for benchmarking spatial transcriptomics methods.
Charitakis N; Salim A; Piers AT; Watt KI; Porrello ER; Elliott DA; Ramialison M.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local en…
Xia X; Zhang F; Li S; Luo X; Peng L; Dong Z; Pausch H; Leonard AS; Crysnanto D; Wang S; Tong B; Lenstra JA; Han J; Li F; Xu T; Gu L; Jin L; Dang R; Huang Y; Lan X; Ren G; Wang Y; Gao Y; Ma Z; Cheng H; Ma Y; Chen H; Pang W; Lei C; Chen N.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fus…
Poszewiecka B; Gogolewski K; Karolak JA; Stankiewicz P; Gambin A.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared
ChromGene: gene-based modeling of epigenomic data.
Jaroszewicz A; Ernst J.
Genome Biol (Unknown)
Published: 2023
5/6 Transparent
Data Code Funding Declared