"Genome Biol"[Journal] - Search Results

Year	Number of Results
2000	69
2001	182
2002	229
2003	194
2004	211
2005	223
2006	239
2007	356
2008	298
2009	222
2010	203
2011	205
2012	204
2013	230
2014	279
2015	293
2016	267
2017	244
2018	229
2019	301
2020	304
2021	351
2022	271
2023	293
2024	324
2025	441
2026	168

1

Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

Naqing F, Yuan Q, Duren Z. Naqing F, et al. Genome Biol. 2026 Apr 15. doi: 10.1186/s13059-026-04071-5. Online ahead of print. Genome Biol. 2026. PMID: 41987329 Free article.

2

Prediction of plant phase-separating proteins using positive-unlabeled learning.

Fu R, Tian Y, Ren H, Zhao A, Lou Y, Mao S, Yang J, Jiang S, Huang X, Wang X. Fu R, et al. Genome Biol. 2026 Apr 15. doi: 10.1186/s13059-026-04075-1. Online ahead of print. Genome Biol. 2026. PMID: 41987292 Free article.

3

Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer.

Moreno-Rodriguez T, Zhang M, Lundberg A, Shrestha R, Sjöström M, Pasam A, Chan J, Devereux L, Foye A, Zhu X, Weinstein AS, Trigos AS, Wyatt AW, Alumkal JJ, Small EJ, Aggarwal R, Dehm SM, Bootsma ML, Zhao SG, Lupien M, Feng FY, Sandhu S, Quigley DA. Moreno-Rodriguez T, et al. Genome Biol. 2026 Apr 15. doi: 10.1186/s13059-026-04074-2. Online ahead of print. Genome Biol. 2026. PMID: 41987223 Free article.

4

Single-cell epigenetic and transcriptomic states across the continuum of monoclonal B cell lymphocytosis to chronic lymphocytic leukemia.

Rathgeber AC, Fernandes SM, Nagler A, Li S, Dorfman DM, Bullinger L, Davids MS, Brown JR, Livak KJ, Ludwig LS, Wu CJ, Penter L. Rathgeber AC, et al. Genome Biol. 2026 Apr 15. doi: 10.1186/s13059-026-04072-4. Online ahead of print. Genome Biol. 2026. PMID: 41987205 Free article.

5

Lineage-specific evolution, structural diversity, and activity of R2 retrotransposons in animals.

Hassan NT, Van Treeck B, Rodríguez-Vargas A, Sheppard AE, Collins K, Adelson DL. Hassan NT, et al. Genome Biol. 2026 Apr 14. doi: 10.1186/s13059-026-04073-3. Online ahead of print. Genome Biol. 2026. PMID: 41981679 Free article.

6

Herpes simplex virus type 1 R-loops are targets for APOBEC-mediated mutagenesis.

Miskei M, Varga D, Hornyák L, Sipos É, Nagy É, Li Q, Karányi Z, Szabó Z, DeWeerd R, Green AM, Szüts D, Csoma E, Székvölgyi L. Miskei M, et al. Genome Biol. 2026 Apr 14. doi: 10.1186/s13059-026-04078-y. Online ahead of print. Genome Biol. 2026. PMID: 41981657 Free article.

7

Proteogenomic decoding of chemotherapy resistance in patients with triple-negative breast cancer.

Lee DK, Kim MH, Hwang Y, Kim SG, Ryu WJ, Kim GU, Yun HM, Park S, Lee JD, Han HJ, Kim GM, Kim KH, Park JB, Kim MJ, Koo JS, Kim JY, Park HS, Kim SI, Gee HY, Park S, Sohn J. Lee DK, et al. Genome Biol. 2026 Apr 14;27(1):125. doi: 10.1186/s13059-026-04053-7. Genome Biol. 2026. PMID: 41975515 Free PMC article.

8

A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

Zhao M, Li J, Jiang Y, Yan J, Tang X, Liang C, Tang J, Guo F. Zhao M, et al. Genome Biol. 2026 Apr 14. doi: 10.1186/s13059-026-04070-6. Online ahead of print. Genome Biol. 2026. PMID: 41975483 Free article.

9

Experimental and computational methods for allelic imbalance analysis from single-nucleus RNA-seq data.

Simmons SK, Adiconis X, Haywood N, Parker J, Lin Z, Liao Z, Tuncali I, Shin A, Jagadeesh K, Gosik K, Gatzen M, Smith JT, El Kodsi DN, Kuras Y, Baecher-Allan C, Serrano GE, Beach TG, Garimella K, Al'Khafaji AM, Rozenblatt-Rosen O, Regev A, Dong X, Scherzer CR, Levin JZ. Simmons SK, et al. Genome Biol. 2026 Apr 11. doi: 10.1186/s13059-026-04062-6. Online ahead of print. Genome Biol. 2026. PMID: 41965748 Free article.

10

DNA damaging properties of G-quadruplex ligand QN-302 are potentiated by the DNA repair inhibitor Olaparib and mitigated by the molecular helicase PhpC.

Psalmon G, Pipier A, Barbotte M, Hudson RHE, Neidle S, Monchaud D. Psalmon G, et al. Genome Biol. 2026 Apr 11. doi: 10.1186/s13059-026-04035-9. Online ahead of print. Genome Biol. 2026. PMID: 41965726 Free article.

11

Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer.

Berman BP, Erdman SA, Wheeler C, Cayford J, Turatsinze JV, Ouzounova M, Piecyk M, Herzog M, Payen-Gay L, Walter T, Kelly TK. Berman BP, et al. Genome Biol. 2026 Apr 10. doi: 10.1186/s13059-026-04060-8. Online ahead of print. Genome Biol. 2026. PMID: 41957676 Free article.

12

Allelic structural variation at the NLR25-1 locus enhances defense against Pseudomonas syringae in kiwifruit.

Wu Y, Wang Y, Lin Y, Zhao M, Huo Y, Zhang T, Wang H, Zhu Y, Wang L, Zheng P, Yue J, Wang S, Liu Y. Wu Y, et al. Genome Biol. 2026 Apr 9. doi: 10.1186/s13059-026-04068-0. Online ahead of print. Genome Biol. 2026. PMID: 41957668 Free article.

13

Transposable element-mediated evolutionary expansion of Sox2- and Brn2-binding regulatory modules for mammalian neural-cell differentiation.

Nishihara H, Komiya A. Nishihara H, et al. Genome Biol. 2026 Apr 9;27(1):114. doi: 10.1186/s13059-026-04050-w. Genome Biol. 2026. PMID: 41952195 Free PMC article.

14

Benchmarking tools for deciphering cellular crosstalk in spatially-resolved transcriptomics.

Ku LT, Bernard V, Min J, Yuan Y, Koay EJ, Maitra A, Li L, Li Z. Ku LT, et al. Genome Biol. 2026 Apr 8. doi: 10.1186/s13059-026-04063-5. Online ahead of print. Genome Biol. 2026. PMID: 41952215 Free article.

15

Benchmarking of sequencing technologies defines optimal strategies for genetic variants detection in a human genome.

Eveleigh RJM, Reiling SJ, Galvez JH, Bourgey M, Ragoussis J, Bourque G. Eveleigh RJM, et al. Genome Biol. 2026 Apr 8;27(1):129. doi: 10.1186/s13059-026-04048-4. Genome Biol. 2026. PMID: 41952156 Free PMC article.

16

Sex and tissue resolved co-expression networks reveal a female placental-brain axis protective against prenatal PCB exposure.

Chau KH, Neier K, Valenzuela AE, Schmidt RJ, Durbin-Johnson B, Lein PJ, Korf I, LaSalle JM. Chau KH, et al. Genome Biol. 2026 Apr 7. doi: 10.1186/s13059-026-04052-8. Online ahead of print. Genome Biol. 2026. PMID: 41943130 Free article.

17

Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.

Hu Y, Jia Y, Yang Z, Lin W, Zhang L, Yin F, Fan C, Zhou Y, Yang QY. Hu Y, et al. Genome Biol. 2026 Apr 7. doi: 10.1186/s13059-026-04047-5. Online ahead of print. Genome Biol. 2026. PMID: 41943068 Free article.

18

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

Gao W, Hu P, Wick B, Qiu Q, Zhang H, Li Y, Kang X, Bedi K, Haeussler M, Sasaki K, Margulies K, Wu H. Gao W, et al. Genome Biol. 2026 Apr 6;27(1):126. doi: 10.1186/s13059-026-04061-7. Genome Biol. 2026. PMID: 41937210 Free PMC article.

19

Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering in Arabidopsis thaliana.

Zhou HR, Doan DTH, Hartwig T, Turck F. Zhou HR, et al. Genome Biol. 2026 Apr 6;27(1):124. doi: 10.1186/s13059-026-04064-4. Genome Biol. 2026. PMID: 41937163 Free PMC article.

20

HistoGWAS: an AI-enabled framework for automated genetic analysis of tissue phenotypes in histology cohorts.

Chaudhary S, Voigts A, Bereket M, Albert ML, Schwamborn K, Zeggini E, Casale FP. Chaudhary S, et al. Genome Biol. 2026 Mar 31;27(1):122. doi: 10.1186/s13059-026-04031-z. Genome Biol. 2026. PMID: 41918129 Free PMC article.

21

The pan-genome provides insights into evolutionary dynamics and fatty acid metabolism in Aceraceae family.

Ma Q, Li S, Xu Z, Zhu L, Wang T, Yan K, Du Y, Li S, Wang L, Ren J, Wang Y, Sun X, Chen Z, Zhu Z, Shen F, Li Q, Jin S. Ma Q, et al. Genome Biol. 2026 Mar 31. doi: 10.1186/s13059-026-04058-2. Online ahead of print. Genome Biol. 2026. PMID: 41918124 Free article.

22

RNA modification-mediated multidimensional crosstalk: a novel perspective on gene expression regulation.

Wang Y, Yang C, Lin R, Ling H, Xu YZ, Wu Q, Zhou Y. Wang Y, et al. Genome Biol. 2026 Mar 31. doi: 10.1186/s13059-026-04037-7. Online ahead of print. Genome Biol. 2026. PMID: 41918117 Free article. Review.

23

MRBEE-TL: improving causal effect estimation in multi-ancestry multivariable Mendelian randomization with transfer learning.

Yang Y, Zhu X. Yang Y, et al. Genome Biol. 2026 Mar 31. doi: 10.1186/s13059-026-04051-9. Online ahead of print. Genome Biol. 2026. PMID: 41913286 Free article.

24

Benchmarking single-cell tumor immune atlases and application for uncovering cell states related to immunotherapy response.

Yang J, Shyr Y, Liu Q. Yang J, et al. Genome Biol. 2026 Mar 31. doi: 10.1186/s13059-026-04055-5. Online ahead of print. Genome Biol. 2026. PMID: 41913233 Free article.

25

A H3K27me3 reader complex couples H3K27me3 accumulation to nascent transcription of transposable elements in Paramecium.

Balan T, Petitalot A, Albert JR, Abbou L, Chevreux G, Al-Sady B, Aygenli BÖ, Bartke T, Margueron R, Duharcourt S. Balan T, et al. Genome Biol. 2026 Mar 30. doi: 10.1186/s13059-026-04045-7. Online ahead of print. Genome Biol. 2026. PMID: 41913290 Free article.

26

Predicting extinction risk of gibbons from genomes of extinct Yunnan lar gibbon.

Luo A, Tian HY, Li S, Roos C, Wang S, Wu DD. Luo A, et al. Genome Biol. 2026 Mar 30. doi: 10.1186/s13059-026-04056-4. Online ahead of print. Genome Biol. 2026. PMID: 41913236 Free article.

27

EMF2b-1 regulates endosperm cell cycling through PRC2 recruitment in maize.

Xu J, Zhang Y, Qing K, Xue N, Chen J, Zhang X, Zhao W, Tian X, Yan H, Li Y, Dong J. Xu J, et al. Genome Biol. 2026 Mar 28. doi: 10.1186/s13059-026-04049-3. Online ahead of print. Genome Biol. 2026. PMID: 41904579 Free article.

28

Functional characterization of transporter genes in rice node at single-cell resolution through multi-omics technologies.

Li H, Jin H, Ning M, Deng F, Chen W, Yang O, Cheng J, Lian X, Shao L, Zhang S, Yamaji N, Hu F, Ma JF, Lei GJ. Li H, et al. Genome Biol. 2026 Mar 27. doi: 10.1186/s13059-026-04046-6. Online ahead of print. Genome Biol. 2026. PMID: 41896984 Free article.

29

DeepISO: deep learning-powered prediction of protein-protein interaction rewiring generated by alternative splicing.

Guo X, Jiang L, Li J, Yuan M, Li D, Shi W, Zhang Z, Wuchty S. Guo X, et al. Genome Biol. 2026 Mar 27. doi: 10.1186/s13059-026-04057-3. Online ahead of print. Genome Biol. 2026. PMID: 41896911 Free article.

30

ImmuSeeker: deep mining of immune-related gene family signatures through lineage reconstruction.

Jiang L, Hurwitz I, Wylezinski LS, Racke MK, Yan F, Ye F, Sheng Q, Leng S, Chung CP, Stein CM, Li CI, Kumar N, Ceccarelli M, Baker SF, Perkins DJ, Spurlock CF 3rd, Han L, Guo Y. Jiang L, et al. Genome Biol. 2026 Mar 26. doi: 10.1186/s13059-026-04039-5. Online ahead of print. Genome Biol. 2026. PMID: 41888873 Free article.

31

Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes.

Lee H, Cao X, Parada GE, Li JD, Iosub IA, Braunschweig U, Rebelo K, Ule J, Wan Y, Blencowe BJ. Lee H, et al. Genome Biol. 2026 Mar 26;27(1):94. doi: 10.1186/s13059-026-04029-7. Genome Biol. 2026. PMID: 41882679 Free PMC article.

32

scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

Jin Z, Tang Z, Li X, Zhang K, Xie Z, Zhang N. Jin Z, et al. Genome Biol. 2026 Mar 24. doi: 10.1186/s13059-026-04043-9. Online ahead of print. Genome Biol. 2026. PMID: 41877186 Free article.

33

ER tethering and active transport govern condensate diffusion during hyperosmotic stress.

Halder B, Gao G, Ahnoud A, Stakenas S, Sumrall ER, Walter NG. Halder B, et al. Genome Biol. 2026 Mar 24. doi: 10.1186/s13059-026-04042-w. Online ahead of print. Genome Biol. 2026. PMID: 41877182 Free article.

34

Unraveling the complexity of the histone code: implications for gene regulation and disease.

Malone KL, Singh AK, Lignos JM, Cook ED, Phillips M, Boyle BW, Kressy IA, Vulikh M, Lathrop AK, McKay KT, Zafar H, Stein JL, Stein GS, Glass KC. Malone KL, et al. Genome Biol. 2026 Mar 24. doi: 10.1186/s13059-026-04011-3. Online ahead of print. Genome Biol. 2026. PMID: 41877173 Free article. Review.

35

Dynamic changes in Lamin B1 and heterochromatin coincide with chromatin condensation during human erythropoiesis.

Wen R, Zhang Q, Li Y, Chen Y, Jiang Y, Lu Y, Zhu J, Kong D, Xu Y, Liu X, Qian P, Zhang M, Huang H, Huo D. Wen R, et al. Genome Biol. 2026 Mar 24. doi: 10.1186/s13059-026-04025-x. Online ahead of print. Genome Biol. 2026. PMID: 41872884 Free article.

36

The cellular landscape of i-motifs: genomic insights, methodological challenges, and the road ahead.

Sengupta P, Sabouri N. Sengupta P, et al. Genome Biol. 2026 Mar 23;27(1):121. doi: 10.1186/s13059-026-04044-8. Genome Biol. 2026. PMID: 41872944 Free PMC article. Review.

37

Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity in autism spectrum disorder.

Lee H, Ko K, Kim S, Lee G, Kim S, Lee J, Song DY, Bong G, Han JH, Lee J, Kim YR, Lee Y, Kim E, Børglum AD, Grove J, Kim SH, Sun W, Yoo HJ, An JY. Lee H, et al. Genome Biol. 2026 Mar 23. doi: 10.1186/s13059-026-04041-x. Online ahead of print. Genome Biol. 2026. PMID: 41872878 Free article.

38

A kingdom-wide full-length RNA atlas reveals the evolutionary landscapes of plant poly(A) tails.

Chen Y, Lu W, He H, Zheng L, Pan X, Sun T, Bu F, Fang Y, Sun Y, Long Y, Wang M, Wu S, Liu L, Jia J, Jiao Y, Hu Z, Zhang Y, Zhai J. Chen Y, et al. Genome Biol. 2026 Mar 23. doi: 10.1186/s13059-026-04040-y. Online ahead of print. Genome Biol. 2026. PMID: 41866516 Free article.

39

Sex chromosome evolution mediated by a large inversion and a possible switch of the sex determination gene.

Mao X, Rafati N, Tellgren-Roth C, Ingvarsson PK, Karrenberg S. Mao X, et al. Genome Biol. 2026 Mar 19;27(1):120. doi: 10.1186/s13059-026-04038-6. Genome Biol. 2026. PMID: 41857659 Free PMC article.

40

Phase separation of β-catenin assembles active loop hubs in colorectal cancer.

Yang J, Sun J, Zhang H, Yu Y, Chen F, Mo J, Luo S, Xu Y, Zhong L, Tan D, Lin Y, Liao Y, Zhang Y, Zhang J, Chen W, Huang X, Peng Y, Gao H, Wang H, Gong Q, Wang J. Yang J, et al. Genome Biol. 2026 Mar 19. doi: 10.1186/s13059-026-04030-0. Online ahead of print. Genome Biol. 2026. PMID: 41857580 Free article.

41

Dynamic and cell-type specific transcriptional reprogramming underlies the floral transition in the maize shoot apical meristem.

Dong L, Sun Y, Kang L, Li Z, Liang Y, Sheng H, Tian F, Jackson D, Yang F. Dong L, et al. Genome Biol. 2026 Mar 18. doi: 10.1186/s13059-026-04033-x. Online ahead of print. Genome Biol. 2026. PMID: 41851888 Free article.

42

IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.

Wang W, Liu JJ, Li Y, Ko S, Feng N, Zhang M, Lin Q, Xia M, Yu YP, Luo JH, Baldoni PL, Tseng GC, Liu S. Wang W, et al. Genome Biol. 2026 Mar 18. doi: 10.1186/s13059-026-04023-z. Online ahead of print. Genome Biol. 2026. PMID: 41851882 Free article.

43

Using reciprocally retained gene families to detect whole-genome multiplications in plants.

Tasdighian S, Sensalari C, Maere S. Tasdighian S, et al. Genome Biol. 2026 Mar 17. doi: 10.1186/s13059-026-04032-y. Online ahead of print. Genome Biol. 2026. PMID: 41845531 Free article.

44

Centromere evolution in annual and perennial soybeans and its implication for hybridization in cultivated species.

Hou J, Wei Y, Liu H, Zhuang B, Chen Z, Zhu X, Han J, Su W, Tan H, Xu W, Lai R, Peng H, Zhang D, Wang Y, Liu Y. Hou J, et al. Genome Biol. 2026 Mar 16;27(1):90. doi: 10.1186/s13059-026-04036-8. Genome Biol. 2026. PMID: 41840677 Free PMC article.

45

Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

Acera-Mateos M, Adiconis X, Li JK, Marchese D, Caratù G, Hon CC, Tiwari P, Kojima M, Vieth B, Murphy MA, Simmons SK, Lefevre T, Claes I, O'Connor CL, Menon R, Otto EA, Ando Y, Vandereyken K, Kretzler M, Bitzer M, Fraenkel E, Voet T, Enard W, Carninci P, Heyn H, Levin JZ, Mereu E. Acera-Mateos M, et al. Genome Biol. 2026 Mar 13;27(1):64. doi: 10.1186/s13059-026-04002-4. Genome Biol. 2026. PMID: 41821037 Free PMC article.

46

The genomic history of Streptococcus mutans from the Mesolithic until modern times.

Thygesen VFDF, Farahani MF, Nielsen SH, Constancias F, Givskov M, Abranches J, Scorrano G, Jørkov MLS, Ebrahimi G, Bendezu-Sarmiento JC, Demeter F, Kristiansen K, Belstrøm D, Sikora M. Thygesen VFDF, et al. Genome Biol. 2026 Mar 12. doi: 10.1186/s13059-026-04018-w. Online ahead of print. Genome Biol. 2026. PMID: 41821123 Free article.

47

Blood proteomics: insights from public data.

Larrea-Sebal A, Dai C, Brenes AJ, Korff K, Neely BA, Geyer PE, Dagley LF, Unwin RD, Naba A, MacCoss MJ, Guo T, Deutsch EW, Martin C, Schwenk JM, Perez-Riverol Y. Larrea-Sebal A, et al. Genome Biol. 2026 Mar 12;27(1):81. doi: 10.1186/s13059-026-04027-9. Genome Biol. 2026. PMID: 41821120 Free PMC article. Review.

48

Recurrent sex chromosome turnover mediated by distinct ARR17 and PISTILLATA duplications in willows.

Wang Y, Xue ZQ, Zhang RG, Zhu ZY, Hörandl E, Wang XR, Mao YF, Charlesworth D, He L. Wang Y, et al. Genome Biol. 2026 Mar 12. doi: 10.1186/s13059-026-04026-w. Online ahead of print. Genome Biol. 2026. PMID: 41821116 Free article.

49

Proteomics and tracer metabolomics link GAPDH ISGylation to glycolytic control.

Eggermont D, Eggermont L, Aslantaş N, Thery F, Boucher K, Beling A, Ghesquière B, Impens F. Eggermont D, et al. Genome Biol. 2026 Mar 11. doi: 10.1186/s13059-026-04034-w. Online ahead of print. Genome Biol. 2026. PMID: 41814427 Free article.

50

Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and evolutionary perspectives.

Shi Y, Liu H, Yang W, Zhai J, Wang H. Shi Y, et al. Genome Biol. 2026 Mar 11. doi: 10.1186/s13059-026-04024-y. Online ahead of print. Genome Biol. 2026. PMID: 41814406 Free article. Review.

51

Comparative centromere genomics reveals evolutionary divergence in Solanaceae genomes.

Wan P, Hu M, Jin H, Tang S, Zhong M, Cheng J, Zhu Z, Cao B, Chen G, Chen C, Chen C, Song J, Liao Y. Wan P, et al. Genome Biol. 2026 Mar 11. doi: 10.1186/s13059-026-04028-8. Online ahead of print. Genome Biol. 2026. PMID: 41814399 Free article.

52

GPU-accelerated linkage disequilibrium scans reveal non-independent assortment of human non-homologous chromosomes.

Lv W, Zou Y, Shang Z, Wei S, Sun C, Xu J, Chen H, Tao J, Tian H, Bi S, Guo X, Dong Y, Zhang C, Zhang M, Lv H, Jiang Y. Lv W, et al. Genome Biol. 2026 Mar 10. doi: 10.1186/s13059-026-04019-9. Online ahead of print. Genome Biol. 2026. PMID: 41808216 Free article.

53

Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies.

Sur A, Noble WS, Myler PJ. Sur A, et al. Genome Biol. 2026 Mar 10;27(1):133. doi: 10.1186/s13059-026-03978-3. Genome Biol. 2026. PMID: 41803952 Free PMC article.

54

Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.

Lefeuvre M, Marsolier MC, Bon C. Lefeuvre M, et al. Genome Biol. 2026 Mar 9;27(1):132. doi: 10.1186/s13059-026-04016-y. Genome Biol. 2026. PMID: 41796349 Free PMC article.

55

Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

Singh M, Qu Y, Pande A, Zadora J, Herse F, Gauster M, Kong X, Zheng R, Anwar R, Stevanovic K, Dechend R, Cohen M, Molvarec A, Wang J, Konkel MK, Zhang B, Feschotte C, Dveksler G, Blois SM, Hurst LD, Izsvák Z. Singh M, et al. Genome Biol. 2026 Mar 9;27(1):73. doi: 10.1186/s13059-026-03944-z. Genome Biol. 2026. PMID: 41796334 Free PMC article.

56

Tribolium madens satellitome reveals a network of highly abundant satellite DNAs in megabase-sized regions hallmarked by macro-dyad symmetries.

Veseljak D, Despot-Slade E, Volarić M, Horvat L, Meštrović N, Mravinac B. Veseljak D, et al. Genome Biol. 2026 Mar 7;27(1):131. doi: 10.1186/s13059-026-04022-0. Genome Biol. 2026. PMID: 41795071 Free PMC article.

57

Augmented CENH3 loading is accompanied by transcriptional and epigenetic reprogramming at rice centromeres during meiosis.

Cao L, Zhao Y, You H, Liu H, Wang B, Run Y, Yang H, Wen M, Chen J, Zhao P, Shen Y, Li Y, Zhang W, Cheng Z. Cao L, et al. Genome Biol. 2026 Mar 5;27(1):130. doi: 10.1186/s13059-026-04020-2. Genome Biol. 2026. PMID: 41787412 Free PMC article.

58

Systematic investigation of interindividual variation of DNA methylation in human whole blood.

Grant OA, Kumari M, Schalkwyk L, Zabet NR. Grant OA, et al. Genome Biol. 2026 Mar 5;27(1):128. doi: 10.1186/s13059-026-04021-1. Genome Biol. 2026. PMID: 41781971 Free PMC article.

59

Multi-context seeds enable fast and high-accuracy read mapping.

Tolstoganov I, Martin M, Buchin N, Sahlin K. Tolstoganov I, et al. Genome Biol. 2026 Feb 28;27(1):118. doi: 10.1186/s13059-026-04017-x. Genome Biol. 2026. PMID: 41764549 Free PMC article.

60

Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.

Michielsen L, Hsu J, Joglekar A, Belchikov N, Reinders MJT, Tilgner HU, Mahfouz A. Michielsen L, et al. Genome Biol. 2026 Feb 28;27(1):119. doi: 10.1186/s13059-026-04015-z. Genome Biol. 2026. PMID: 41764538 Free PMC article.

61

Centromere organization and epigenetic regulation in Aristolochia fimbriata.

Li K, Li J, Zhao R, Qin L, Wang Y, Ren J, Ke L, Wang J, Yi X, Zhou Y, Jiao Y. Li K, et al. Genome Biol. 2026 Feb 27;27(1):115. doi: 10.1186/s13059-026-04014-0. Genome Biol. 2026. PMID: 41761339 Free PMC article.

62

Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone.

Vilgalys TP, Anderson JA, Fogel AS, Lin D, Archie EA, Alberts SC, Tung J. Vilgalys TP, et al. Genome Biol. 2026 Feb 27;27(1):116. doi: 10.1186/s13059-026-04013-1. Genome Biol. 2026. PMID: 41761253 Free PMC article.

63

Translational buffering tunes gene expression in mice and humans.

Rao S, Le AY, Persyn L, Cenik C. Rao S, et al. Genome Biol. 2026 Feb 26;27(1):113. doi: 10.1186/s13059-026-04010-4. Genome Biol. 2026. PMID: 41749359 Free PMC article.

64

RIMap-RISC: a transcriptome-wide database of structurally modeled human microRNA interactions.

Chasles S, Gaillard-Duchassin Z, Quenneville J, Lemaire M, Gagnon E, Major F. Chasles S, et al. Genome Biol. 2026 Feb 26;27(1):112. doi: 10.1186/s13059-026-04008-y. Genome Biol. 2026. PMID: 41749322 Free PMC article.

65

Benchmarking LLM-based agents for single-cell omics analysis.

Liu Y, Zhou L, Du X, He R, Zhang X, Shen R, Li Y. Liu Y, et al. Genome Biol. 2026 Feb 25;27(1):123. doi: 10.1186/s13059-026-03998-z. Genome Biol. 2026. PMID: 41742311 Free PMC article.

66

iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.

Mehta S, Wagner R, Do KT, Johnson JE, Yu F, Jubenville T, Richards K, Coleman S, Popescu FE, Nesvizhskii AI, Largaespada DA, Jagtap PD, Griffin TJ. Mehta S, et al. Genome Biol. 2026 Feb 25;27(1):111. doi: 10.1186/s13059-026-04012-2. Genome Biol. 2026. PMID: 41742304 Free PMC article.

67

A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification.

Wissel D, Mehlferber MM, Nguyen KM, Pavelko V, Tseng E, Robinson MD, Sheynkman GM. Wissel D, et al. Genome Biol. 2026 Feb 25;27(1):110. doi: 10.1186/s13059-026-03988-1. Genome Biol. 2026. PMID: 41742281 Free PMC article.

68

Reducing demographic bias in biomedical machine learning for cancer detection using cfDNA methylation.

Li S, Zeng W, Li W, Liu CC, Zhou Y, Ni X, Stackpole ML, Yeh AH, Melehy A, Lu DS, Raman SS, Hsu W, Mishra L, Shetty K, Tran B, Yokomizo M, Ahuja P, Zhu Y, Tseng HR, Aberle DR, Agopian VG, Han SB, French SW, Dubinett SM, Zhou XJ, Wong WH. Li S, et al. Genome Biol. 2026 Feb 25. doi: 10.1186/s13059-026-04006-0. Online ahead of print. Genome Biol. 2026. PMID: 41736096 Free article.

69

Integrating scRNA-seq and snRNA-seq with spatial transcriptomics to unlock the xylem puzzle.

Wei M, Hsieh JA, Dang JF, Tong B, Li H, Sederoff R, Lin YJ, Li Q. Wei M, et al. Genome Biol. 2026 Feb 23;27(1):109. doi: 10.1186/s13059-026-04007-z. Genome Biol. 2026. PMID: 41724975 Free PMC article.

70

krepp: a k-mer-based maximum pseudo-likelihood method for estimating read distances and genome-wide phylogenetic placement.

Şapcı AOB, Mirarab S. Şapcı AOB, et al. Genome Biol. 2026 Feb 21;27(1):108. doi: 10.1186/s13059-026-03999-y. Genome Biol. 2026. PMID: 41723514 Free PMC article.

71

Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.

Assari M, Chew BJ, Bayat Tork MA, Sobczyk M, Zhu C, Tran HAV, Rudzka D, Zhang W, Pan T. Assari M, et al. Genome Biol. 2026 Feb 20;27(1):106. doi: 10.1186/s13059-026-04009-x. Genome Biol. 2026. PMID: 41721424 Free PMC article.

72

Genomic and epidemiological identification of Pseudomonas aeruginosa transmission chains and in hospital ICUs.

Graña-Miraglia L, Hu X, Volling C, Mataseje L, Mulvey MR, McGeer A, Guttman DS; Toronto Invasive Bacterial Diseases Network (TIBDN). Graña-Miraglia L, et al. Genome Biol. 2026 Feb 20;27(1):107. doi: 10.1186/s13059-026-04005-1. Genome Biol. 2026. PMID: 41721420 Free PMC article.

73

Network-based framework for studying etiology and phenotypic diversity in primary ciliopathies.

Aarts EM, Laman Trip DS, Neatu R, Martin CG, Riley B, Kraus A, Green A, Al-Hamed MH, Armstrong RE, Sayer JA, Bachmann-Gagescu R, Beltrao P. Aarts EM, et al. Genome Biol. 2026 Feb 19;27(1):105. doi: 10.1186/s13059-025-03899-7. Genome Biol. 2026. PMID: 41715205 Free PMC article.

74

A comprehensive evaluation of long-read de novo transcriptome assembly.

Yan F, Baldoni PL, Lancaster J, Ritchie ME, Lewsey MG, Gouil Q, Davidson NM. Yan F, et al. Genome Biol. 2026 Feb 18;27(1):102. doi: 10.1186/s13059-026-04001-5. Genome Biol. 2026. PMID: 41709347 Free PMC article.

75

saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.

Segers A, Gilis J, Van Heetvelde M, Risso D, De Baere E, Clement L. Segers A, et al. Genome Biol. 2026 Feb 18;27(1):103. doi: 10.1186/s13059-026-03973-8. Genome Biol. 2026. PMID: 41709279 Free PMC article.

76

Rootless hair as a reliable source of forensic genetic information.

Kapp JD, Wanket C, Nguyen R, Tzadikario T, Neadeau H, Shapiro B, Sacco S, Schwartz C, Valencia C, Harkins K, Green RE. Kapp JD, et al. Genome Biol. 2026 Feb 18;27(1):104. doi: 10.1186/s13059-026-03981-8. Genome Biol. 2026. PMID: 41703596 Free PMC article.

77

Non-disruptive in vitro monitoring of cellular states with cell-free DNA methylation.

Hess A, Kovacsovics A, Bachinger F, Vallier L, Kretzmer H, Meissner A. Hess A, et al. Genome Biol. 2026 Feb 17;27(1):59. doi: 10.1186/s13059-026-03996-1. Genome Biol. 2026. PMID: 41703631 Free PMC article.

78

Sequence bias in chromatin fragmentation leads to misinterpretation of protein-DNA interactions in vivo.

Durán L, Rodríguez L, García A, Santamaría R, Sánchez M, Antequera F. Durán L, et al. Genome Biol. 2026 Feb 16;27(1):101. doi: 10.1186/s13059-026-04004-2. Genome Biol. 2026. PMID: 41699733 Free PMC article.

79

Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species.

Hoff SNK, Maurstad MF, Tørresen OK, Araya RA, Berg PR, Præbel K, Jakobsen KS, Jentoft S. Hoff SNK, et al. Genome Biol. 2026 Feb 16;27(1):100. doi: 10.1186/s13059-026-03975-6. Genome Biol. 2026. PMID: 41699629 Free PMC article.

80

Predicting disease-specific histone modifications and functional effects of non-coding variants by leveraging DNA language models.

Wang X, Pan T, Chen S, Webb GI, Jiang Y, Rozowsky J, Gerstein M, Song J. Wang X, et al. Genome Biol. 2026 Feb 14;27(1):97. doi: 10.1186/s13059-026-04003-3. Genome Biol. 2026. PMID: 41691336 Free PMC article.

81

Modeling nascent transcription from chromatin landscape and structure with CLASTER.

Pielies Avellí M, Sigurdsson AI, Ollé López J, Narita T, Krietenstein N, Choudhary C, Rasmussen S. Pielies Avellí M, et al. Genome Biol. 2026 Feb 14;27(1):98. doi: 10.1186/s13059-026-03992-5. Genome Biol. 2026. PMID: 41691282 Free PMC article.

82

Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs.

Piri RD, Wang M, Romay MC, Buckler ES, Dawe RK. Piri RD, et al. Genome Biol. 2026 Feb 14;27(1):99. doi: 10.1186/s13059-026-03993-4. Genome Biol. 2026. PMID: 41691274 Free PMC article.

83

Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.

Priebe O, Solan R, Messer C, Chu C, Hess J, Getz G. Priebe O, et al. Genome Biol. 2026 Feb 14;27(1):83. doi: 10.1186/s13059-026-03971-w. Genome Biol. 2026. PMID: 41689134 Free PMC article.

84

Hidden in plain sight: illuminating the tRNA landscape by sequencing.

Marlow K, Su Z. Marlow K, et al. Genome Biol. 2026 Feb 13;27(1):95. doi: 10.1186/s13059-026-03995-2. Genome Biol. 2026. PMID: 41689121 Free PMC article. Review.

85

PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns.

Zhuang H, Ji Z. Zhuang H, et al. Genome Biol. 2026 Feb 12;27(1):93. doi: 10.1186/s13059-026-03994-3. Genome Biol. 2026. PMID: 41673899 Free PMC article.

86

Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus.

Ko S, Cummins EA, Monteith W, Sheppard SK. Ko S, et al. Genome Biol. 2026 Feb 11;27(1):91. doi: 10.1186/s13059-026-04000-6. Genome Biol. 2026. PMID: 41673895 Free PMC article.

87

DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

Wang Y, Li Y, Ye C, Irkliyenko I, Gao L, Bissonnette M, Dai Q, Tang W, He C. Wang Y, et al. Genome Biol. 2026 Feb 11. doi: 10.1186/s13059-026-03991-6. Online ahead of print. Genome Biol. 2026. PMID: 41673887 Free article.

88

A geometric deep learning framework for genome-wide prediction of enzyme turnover number.

Pan T, Cui X, Koh HY, Bi Y, Wang X, Zhang Y, Hu S, Webb GI, Kurgan L, Zhang G, Song J. Pan T, et al. Genome Biol. 2026 Feb 11;27(1):92. doi: 10.1186/s13059-026-03986-3. Genome Biol. 2026. PMID: 41673757 Free PMC article.

89

Dissecting the genetic architecture of seed-related traits in Brassica napus by integrating multi-omics analysis and VIS-NIR hyperspectral imaging.

Tan Z, Liu Y, Wu X, Song J, Lu B, Chen Y, Fan R, Chen J, Yang W, Feng H, Guo L, Yao X. Tan Z, et al. Genome Biol. 2026 Feb 10;27(1):88. doi: 10.1186/s13059-026-03990-7. Genome Biol. 2026. PMID: 41668184 Free PMC article.

90

ICE: robust detection of cellular senescence from weak single-cell signatures using imputation-based marker refinement.

Xu P, Zhang H, Zhu S, Kong Y. Xu P, et al. Genome Biol. 2026 Feb 10;27(1):89. doi: 10.1186/s13059-026-03997-0. Genome Biol. 2026. PMID: 41668152 Free PMC article.

91

Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.

Ammari M, Choudhary A, Zander M. Ammari M, et al. Genome Biol. 2026 Feb 10;27(1):87. doi: 10.1186/s13059-026-03979-2. Genome Biol. 2026. PMID: 41668066 Free PMC article. Review.

92

Single-cell transcriptomic analysis of plant quiescent center by third-generation sequencing reveals developmental trajectories.

Hu G, Li C, Guo W, Li D, Yang L, Gu X. Hu G, et al. Genome Biol. 2026 Feb 9;27(1):86. doi: 10.1186/s13059-026-03989-0. Genome Biol. 2026. PMID: 41664205 Free PMC article.

93

Ubiquitination degradation of GATA4 by CUL4B promotes ovarian cancer metastasis by inducing lysosomal acidification.

Yin X, Gao R, Geng Y, Mu X, Zhang Y, Ma Y, Chen X, Han F, Chen Z, Li F, He J. Yin X, et al. Genome Biol. 2026 Feb 9;27(1):85. doi: 10.1186/s13059-026-03982-7. Genome Biol. 2026. PMID: 41664169 Free PMC article.

94

The gene expression landscape of disease genes.

García-González J, Cote AC, Garcia-Gonzalez S, Liou L, O'Reilly PF. García-González J, et al. Genome Biol. 2026 Feb 9;27(1):84. doi: 10.1186/s13059-026-03958-7. Genome Biol. 2026. PMID: 41664080 Free PMC article.

95

Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis.

Psonis N, Tabakaki E, Vassou D, Papadantonakis S, Souleles A, Nafplioti A, Kousis Tsampazis G, Papadopoulou A, Xanthopoulos K, Panailidis P, Georgiadou A, Papakosta D, Koursioti S, Evangelinou M, Papadopoulou V, Evaggeloglou P, Korka E, Christidis I, Ioannou M, Kontogianni T, Arkoumanis A, Stamatakis A, Poulakakis N, Papageorgopoulou C, Pavlidis P. Psonis N, et al. Genome Biol. 2026 Feb 7;27(1):96. doi: 10.1186/s13059-026-03968-5. Genome Biol. 2026. PMID: 41654922 Free PMC article.

96

Genetic impacts on within-pair DNA methylation variance in monozygotic twins capture gene-environment interactions and cell-type effects.

Zhang X, Yet I, Villicaña S, Castillo-Fernandez J, Mangino M, Hottenga JJ, Tsai PC, Min JL, Falchi M, Wong A, Boomsma DI, Ong KK, van Dongen J, Bell JT. Zhang X, et al. Genome Biol. 2026 Feb 7;27(1):80. doi: 10.1186/s13059-026-03947-w. Genome Biol. 2026. PMID: 41654882 Free PMC article.

97

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.

Saidi S, Blaison M, Del Pilar Rodríguez-Ordóñez M, Confais J, Quesneville H. Saidi S, et al. Genome Biol. 2026 Feb 7;27(1):117. doi: 10.1186/s13059-026-03984-5. Genome Biol. 2026. PMID: 41654859 Free PMC article.

98

PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignment.

Ji Y, Guan J, Liao H, Shang J, Sun Y. Ji Y, et al. Genome Biol. 2026 Feb 7;27(1):79. doi: 10.1186/s13059-026-03966-7. Genome Biol. 2026. PMID: 41654842 Free PMC article.

99

FungiGuard: identification of plant antifungal peptides with artificial intelligence.

Li X, Fang Y, Wu Y, Yu X. Li X, et al. Genome Biol. 2026 Feb 6;27(1):78. doi: 10.1186/s13059-026-03983-6. Genome Biol. 2026. PMID: 41645295 Free PMC article.

100

Quantitative proteomics and phosphoproteomics reveal glucocorticoid stimulation of TLR and Rho GTPase signaling in neutrophil-like cells.

Cho H, Nielsen ML, Olsen JV. Cho H, et al. Genome Biol. 2026 Feb 5;27(1):77. doi: 10.1186/s13059-026-03985-4. Genome Biol. 2026. PMID: 41645235 Free PMC article.

101

UniSyn: a multi-modal framework with knowledge transfer for anti-cancer drug synergy prediction.

Chen Y, Zhang Y, Niu M, Wang J, Ren Z, Zou Q, Song J, Luo X. Chen Y, et al. Genome Biol. 2026 Feb 4;27(1):74. doi: 10.1186/s13059-026-03972-9. Genome Biol. 2026. PMID: 41639919 Free PMC article.

102

SAKURA: a knowledge-guided approach to recovering important, rare signals from single-cell data.

Zhang Z, Chen J, Wu H, Li KY, Adams PD, Itkin-Ansari P, Yip KY. Zhang Z, et al. Genome Biol. 2026 Feb 4;27(1):76. doi: 10.1186/s13059-026-03965-8. Genome Biol. 2026. PMID: 41639748 Free PMC article.

103

Sex-specific nonlinear DNA methylation aging trajectories reveal biomarkers of cancer risk and inflammation.

Grolaux R, Jacques M, Jones-Freeman B, Horvath S, Teschendorff A, Eynon N. Grolaux R, et al. Genome Biol. 2026 Feb 4;27(1):2. doi: 10.1186/s13059-026-03952-z. Genome Biol. 2026. PMID: 41634811 Free PMC article.

104

Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.

Xiao PX, Tan L, Dong J, Huang J, Huang Y, He JB, Su H, Song B, Jiao WB. Xiao PX, et al. Genome Biol. 2026 Feb 3;27(1):70. doi: 10.1186/s13059-026-03980-9. Genome Biol. 2026. PMID: 41634861 Free PMC article.

105

Self-supervised pretraining with NuSPIRe unlocks nuclear morphology-driven insights in spatial omics.

Hua Y, Li S, Zhang Y. Hua Y, et al. Genome Biol. 2026 Feb 3;27(1):71. doi: 10.1186/s13059-026-03987-2. Genome Biol. 2026. PMID: 41634826 Free PMC article.

106

A comprehensive functional atlas of ALK kinase domain variants reveals resistance landscape to ALK inhibitors.

Oh HC, Han Y, Chang Y, Kim HH. Oh HC, et al. Genome Biol. 2026 Feb 3;27(1):72. doi: 10.1186/s13059-026-03977-4. Genome Biol. 2026. PMID: 41630044 Free PMC article.

107

smoppix: unified nonparametric analysis of single-molecule spatial omics data using probabilistic indices.

Hawinkel S, Yang X, Poelmans W, Motte H, Beeckman T, Maere S. Hawinkel S, et al. Genome Biol. 2026 Feb 2;27(1):68. doi: 10.1186/s13059-026-03976-5. Genome Biol. 2026. PMID: 41630030 Free PMC article.

108

Functional correction and genome integrity with duplex base editing of β-thalassemic hematopoietic stem cells.

Papaioannou NY, Patsali P, Klermund J, Papasavva PL, Andrieux G, Koniali L, Naiisseh B, Christou S, Sitarou M, Kleanthous M, Cathomen T, Lederer CW. Papaioannou NY, et al. Genome Biol. 2026 Feb 2;27(1):67. doi: 10.1186/s13059-026-03974-7. Genome Biol. 2026. PMID: 41629994 Free PMC article.

109

The evolutionary history of the field vole species complex revealed by modern and ancient genomes.

Baca M, Bujalska B, Popović D, Golubiński M, Alves PC, Bard E, Berto C, Cuenca-Bescós G, Dalén L, Fewlass H, Fadeeva T, Herman J, Horáček I, Krajcarz M, Law M, Lemanik A, López-García JM, Luzi E, Murelaga X, Mahmoudi A, Peresani M, Parfitt S, Pauperio J, Pavlova SV, Pazonyi P, Rodríguez IR, Searle JB, Stojak J, Strukova T, Wójcik JM, Nadachowski A. Baca M, et al. Genome Biol. 2026 Feb 2;27(1):69. doi: 10.1186/s13059-026-03961-y. Genome Biol. 2026. PMID: 41629962 Free PMC article.

110

PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.

Ye W, Cheng X, Bi X, Wu X. Ye W, et al. Genome Biol. 2026 Jan 31;27(1):65. doi: 10.1186/s13059-026-03963-w. Genome Biol. 2026. PMID: 41620776 Free PMC article.

111

MER57E3 transposable elements regulate gene expression in a human cell model of neural development.

Almeida da Paz M, Yildiz U, Kim M, Campos-Fornés V, Pinkasz M, Dahlet T, Noh KM, Taher L. Almeida da Paz M, et al. Genome Biol. 2026 Jan 31;27(1):66. doi: 10.1186/s13059-026-03946-x. Genome Biol. 2026. PMID: 41620616 Free PMC article.

112

Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effects.

Pahlevan Kakhki M, Rangani F, Ewing E, Starvaggi Cucuzza C, Zheleznyakova G, Kalomoiri M, Kenny L, Raghavan A, Rao Prakash C, van den Hoeven G, Venkata S Badam T, Covacu R, Andreou I, Needhamsen M, Kular L, Jagodic M. Pahlevan Kakhki M, et al. Genome Biol. 2026 Jan 31;27(1):52. doi: 10.1186/s13059-026-03967-6. Genome Biol. 2026. PMID: 41620608 Free PMC article.

113

An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage.

Chen Q, Yang T, Hou Y, Wang K, Li T, Wang L, Dou C, Cheng P, Shi M, Li W. Chen Q, et al. Genome Biol. 2026 Jan 30;27(1):63. doi: 10.1186/s13059-025-03902-1. Genome Biol. 2026. PMID: 41618446 Free PMC article.

114

Resolving sampling and population-size biases in domestication genomics supports a South Asian origin of walnuts.

Chen CJ, Pang XX, Ding YM, Zhang WP, Yang Y, Liu J, Nersesyan A, Zhang BW, Renner SS, Zhang DY, Bai WN. Chen CJ, et al. Genome Biol. 2026 Jan 30;27(1):61. doi: 10.1186/s13059-026-03959-6. Genome Biol. 2026. PMID: 41618441 Free PMC article.

115

Parameter-efficient fine-tuning enables scalable transfer of regulatory sequence models to novel contexts.

Yuan H, Linder J, Kelley DR. Yuan H, et al. Genome Biol. 2026 Jan 30;27(1):60. doi: 10.1186/s13059-026-03935-0. Genome Biol. 2026. PMID: 41618434 Free PMC article.

116

Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.

Wang Y, Zuo W, Huang J, Sun F, Du Y. Wang Y, et al. Genome Biol. 2026 Jan 30;27(1):75. doi: 10.1186/s13059-026-03970-x. Genome Biol. 2026. PMID: 41618433 Free PMC article.

117

RNA2seg: a generalist model for cell segmentation in image-based spatial transcriptomics.

Defard T, Blondel A, Bellow S, Coleon A, Dias de Melo G, Mueller F, Walter T. Defard T, et al. Genome Biol. 2026 Jan 30;27(1):62. doi: 10.1186/s13059-025-03908-9. Genome Biol. 2026. PMID: 41618375 Free PMC article.

118

Understanding liquid-liquid phase separation through TDP-43: fundamental principles, subcellular compartmentalisation, and role of solid inclusion formation.

Bigi A, Chiti F. Bigi A, et al. Genome Biol. 2026 Jan 29;27(1):57. doi: 10.1186/s13059-026-03956-9. Genome Biol. 2026. PMID: 41612406 Free PMC article. Review.

119

Genetic dynamics drive maize growth and breeding.

Wu C, Geng Z, Li W, Ye J, Hao X, Xu J, Jin M, Wu X, Du Y, Chen Y, Ma C, Gao Y, Chen Y, Xie T, Gui S, Chen Y, Luo J, Liu Y, Yang W, Yan J, Yang W, Xiao Y. Wu C, et al. Genome Biol. 2026 Jan 29;27(1):56. doi: 10.1186/s13059-026-03957-8. Genome Biol. 2026. PMID: 41612384 Free PMC article.

120

Resolving clonal evolution and selection of extrachromosomal DNA at single-cell resolution.

Hendriksen JD, Locallo A, Schlotmann BC, González FGR, Skjøth-Rasmussen J, Yde CW, Nørøxe DS, Poulsen HS, Lassen U, Weischenfeldt J. Hendriksen JD, et al. Genome Biol. 2026 Jan 29;27(1):10. doi: 10.1186/s13059-026-03933-2. Genome Biol. 2026. PMID: 41606654 Free PMC article.

121

3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice.

Li Y, Zhang Z, Qiu L, Zheng R, Li H, Cao Z, Guo M, Wang S, Xie L, Guan P, Huang X, Shen C, Wu H, Li W, Ouyang W, Zhang Y, Chen G, Foda M, Yan J, Wu C, Ouyang X, Li G, Xing Y, Li X. Li Y, et al. Genome Biol. 2026 Jan 29;27(1):58. doi: 10.1186/s13059-026-03940-3. Genome Biol. 2026. PMID: 41606643 Free PMC article.

122

Cosmopolitanism in the depths of Barbaricum evidenced by archaeogenomic data from the Late Iron Age Goth community of the Masłomęcz group.

Golubiński M, Baca M, Popović D, Speidel L, Schiffels S, Niezabitowska-Wiśniewska B, Kokowski A, Molak M. Golubiński M, et al. Genome Biol. 2026 Jan 28;27(1):50. doi: 10.1186/s13059-026-03969-4. Genome Biol. 2026. PMID: 41606683 Free PMC article.

123

Genetic associations of circulating plasma proteins with cardiometabolic diseases.

Zhou R, Qiao J, Zhang X, Yang X, Hong W, Cai L, Zhang P, Pauklin S, Yang Y, Xu Z, Feng Y. Zhou R, et al. Genome Biol. 2026 Jan 28;27(1):55. doi: 10.1186/s13059-026-03962-x. Genome Biol. 2026. PMID: 41606682 Free PMC article.

124

stGCL: a versatile cross-modality fusion method based on multi-modal graph contrastive learning for spatial transcriptomics.

Yu N, Zhang D, Zhang W, Liu Z, Qiao X, Wang C, Zhao M, Yue W, Li W, De Marinis Y, Gao R. Yu N, et al. Genome Biol. 2026 Jan 28;27(1):51. doi: 10.1186/s13059-025-03896-w. Genome Biol. 2026. PMID: 41606649 Free PMC article.

125

Rational engineering of combinatorial bacterial therapies for cancer.

Steppe P, O'Connor K, Hasty J. Steppe P, et al. Genome Biol. 2026 Jan 28;27(1):53. doi: 10.1186/s13059-026-03951-0. Genome Biol. 2026. PMID: 41606628 Free PMC article. Review.

126

SCITO-seq2: ultra-high-throughput single-cell transcriptome and epitope sequencing.

Lee SH, Jin BY, Lee CR, Kim DR, Shin A, Park SG, Kim YJ, Kim SH, Choi M, Hwang B. Lee SH, et al. Genome Biol. 2026 Jan 27;27(1):45. doi: 10.1186/s13059-026-03954-x. Genome Biol. 2026. PMID: 41593779 Free PMC article.

127

Expression spectrum of TE-driven transcripts in human adult tissues.

Miao B, Luo X, Ademovic A, Yang Y, Wu TP, Zhang BA. Miao B, et al. Genome Biol. 2026 Jan 27;27(1):54. doi: 10.1186/s13059-025-03898-8. Genome Biol. 2026. PMID: 41593763 Free PMC article.

128

Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.

Lin L, Zheng X, Tao Y, Zhu W, Guan LL, Mao S. Lin L, et al. Genome Biol. 2026 Jan 27;27(1):44. doi: 10.1186/s13059-026-03960-z. Genome Biol. 2026. PMID: 41593747 Free PMC article.

129

Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace.

Freudenberg J, Rao J, Howard MK, Macdonald C, Greenwald NF, Coyote-Maestas W, Pimentel H. Freudenberg J, et al. Genome Biol. 2026 Jan 27;27(1):48. doi: 10.1186/s13059-026-03934-1. Genome Biol. 2026. PMID: 41593735 Free PMC article.

130

Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.

Yao X, Xu Z, Xi Y, He X, Gao Q, Lu J, Fu P. Yao X, et al. Genome Biol. 2026 Jan 27;27(1):43. doi: 10.1186/s13059-025-03904-z. Genome Biol. 2026. PMID: 41593733 Free PMC article.

131

Campolina: a deep neural framework for accurate segmentation of nanopore signals.

Bakić S, Friganović K, Hooi B, Šikić M. Bakić S, et al. Genome Biol. 2026 Jan 27;27(1):46. doi: 10.1186/s13059-026-03950-1. Genome Biol. 2026. PMID: 41593700 Free PMC article.

132

Engineering hypercompact IscB nucleases for efficient and versatile genome editing in rice.

Zhu J, Li Y, Yu C, Huang W, Chen J, Liu X, Qin R, Li J, Xu R, Wei P. Zhu J, et al. Genome Biol. 2026 Jan 27;27(1):49. doi: 10.1186/s13059-026-03953-y. Genome Biol. 2026. PMID: 41593699 Free PMC article.

133

Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes.

Shi LD, Penev PI, Nissley AJ, Nayak DD, Sachdeva R, Cate JHD, Banfield JF. Shi LD, et al. Genome Biol. 2026 Jan 27;27(1):42. doi: 10.1186/s13059-025-03903-0. Genome Biol. 2026. PMID: 41593673 Free PMC article.

134

omnideconv: a unifying framework for using and benchmarking single-cell-informed deconvolution of bulk RNA-seq data.

Dietrich A, Merotto L, Pelz K, Eder B, Zackl C, Reinisch K, Edenhofer F, Marini F, Sturm G, List M, Finotello F. Dietrich A, et al. Genome Biol. 2026 Jan 26;27(1):6. doi: 10.1186/s13059-026-03955-w. Genome Biol. 2026. PMID: 41582216 Free PMC article.

135

Multiomics profiling reveals the adaptive responses of largemouth bass to high temperature stress.

Guan W, Yu Y, Zhang J, Jian J, Niu B, Lou B, Hu D, Xu X. Guan W, et al. Genome Biol. 2026 Jan 22;27(1):40. doi: 10.1186/s13059-026-03964-9. Genome Biol. 2026. PMID: 41572355 Free PMC article.

136

Evaluating deconvolution methods using real bulk RNA-expression data for robust prognostic insights across cancer types.

Li M, Su Y, Tang Y, Lee Y, Tian W. Li M, et al. Genome Biol. 2026 Jan 21;27(1):38. doi: 10.1186/s13059-026-03942-1. Genome Biol. 2026. PMID: 41566530 Free PMC article.

137

Harmonizing single-cell 3D genome data with STARK and scNucleome.

Jiang WJ, Cai K, Sun Y, Liu A, Zhu H, Gao R, Zhong C, Wei N, Lai F, Fei T, Wang YJ, Zheng X, Xu M, Wu HJ. Jiang WJ, et al. Genome Biol. 2026 Jan 21;27(1):82. doi: 10.1186/s13059-026-03938-x. Genome Biol. 2026. PMID: 41566400 Free PMC article.

138

Comprehensive assessment of activity, specificity, and safety of hypercompact TnpB systems for gene editing.

Xin C, Xiang G, Cao S, Wang Y, Yuan S, Liu X, Huo Y, Sun J, Wan X, Liu D, Hong J, Hu J, Wang H. Xin C, et al. Genome Biol. 2026 Jan 21;27(1):39. doi: 10.1186/s13059-026-03949-8. Genome Biol. 2026. PMID: 41566394 Free PMC article.

139

Dissecting the contribution of transposable elements to interphase chromosome structure.

Shi L, Xiao Z, Zhou X, Babarinde IA, Fu X, Ma G, Huang Z, Sun L, He J, Strunnikov A, Hutchins AP. Shi L, et al. Genome Biol. 2026 Jan 20;27(1):36. doi: 10.1186/s13059-026-03945-y. Genome Biol. 2026. PMID: 41559820 Free PMC article.

140

Blood-based DNA methylation captures variance in adult height.

Hatton AA, Hillary RF, McCartney DL, Harris SE, Cox SR, Evans KL, Walker RM, Suderman M, Yousefi P, McRae AF, Marioni RE. Hatton AA, et al. Genome Biol. 2026 Jan 20;27(1):37. doi: 10.1186/s13059-025-03918-7. Genome Biol. 2026. PMID: 41559797 Free PMC article.

141

Genomic basis underlying alternative transcripts-mediated drought tolerance in maize.

Hao S, Han S, He Z, Dou N, Yu Z, Liu X, Wang X, Zhang Y, Dai M, Sun X. Hao S, et al. Genome Biol. 2026 Jan 20;27(1):47. doi: 10.1186/s13059-026-03939-w. Genome Biol. 2026. PMID: 41559689 Free PMC article.

142

CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

He Z, Sun Y, Li H, Sun C, Yang X, Chen H, Liao M, Bo X. He Z, et al. Genome Biol. 2026 Jan 19;27(1):35. doi: 10.1186/s13059-026-03948-9. Genome Biol. 2026. PMID: 41555433 Free PMC article.

143

TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data.

Herrmann M, Krebs Y, Acosta FM, Parusel S, Siering O, Andres FGM, Taye B, Miskey C, Pfaller CK. Herrmann M, et al. Genome Biol. 2026 Jan 19;27(1):5. doi: 10.1186/s13059-026-03941-2. Genome Biol. 2026. PMID: 41549280 Free PMC article.

144

Exploring differences in the human gut microbiome between Han Chinese and non-Chinese populations.

Wang J, Zhang Z, Chen Y, Zhou X, Xiang J, Yang C, Rodionov DA, Osterman AL, Qiu Q, Deng Y, Liu Y, Wang C, Shang X, Huang L, Sun C, Guo J, Yang Z, Zhai L, Bian Z, Lyu A, Han L, Jia W, Fang X, Zhang L. Wang J, et al. Genome Biol. 2026 Jan 17;27(1):34. doi: 10.1186/s13059-026-03932-3. Genome Biol. 2026. PMID: 41545888 Free PMC article.

145

An inflammatory and quiescent HSC subpopulation expands with age in humans.

Safina KR, Salik B, Kotliar D, Curtis M, Good JD, Weng C, David S, Raychaudhuri S, Kreso A, Trowbridge JJ, Sankaran VG, van Galen P. Safina KR, et al. Genome Biol. 2026 Jan 16;27(1):30. doi: 10.1186/s13059-026-03936-z. Genome Biol. 2026. PMID: 41546063 Free PMC article.

146

Neighborhood nonnegative matrix factorization identifies patterns and spatially-variable genes in large-scale spatial transcriptomics data.

Laursen R, Chen H, Demaray J, Pelka K, Engelhardt BE. Laursen R, et al. Genome Biol. 2026 Jan 16;27(1):31. doi: 10.1186/s13059-025-03846-6. Genome Biol. 2026. PMID: 41546049 Free PMC article.

147

Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress.

Fulcher JM, Dawar P, Balasubramanian VK, Williams SM, Nadeau KD, Winkler TE, Markillie LM, Mitchell HD, Ahkami AH, Paša-Tolić L, Zhu Y. Fulcher JM, et al. Genome Biol. 2026 Jan 16;27(1):32. doi: 10.1186/s13059-025-03919-6. Genome Biol. 2026. PMID: 41546014 Free PMC article.

148

Tracing bronze to iron age population dynamics in Northwest Xinjiang using ancient time-series genomic data.

Zhao X, Zhang D, Sun B, Yang S, Qi Y, An W, Li C, Niyazi A, Wang K, Cui Y. Zhao X, et al. Genome Biol. 2026 Jan 16;27(1):33. doi: 10.1186/s13059-026-03943-0. Genome Biol. 2026. PMID: 41540458 Free PMC article.

149

Ancient DNA study provides clues to leprosy susceptibility in medieval Europe.

Romeyer-Dherbey JH, Caliebe A, Ӧzer O, da Silva NA, Mejía NM, Myburgh DA, Fuchs K, Pedersen DD, Boldsen J, Larsen LA, Seeberg L, Søvsø M, Rieger D, Prescher A, Nebel A, Krause-Kyora B. Romeyer-Dherbey JH, et al. Genome Biol. 2026 Jan 16;27(1):4. doi: 10.1186/s13059-025-03925-8. Genome Biol. 2026. PMID: 41540446 Free PMC article.

150

VIST: variational inference for single cell time series.

Xu B, Braun R. Xu B, et al. Genome Biol. 2026 Jan 15;27(1):29. doi: 10.1186/s13059-025-03874-2. Genome Biol. 2026. PMID: 41535949 Free PMC article.

151

Whole genome sequence analysis of pulmonary function and COPD in 44,287 multi-ancestry participants.

Kim W, Hu X, Kim K, Chun S, Orchard P, Qiao D, Ruczinski I, Saferali A, Aguet F, Antonacci-Fulton L, Balte PP, Bartz TM, Anamika WJ, Zhou X, Duan J, Brody JA, Cade BE, Daviglus ML, Doddapaneni H, Dugan-Perez S, Dutcher SK, Frazar CD, Gabriel SB, Gharib SA, Gupta N, Hobbs BD, Kasela S, Loehr LR, Metcalf GA, Muzny DM, Oelsner EC, Rasmussen-Torvik LJ, Sitlani CM, Smith J, Sofer T, Xu H, Yu B, Zhang D, Ziniti J, Barr RG, Carson AP, Fornage M, Hou L, Kalhan R, Kaplan R, Lappalainen T, London SJ, Morrison AC, O'Connor GT, Psaty BM, Raffield LM, Redline S, Rich SS, Rotter JI, Silverman EK, Manichaikul A, Cho MH. Kim W, et al. Genome Biol. 2026 Jan 15;27(1):28. doi: 10.1186/s13059-025-03921-y. Genome Biol. 2026. PMID: 41535900 Free PMC article.

152

FSBLUP: a novel strategy of fusion similarity matrix construction via optimally integrating intermediate omics data to enhance genomic prediction.

Xue Y, Zhou L, Zhuo Y, Li W, Ma S, Du H, Li W, Jiang J, Liu JF. Xue Y, et al. Genome Biol. 2026 Jan 14;27(1):27. doi: 10.1186/s13059-026-03931-4. Genome Biol. 2026. PMID: 41535974 Free PMC article.

153

Non-negative matrix factorization and deconvolution as a dual simplex problem.

Kleverov D, Aladyeva E, Serdyukov A, Artyomov MN. Kleverov D, et al. Genome Biol. 2026 Jan 14;27(1):25. doi: 10.1186/s13059-025-03910-1. Genome Biol. 2026. PMID: 41535969 Free PMC article.

154

O-GlcNAcylation of NONO mediates alternative splicing of SETMAR and facilitates NHEJ repair.

Li M, Tian H, Zhou Z, Jiang Y, Guo X, Qin W, Zhang H, Jiao Y, Guo S, Wu C. Li M, et al. Genome Biol. 2026 Jan 14;27(1):26. doi: 10.1186/s13059-026-03930-5. Genome Biol. 2026. PMID: 41535889 Free PMC article.

155

baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.

Roskams-Hieter B, Almelid Ø, Ponting CP. Roskams-Hieter B, et al. Genome Biol. 2026 Jan 13;27(1):24. doi: 10.1186/s13059-025-03916-9. Genome Biol. 2026. PMID: 41526967 Free PMC article.

156

SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.

Munteanu V, Saldana MA, Dreifuss D, Ouyang WO, Ferdous J, Mohebbi F, Roseberry JS, Ciorba D, Bostan V, Gordeev V, Drabcinski N, Su JM, Kasianchuk N, Sharma NK, Knyazev S, Aßmann E, Lobiuc A, Covasa M, Crandall KA, Wu NC, Mason CE, Tierney BT, Lucaci AG, Ophoff RA, Gibas C, Rzymski P, Skums P, Solo-Gabriele H, Niko B, Zelikovsky A, Hölzer M, Smith A, Mangul S. Munteanu V, et al. Genome Biol. 2026 Jan 12;27(1):1. doi: 10.1186/s13059-025-03927-6. Genome Biol. 2026. PMID: 41526978 Free PMC article. Review.

157

A technical comparison of spatial transcriptomics platforms across six cancer types.

Cervilla S, Grases D, Perez E, Real FX, Musulen E, Aprea J, Esteller M, Porta-Pardo E. Cervilla S, et al. Genome Biol. 2026 Jan 12;27(1):22. doi: 10.1186/s13059-026-03937-y. Genome Biol. 2026. PMID: 41526977 Free PMC article.

158

SDrecall: a sensitive approach for variant detection in segmental duplications.

Yang XT, She CH, Zhang C, Leung D, Yang J, Chan KW, Duque JSR, Lau YL, Yang W. Yang XT, et al. Genome Biol. 2026 Jan 12;27(1):23. doi: 10.1186/s13059-025-03928-5. Genome Biol. 2026. PMID: 41526966 Free PMC article.

159

Differential expression analysis for spatially correlated data using smiDE.

Vasconcelos AG, McGuire D, Simon N, Danaher P, Shojaie A. Vasconcelos AG, et al. Genome Biol. 2026 Jan 10;27(1):21. doi: 10.1186/s13059-025-03867-1. Genome Biol. 2026. PMID: 41519776 Free PMC article.

160

Cross-species prediction of histone modifications in plants via deep learning.

Lv T, Han Q, Li Y, Liang C, Ruan Z, Chao H, Chen M, Chen D. Lv T, et al. Genome Biol. 2026 Jan 9;27(1):20. doi: 10.1186/s13059-025-03929-4. Genome Biol. 2026. PMID: 41514301 Free PMC article.

161

Predicting enviromically adapted varieties with big data.

Gogna A, Kamali B, Wimmer V, Schmidt RH, Rezaei EE, Eckhoff WM, Reif JC, Zhao Y. Gogna A, et al. Genome Biol. 2026 Jan 7;27(1):3. doi: 10.1186/s13059-025-03914-x. Genome Biol. 2026. PMID: 41495804 Free PMC article.

162

Deep-learning prediction of gene expression from personal genomes.

Drusinsky S, Whalen S, Pollard KS. Drusinsky S, et al. Genome Biol. 2026 Jan 6;27(1):19. doi: 10.1186/s13059-025-03926-7. Genome Biol. 2026. PMID: 41495833 Free PMC article.

163

Genetic diversity and architectural dynamics of soybean centromeres.

Huang Y, Guan E, Song S, Koo DH, Schmidt MA, Su H, Chen C, Zhang J. Huang Y, et al. Genome Biol. 2026 Jan 5;27(1):17. doi: 10.1186/s13059-025-03924-9. Genome Biol. 2026. PMID: 41491959 Free PMC article.

164

Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.

Wang R, Zhang W, He Z, Zhou Y, Chen C, Song K, Shang Q, Wu Y, Gu P, Shu D, Zhao L. Wang R, et al. Genome Biol. 2026 Jan 5;27(1):13. doi: 10.1186/s13059-025-03905-y. Genome Biol. 2026. PMID: 41491699 Free PMC article.

165

Haplotype applications in genomic selection.

MacNish TR, Bergmann T, Edwards D. MacNish TR, et al. Genome Biol. 2026 Jan 5;27(1):18. doi: 10.1186/s13059-025-03913-y. Genome Biol. 2026. PMID: 41491493 Free PMC article. Review.

166

Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.

Wen M, Liang X, Shi K, Fei L, Wang Y, Zhou Y, Wang K. Wen M, et al. Genome Biol. 2026 Jan 2;27(1):12. doi: 10.1186/s13059-025-03907-w. Genome Biol. 2026. PMID: 41484656 Free PMC article.

167

Unravelling the progression of the zebrafish primary body axis with reconstructed spatiotemporal transcriptomics.

Dong Y, Cheng T, Liu X, Fu XX, Hu Y, Yang XF, Yang LE, Li HR, Bian ZW, Jing N, Liao J, Fan X, Xu PF. Dong Y, et al. Genome Biol. 2026 Jan 2;27(1):11. doi: 10.1186/s13059-025-03917-8. Genome Biol. 2026. PMID: 41484648 Free PMC article.

168

The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks.

Ronai I, de Paula Baptista R, Paulat NS, Frederick JC, Azagi T, Bakker JW, Dillon KC, Sprong H, Ray DA, Glenn TC. Ronai I, et al. Genome Biol. 2026 Jan 2;27(1):41. doi: 10.1186/s13059-025-03909-8. Genome Biol. 2026. PMID: 41484638 Free PMC article.

169

Coordinated single-nucleus responses for quantitative disease resistance involve a calcium-associated switch in transcriptional noise.

Jones DAB, Delplace F, Khafif M, Zaffuto M, Xiong TC, Barbacci A, Raffaele S. Jones DAB, et al. Genome Biol. 2025 Dec 31;27(1):14. doi: 10.1186/s13059-025-03906-x. Genome Biol. 2025. PMID: 41469724 Free PMC article.

170

Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.

Catry A, Abrouk D, Fierling N, Mendoza AIS, Rey M, Vesga P, Heiman CM, Garrido-Sanz D, Bouffaud ML, Buscot F, Giongo A, Smalla K, Comte G, Keel C, Muller D, Moënne-Loccoz Y. Catry A, et al. Genome Biol. 2025 Dec 28;27(1):16. doi: 10.1186/s13059-025-03911-0. Genome Biol. 2025. PMID: 41457274 Free PMC article.

171

BASCULE: bayesian inference and clustering of mutational signatures leveraging biological priors.

Buscaroli E, Sadr A, Bergamin R, Milite S, Villegas Garcia EN, Tasciotti A, Ansuini A, Ramazzotti D, Calonaci N, Caravagna G. Buscaroli E, et al. Genome Biol. 2025 Dec 27;27(1):15. doi: 10.1186/s13059-025-03835-9. Genome Biol. 2025. PMID: 41456010 Free PMC article.

172

HUBMet: an integrative database and analytical platform for human blood metabolites and metabolite-protein associations.

Wang X, Qiao X, Zenere A, Barde S, Wang J, Zhong W. Wang X, et al. Genome Biol. 2025 Dec 27;27(1):7. doi: 10.1186/s13059-025-03922-x. Genome Biol. 2025. PMID: 41455991 Free PMC article.

173

The differential subcellular localization of soybean transcripts, an additional regulatory mechanism of gene activity.

Tennant S, Amezquita EJ, Li Y, Smith B, Subramanyam SSMV, Cervantes-Pérez SA, Thibivilliers S, Bhattacharya S, Klaver J, Libault M. Tennant S, et al. Genome Biol. 2025 Dec 27;27(1):9. doi: 10.1186/s13059-025-03920-z. Genome Biol. 2025. PMID: 41454350 Free PMC article.

174

Correction: Fine-tuning sugar content in strawberry.

Xing S, Chen K, Zhu H, Zhang R, Zhang H, Li B, Gao C. Xing S, et al. Genome Biol. 2025 Dec 24;26(1):435. doi: 10.1186/s13059-025-03894-y. Genome Biol. 2025. PMID: 41444675 Free PMC article. No abstract available.

175

Sorghum embryos undergoing B chromosome elimination express B-variants of mitotic-related genes.

Bojdová T, Hloušková L, Holušová K, Svačina R, Hřibová E, Ilíková I, Thiel J, Kim G, Pleskot R, Houben A, Bartoš J, Karafiátová M. Bojdová T, et al. Genome Biol. 2025 Dec 24;27(1):8. doi: 10.1186/s13059-025-03915-w. Genome Biol. 2025. PMID: 41437077 Free PMC article.

176

PepQueryMHC: rapid and comprehensive tumor antigen prioritization from immunopeptidomics data.

Choi S, Zhang B. Choi S, et al. Genome Biol. 2025 Dec 23;26(1):434. doi: 10.1186/s13059-025-03923-w. Genome Biol. 2025. PMID: 41437377 Free PMC article.

177

Comparative assessment of SNP genotyping assays for challenging forensic samples utilizing ancient DNA methods.

Staadig A, Krzewińska M, Sidstedt M, Kling D, Fagerholm SA, Ansell R, Götherström A, Tillmar A. Staadig A, et al. Genome Biol. 2025 Dec 23;26(1):433. doi: 10.1186/s13059-025-03912-z. Genome Biol. 2025. PMID: 41430704 Free PMC article.

178

Multi-omics dissection of the genetic regulation underlying fatty acid composition in cattle.

Zhang T, Niu Q, Wang T, Wu J, Zhu B, Wang Z, Gao X, Chen Y, Gao H, Zhang L, Fu T, Gao T, Liu GE, Li J, Xu L. Zhang T, et al. Genome Biol. 2025 Dec 22;26(1):432. doi: 10.1186/s13059-025-03885-z. Genome Biol. 2025. PMID: 41430323 Free PMC article.

179

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.

D'Asaro D, Arbona JM, Piveteau V, Piazza A, Vaillant C, Jost D. D'Asaro D, et al. Genome Biol. 2025 Dec 22;26(1):431. doi: 10.1186/s13059-025-03872-4. Genome Biol. 2025. PMID: 41430292 Free PMC article.

180

Antisense transcription can induce expression memory via stable promoter repression.

Mutzel V, Schwämmle T, Oeverdieck S, Librenjak L, Boesen B, Bothe M, Gjaltema RAF, Dunkel I, Noviello G, Schulz EG. Mutzel V, et al. Genome Biol. 2025 Dec 20;26(1):430. doi: 10.1186/s13059-025-03875-1. Genome Biol. 2025. PMID: 41422243 Free PMC article.

181

A robust workflow to benchmark deconvolution of multi-omic data.

Amblard E, Bertrand V, Barbot H, Martin Peña L, Karkar S, Chuffart F, Ayadi M, Baurès A, Armenoult L, Kermezli Y, Causeur D, Cros J, Blum Y, Richard M. Amblard E, et al. Genome Biol. 2025 Dec 17;26(1):429. doi: 10.1186/s13059-025-03897-9. Genome Biol. 2025. PMID: 41408313 Free PMC article.

182

ST-FFPE-mIF: integrating spatial transcriptomics and multiplex immunofluorescence in formalin-fixed paraffin-embedded tissues using Stereo-seq.

Zhang X, Zhang M, Xu Y, Song Y, Yang X, Wu Y, Zhao X, Ran D, Liu X, Huang H, Lei W, Li H, Zhang Y, Xi F, Li G, Liu X, Xu L, Chen A, Liao S, Zhang J. Zhang X, et al. Genome Biol. 2025 Dec 16;26(1):428. doi: 10.1186/s13059-025-03900-3. Genome Biol. 2025. PMID: 41402878 Free PMC article.

183

Spatial transcriptomic alignment, integration, and 3D reconstruction by STAIR.

Yu Y, Xie Z. Yu Y, et al. Genome Biol. 2025 Dec 15;26(1):427. doi: 10.1186/s13059-025-03895-x. Genome Biol. 2025. PMID: 41398698 Free PMC article.

184

The repertoire of short tandem repeats across the tree of life.

Chantzi N, Georgakopoulos-Soares I. Chantzi N, et al. Genome Biol. 2025 Dec 12;26(1):425. doi: 10.1186/s13059-025-03893-z. Genome Biol. 2025. PMID: 41388549 Free PMC article.

185

A single-cell atlas of RNA alternative splicing in the glioma-immune ecosystem.

Song X, Tiek D, Lu M, Yu X, Wu R, Walker M, He Q, Sisbarro D, Hu B, Cheng SY. Song X, et al. Genome Biol. 2025 Dec 12;26(1):426. doi: 10.1186/s13059-025-03889-9. Genome Biol. 2025. PMID: 41387900 Free PMC article.

186

A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing.

Zhao R, Lu J, Li Y, Zhou W, Zhao N, Ji H. Zhao R, et al. Genome Biol. 2025 Dec 11;26(1):424. doi: 10.1186/s13059-025-03887-x. Genome Biol. 2025. PMID: 41382205 Free PMC article.

187

Correction: iNOME-seq: in vivo simultaneous genome-wide mapping of chromatin accessibility, nucleosome positioning, DNA-binding protein sites, and DNA methylation in Arabidopsis.

Hussain N, Merritt R, Engelhorn J, Antunez-Sanchez J, Wibowo A, Latrasse D, Wrightsman T, Collenberg M, Bezrukov I, Alotaibi H, Carrasco E, Benhamed M, Weigel D, Zabet NR, Gutierrez-Marcos J. Hussain N, et al. Genome Biol. 2025 Dec 10;26(1):423. doi: 10.1186/s13059-025-03888-w. Genome Biol. 2025. PMID: 41373012 Free PMC article. No abstract available.

188

Transcriptional dynamics and chromatin accessibility in the regulation of shade-responsive genes in Arabidopsis.

Paulišić S, Boccaccini A, Dreos R, Ambrosini G, Guex N, Benstein RM, Schmid M, Fankhauser C. Paulišić S, et al. Genome Biol. 2025 Dec 10;26(1):422. doi: 10.1186/s13059-025-03901-2. Genome Biol. 2025. PMID: 41372949 Free PMC article.

189

Ancient genomes give insight into 160,000 years of East Asian population dynamics and biological adaptation.

He G, Sun Y, Duan S, Luo L, Sun Q, Li B, Yun L, Liu C, Wang M. He G, et al. Genome Biol. 2025 Dec 10;26(1):420. doi: 10.1186/s13059-025-03859-1. Genome Biol. 2025. PMID: 41372915 Free PMC article. Review.

190

RAMEN: Dissecting individual, additive and interactive gene-environment contributions to DNA methylome variability in cord blood.

Navarro-Delgado EI, Czamara D, Edwards K, Fu MP, Merrill SM, Konwar C, MacIsaac JL, Lin DTS, Mandhane P, Simons E, Subbarao P, Moraes TJ, Lahti J, Miller GE, Binder EB, Räikkönen K, Turvey SE, Korthauer K, Kobor MS. Navarro-Delgado EI, et al. Genome Biol. 2025 Dec 10;26(1):421. doi: 10.1186/s13059-025-03864-4. Genome Biol. 2025. PMID: 41372765 Free PMC article.

191

Distinct roles of histone H2B ubiquitination at promoters and coding regions of Pol II-transcribed stress genes.

Barrios R, Vega M, Gracia-Domingo R, Boronat S, García-Santamarina S, Tanny JC, Ayté J, Hidalgo E. Barrios R, et al. Genome Biol. 2025 Dec 9;26(1):419. doi: 10.1186/s13059-025-03891-1. Genome Biol. 2025. PMID: 41366798 Free PMC article.

192

AP1 is a pioneer transcription factor that programmes cell fate through MADS-domain protein tetramerisation.

Xu X, Neumann M, Carew F, Chen P, Braeuning C, Zubieta C, Muino JM, Smaczniak C, Kaufmann K. Xu X, et al. Genome Biol. 2025 Dec 9;26(1):418. doi: 10.1186/s13059-025-03884-0. Genome Biol. 2025. PMID: 41366461 Free PMC article.

193

Identifying cell-type-specific spatially variable genes with ctSVG.

Zhuang H, Shang X, Hou W, Ji Z. Zhuang H, et al. Genome Biol. 2025 Dec 8;26(1):416. doi: 10.1186/s13059-025-03870-6. Genome Biol. 2025. PMID: 41361894 Free PMC article.

194

Methylome-wide association studies and epigenetic biomarker development for 133 mass spectrometry-assessed circulating proteins in 14,671 Generation Scotland participants.

Robertson JA, Bajzik J, Vernardis S, Chybowska AD, McCartney DL, Grauslys A, Mur J, Smith HM, Campbell A, Drake C, Grant H, Pearce J, Russ TC, Adkin P, White M, Brigden C, Messner CB, Porteous DJ, Hayward C, Cox SR, Zelezniak A, Ralser M, Robinson MR, Marioni RE. Robertson JA, et al. Genome Biol. 2025 Dec 8;26(1):417. doi: 10.1186/s13059-025-03892-0. Genome Biol. 2025. PMID: 41361833 Free PMC article.

195

Unraveling genome- and immunome-wide genetic diversity in modern and historical Jaguars.

Meißner R, Winter S, Elbers JP, Plášil M, Futas J, Mohandesan E, Sharif MB, Horin P, Prost S, Burger P. Meißner R, et al. Genome Biol. 2025 Dec 8;26(1):415. doi: 10.1186/s13059-025-03868-0. Genome Biol. 2025. PMID: 41361788 Free PMC article.

196

3D chromatin-based variant-to-gene maps across 57 human cell types reveal the cellular and genetic architecture of autoimmune disease susceptibility.

Trang KB, Sharma P, Cook L, Mount Z, Thomas RM, Kulkarni NN, Cabrera EC, Rachimi S, Pahl MC, Pippin JA, Su C, Kaestner KH, O'Brien JM, Wagley Y, Hankenson KD, Jermusyk A, Hoskins JW, Amundadottir LT, Xu M, Brown KM, Anderson SA, Yang W, Titchenell PM, Seale P, Zemel BS, Chesi A, Romberg N, Levings MK, Grant SFA, Wells AD. Trang KB, et al. Genome Biol. 2025 Dec 8;26(1):414. doi: 10.1186/s13059-025-03880-4. Genome Biol. 2025. PMID: 41361473 Free PMC article.

197

Large DNA and protein language models enhance discovery of deleterious mutations in maize.

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Bamdam: a post-mapping authentication toolkit for ancient metagenomics.

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CRISPR-Cas9-induced double-strand breaks disrupt maintenance of epigenetic information.

Wang M, Zhang Y, Bi C, Li M. Wang M, et al. Genome Biol. 2025 Dec 3;26(1):411. doi: 10.1186/s13059-025-03851-9. Genome Biol. 2025. PMID: 41331675 Free PMC article.

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SwitchTFI: identifying transcription factors driving cell differentiation.

Martini P, Hartebrodt A, de Almeida GP, Hackstein CP, Zehn D, Blumenthal DB. Martini P, et al. Genome Biol. 2025 Dec 2;26(1):410. doi: 10.1186/s13059-025-03876-0. Genome Biol. 2025. PMID: 41331466 Free PMC article.

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