"Gigascience"[Journal] - Search Results

Year	Number of Results
2012	18
2013	17
2014	36
2015	65
2016	50
2017	126
2018	169
2019	173
2020	163
2021	105
2022	239
2023	7
2024	118
2025	169
2026	58

1

MIFE and MIFD: Minimum information for fermentation experiments and devices.

Georgakilas GK, Metcalfe B, Bize A, Crowther M, Fernandez E, Alonso Villela SM, Owen S, Wittner R, Corrales DC, von Gladiss A, Blomberg P, Andrabi M, Aceves Lara CA, Mattila H, Wiebe M, Dalamagas T, Koehorst JJ. Georgakilas GK, et al. Gigascience. 2026 Apr 9:giag038. doi: 10.1093/gigascience/giag038. Online ahead of print. Gigascience. 2026. PMID: 41967014 Free article.

2

Community-curated Galaxy interfaces with the Galaxy Labs Engine.

Hyde CJ, Syme A, Batut B, Zierep PF, Mok W, Bacon WA, Price GR. Hyde CJ, et al. Gigascience. 2026 Apr 8:giag041. doi: 10.1093/gigascience/giag041. Online ahead of print. Gigascience. 2026. PMID: 41964931 Free article.

3

GEfetch2R: fetching single-cell/bulk RNA-seq data from public repositories to R and benchmarking the subsequent format conversion tools.

Song Y, Wang J, Gao J. Song Y, et al. Gigascience. 2026 Apr 8:giag039. doi: 10.1093/gigascience/giag039. Online ahead of print. Gigascience. 2026. PMID: 41964930 Free article.

4

HVRLocator: A Computationally Efficient Tool for Identifying Hypervariable Regions in Large 16S rRNA Datasets.

Arboleda-Baena C, Correa FB, Saraiva JP, Castillo-Rivadeneira S, Kasmanas JC, Chatzinotas A, Jurburg SD. Arboleda-Baena C, et al. Gigascience. 2026 Apr 8:giag040. doi: 10.1093/gigascience/giag040. Online ahead of print. Gigascience. 2026. PMID: 41964929 Free article.

5

Comparative analysis of 163 ant genomes reveals recurrent horizontal gene transfer from bacteria to ants.

Rinke JL, Franke L, He D, Fischer ML, Vizueta J, Eicholt LA, Larsen RS, Xiong Z, Cunningham P, Henry LM, Kaltenpoth M, Gadau J, Zhang G, Boomsma JJ, Schrader L. Rinke JL, et al. Gigascience. 2026 Apr 6:giag043. doi: 10.1093/gigascience/giag043. Online ahead of print. Gigascience. 2026. PMID: 41947428 Free article.

6

NEXT-scASV: A Nextflow Pipeline for Allele-Specific Variants Calling from single cell RNA-seq data.

Shevtsov A, Buyan A, Nozdrin V, Akhtyamov P, Stupnikov A, Meshcheryakov G, Kulakovskiy IV, Medvedeva YA. Shevtsov A, et al. Gigascience. 2026 Apr 6:giag042. doi: 10.1093/gigascience/giag042. Online ahead of print. Gigascience. 2026. PMID: 41947412 Free article.

7

MicroFinder: conserved gene-set mapping and assembly ordering for manual curation of bird dot microchromosomes.

Mathers TC, Paulini M, Sotero-Caio CG, Wood JMD. Mathers TC, et al. Gigascience. 2026 Apr 3:giag036. doi: 10.1093/gigascience/giag036. Online ahead of print. Gigascience. 2026. PMID: 41934175 Free article.

8

Cancer genome standards for long-read sequencing using cancer cell line mixtures.

Zhang J, Wong HY, Liu L, Koufariotis LT, Wood S, Fitzpatrick N, Quiatchon J, Collins P, Pearson JV, Waddell N. Zhang J, et al. Gigascience. 2026 Apr 3:giag037. doi: 10.1093/gigascience/giag037. Online ahead of print. Gigascience. 2026. PMID: 41934171 Free article.

9

scDenorm: a denormalisation tool for integrating single-cell transcriptomics data.

Huang Y, Pournara AV, Ao Y, Huang Z, Zhang H, Zhang Y, Liu S, Brazma A, Papatheodorou I, Yang X, Shi M, Miao Z. Huang Y, et al. Gigascience. 2026 Mar 31:giag032. doi: 10.1093/gigascience/giag032. Online ahead of print. Gigascience. 2026. PMID: 41915012 Free article.

10

What needs to be standardized for reliable, reproducible, and robust tractography?

Legarreta JH, Schiavi S, Tang W, Banks G, Cieslak M, Schilling K, De Luca A, Tournier JD, Kruper J, Rheault F, Sotiropoulos SN, Pestilli F, Veraart J, Yang JY, Descoteaux M, Heilbronner S, Rokem A. Legarreta JH, et al. Gigascience. 2026 Mar 25:giag034. doi: 10.1093/gigascience/giag034. Online ahead of print. Gigascience. 2026. PMID: 41880537 Free article.

11

Dissecting glioblastoma risk signatures in the tumor immune microenvironment based on multi-dimensional transcriptomics.

Li T, Mi W, Yan H, Ma Y, Jiang H, Yang X, Zhang Y, Hu C. Li T, et al. Gigascience. 2026 Mar 25:giag035. doi: 10.1093/gigascience/giag035. Online ahead of print. Gigascience. 2026. PMID: 41880523 Free article.

12

SMIntegration: A Web Tool for Comprehensive Spatial Metabolomics and Transcriptomics Integrated Analysis and Visualization.

Deng H, Ning X, Lin X, Zong L, Zheng S, Zhao Y, Wang J, Chen L, Zi J, Mei Z. Deng H, et al. Gigascience. 2026 Mar 24:giag033. doi: 10.1093/gigascience/giag033. Online ahead of print. Gigascience. 2026. PMID: 41874432 Free article.

13

Sex Chromosome Turnover and Structural Genome Divergence Shapes Meiotic Outcomes in Hybridising Cobitis.

Schlebusch SA, Trifonov V, Halenková Z, Klianitskaya M, Dedukh D, Ruiz-Herrera A, Álvarez-González L, Pujol G, Hřibová E, Andjel L, Bartoš O, Pajer P, Tichopád T, Kulik D, Kotusz J, Kaštánková Doležálková M, Böhne A, Marta A, Horna P, Reifová R, Guiguen Y, Kuhl H, Pačes J, Janko K. Schlebusch SA, et al. Gigascience. 2026 Mar 24:giag031. doi: 10.1093/gigascience/giag031. Online ahead of print. Gigascience. 2026. PMID: 41874414 Free article.

14

MADRe: Strain-level Metagenomic Classification Through Assembly-Driven Database Reduction.

Lipovac J, Šikić M, Vicedomini R, Križanović K. Lipovac J, et al. Gigascience. 2026 Mar 23:giag030. doi: 10.1093/gigascience/giag030. Online ahead of print. Gigascience. 2026. PMID: 41871361 Free article.

15

Characterising a species-rich and understudied tropical insect fauna using DNA barcoding.

Hemprich-Bennett DR, Donkor E, Adams B, Acquaah NA, Ofori ED, Anie-Amoah S, Bailey A, Godfray HCJ, Lewis OT, Aboagye-Antwi F, Hackett TD. Hemprich-Bennett DR, et al. Gigascience. 2026 Mar 17:giag028. doi: 10.1093/gigascience/giag028. Online ahead of print. Gigascience. 2026. PMID: 41842855 Free article.

16

Multiplatform comparisons and annotation of structural variants highlight the utility of the T2T reference genome in human diagnostics.

Savara J, Novosad T, Gajdos P, Petrackova A, Behalek M, Manakova J, Ctvrtlik F, Minarik J, Papajik T, Kriegova E. Savara J, et al. Gigascience. 2026 Mar 9:giag027. doi: 10.1093/gigascience/giag027. Online ahead of print. Gigascience. 2026. PMID: 41802198 Free article.

17

ZNF331 Modulates Early Embryonic Transcription During Zygotic Genome Activation in Goat.

Yang Y, Zhang J, Chen X, Chen H, Li D, Wan Y, Deng M, Wang F. Yang Y, et al. Gigascience. 2026 Mar 5:giag025. doi: 10.1093/gigascience/giag025. Online ahead of print. Gigascience. 2026. PMID: 41784530 Free article.

18

Patterns of aDNA Damage Through Time and Environments - lessons from herbarium specimens.

Porrelli S, Fornasiero A, Le HP, Yin W, Rodriguez MN, Mohammed N, Himmelbach A, Clarke AC, Stein N, Kersey PJ, Wing RA, Gutaker RM. Porrelli S, et al. Gigascience. 2026 Mar 5:giag026. doi: 10.1093/gigascience/giag026. Online ahead of print. Gigascience. 2026. PMID: 41784526 Free article.

19

Toward total recall: Enhancing data FAIRness through AI-driven metadata standardization.

Sundaram SS, Gonçalves RS, Musen MA. Sundaram SS, et al. Gigascience. 2026 Mar 3:giag019. doi: 10.1093/gigascience/giag019. Online ahead of print. Gigascience. 2026. PMID: 41773962 Free article.

20

Chromosome-level genome assembly and transcriptomes of the leaf insect Cryptophyllium westwoodii provide insights into the evolution of leaf-like masquerade.

Mao C, Dong Z, Li Z, Zhou B, Hu Y, Li J, Liu G, Zhou Z, He J, Wu Y, Wan W, Gao H, Zhao R, Nie W, Wang W, Li X. Mao C, et al. Gigascience. 2026 Mar 2:giag022. doi: 10.1093/gigascience/giag022. Online ahead of print. Gigascience. 2026. PMID: 41770032 Free article.

21

Stereo-cell deciphers the spatial and functional heterogeneity of polyploid hepatocytes.

Yang Y, Luo J, Cai Y, Guo P, Guo Q, Wu H, Liu L, Hao S. Yang Y, et al. Gigascience. 2026 Mar 2:giag023. doi: 10.1093/gigascience/giag023. Online ahead of print. Gigascience. 2026. PMID: 41770024 Free article.

22

MIReVTD, a Minimum Information Standard for Reporting Vector Trait Data.

Ryan SJ, Huxley PJ, Lippi CA, Pawar S, Cator L, Rund SSC, Johnson LR. Ryan SJ, et al. Gigascience. 2026 Feb 28:giag020. doi: 10.1093/gigascience/giag020. Online ahead of print. Gigascience. 2026. PMID: 41762157 Free article.

23

A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.

Feng T, Wu Y, Xu Y, Chen WH. Feng T, et al. Gigascience. 2026 Feb 25:giag016. doi: 10.1093/gigascience/giag016. Online ahead of print. Gigascience. 2026. PMID: 41738843 Free article.

24

Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.

Zabala A, Ascensión AM, Prada-Luengo I, Otaegui D. Zabala A, et al. Gigascience. 2026 Feb 25:giag017. doi: 10.1093/gigascience/giag017. Online ahead of print. Gigascience. 2026. PMID: 41738836 Free article.

25

Improved genome assembly of whale shark, the world's biggest fish: revealing intragenomic heterogeneity in molecular evolution.

Kawaguchi YW, Matsumoto R, Kuraku S. Kawaguchi YW, et al. Gigascience. 2026 Feb 6:giag014. doi: 10.1093/gigascience/giag014. Online ahead of print. Gigascience. 2026. PMID: 41649419 Free article.

26

A Proposed Unified, Scalable Platform for Integrative Research on Venomous Species.

Mehr S, Castoe T, Daly M, Jungo F, Kirchhoff KN, Koludarov I, Mackessy SP, Macrander J, Naidu P, Modica MV, Sanchez EE, Zancolli G, Holford M. Mehr S, et al. Gigascience. 2026 Jan 31:giaf153. doi: 10.1093/gigascience/giaf153. Online ahead of print. Gigascience. 2026. PMID: 41618863 Free article.

27

Interactive analysis of single-cell trajectories in 3D space with Cell Journey.

Panas D, Tabaka M. Panas D, et al. Gigascience. 2026 Jan 21;15:giag021. doi: 10.1093/gigascience/giag021. Gigascience. 2026. PMID: 41773942 Free PMC article.

28

HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.

Silva JM, Martins I, Almeida JR. Silva JM, et al. Gigascience. 2026 Jan 21;15:giag024. doi: 10.1093/gigascience/giag024. Gigascience. 2026. PMID: 41770016 Free PMC article.

29

ChronoRoot 2.0: an open AI-powered platform for 2D temporal plant phenotyping.

Gaggion N, Boccardo NA, Bonazzola R, Legascue MF, Mammarella MF, Rodriguez FS, Aballay FE, Catulo FB, Barrios A, Santoro LJ, Accavallo F, Villarreal SN, Pereyra-Bistrain LI, Benhamed M, Crespi M, Ricardi MM, Petrillo E, Blein T, Ariel F, Ferrante E. Gaggion N, et al. Gigascience. 2026 Jan 21;15:giag018. doi: 10.1093/gigascience/giag018. Gigascience. 2026. PMID: 41762156 Free PMC article.

30

Enhanced semantic classification of microbiome sample origins using large language models (LLMs).

Gaio D, Tackmann J, Perez-Molphe-Montoya E, Näpflin N, Patsch D, Malfertheiner L, Peluso ME, von Mering C. Gaio D, et al. Gigascience. 2026 Jan 21;15:giag015. doi: 10.1093/gigascience/giag015. Gigascience. 2026. PMID: 41677795 Free PMC article.

31

An interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis.

Wang Z, Zhan Q, Yang S, Zhou Z, Kan M, Zhai T, Shen L. Wang Z, et al. Gigascience. 2026 Jan 21;15:giag012. doi: 10.1093/gigascience/giag012. Gigascience. 2026. PMID: 41661124 Free PMC article.

32

Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat.

Li R, Duan S, Deng Q, Ma W, Liu C, Gao P, Lu L, Yuan Y. Li R, et al. Gigascience. 2026 Jan 21;15:giag013. doi: 10.1093/gigascience/giag013. Gigascience. 2026. PMID: 41632074 Free PMC article.

33

Expression-driven genetic dependency reveals targets for precision oncology.

Elmas A, Layden HM, Ellis JD, Bartlett LN, Zhao X, Kawabata-Iwakawa R, Wang Z, Obinata H, Hiebert SW, Huang KL. Elmas A, et al. Gigascience. 2026 Jan 21;15:giag011. doi: 10.1093/gigascience/giag011. Gigascience. 2026. PMID: 41609417 Free PMC article.

34

ViralBindPredict: empowering viral protein-ligand binding sites through deep learning and protein sequence-derived insights.

Amorim AMB, Marques-Pereira C, Almeida T, Rosário-Ferreira N, Pinto HS, Vaz C, Francisco A, Moreira IS. Amorim AMB, et al. Gigascience. 2026 Jan 21;15:giag010. doi: 10.1093/gigascience/giag010. Gigascience. 2026. PMID: 41578956 Free PMC article.

35

High-definition likelihood inference of genetic colocalization reveals protein biomarkers for human complex diseases.

Li Y, Zhai R, Yang Z, Li T, Pawitan Y, Shen X. Li Y, et al. Gigascience. 2026 Jan 21;15:giaf155. doi: 10.1093/gigascience/giaf155. Gigascience. 2026. PMID: 41574934 Free PMC article.

36

nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.

Karatzas E, Beracochea M, Baltoumas FA, Aplakidou E, Richardson L, Fellows Yates JA, Lundin D; nf-core community; Buluç A, Kyrpides NC, Georgakopoulos-Soares I, Pavlopoulos GA, Finn RD. Karatzas E, et al. Gigascience. 2026 Jan 21;15:giag009. doi: 10.1093/gigascience/giag009. Gigascience. 2026. PMID: 41563008 Free PMC article.

37

MBGC2: Boosting compression via efficient encoding of approximate matches in genome collections.

Kowalski TM. Kowalski TM. Gigascience. 2026 Jan 21;15:giag008. doi: 10.1093/gigascience/giag008. Gigascience. 2026. PMID: 41562940 Free PMC article.

38

SpaceBF: spatial coexpression analysis using Bayesian fused approaches in spatial omics datasets.

Seal S, Neelon B. Seal S, et al. Gigascience. 2026 Jan 21;15:giag006. doi: 10.1093/gigascience/giag006. Gigascience. 2026. PMID: 41556565 Free PMC article.

39

Beyond volume and toward coherence: a research parasite's perspective.

Turco G. Turco G. Gigascience. 2026 Jan 21;15:giag001. doi: 10.1093/gigascience/giag001. Gigascience. 2026. PMID: 41556558 Free PMC article.

40

Generalizable machine learning models for rapid antimicrobial resistance prediction in unseen health care settings.

Duroux D, Meyer PP, Visonà G, Beerenwinkel N. Duroux D, et al. Gigascience. 2026 Jan 21;15:giaf156. doi: 10.1093/gigascience/giaf156. Gigascience. 2026. PMID: 41553357 Free PMC article.

41

Dynamont: A comprehensive cross-species comparison of ONT segmentation tools.

Spangenberg J, Siederdissen CHZ, Goettsch W, Köhler L, Luke LM, Papenfort K, Marz M. Spangenberg J, et al. Gigascience. 2026 Jan 21;15:giag005. doi: 10.1093/gigascience/giag005. Gigascience. 2026. PMID: 41553355 Free PMC article.

42

Federated knowledge retrieval elevates large language model performance on biomedical benchmarks.

Joy J, Su AI. Joy J, et al. Gigascience. 2026 Jan 21;15:giag007. doi: 10.1093/gigascience/giag007. Gigascience. 2026. PMID: 41553353 Free PMC article.

43

Cord blood DNA methylation and cell-type composition are not significantly associated with severe preeclampsia after cell-type and clinical covariate adjustment.

Yang X, Liu W, Mao Z, Du Y, Lassiter C, Alakwaa FM, Benny PA, Garmire LX. Yang X, et al. Gigascience. 2026 Jan 21;15:giag002. doi: 10.1093/gigascience/giag002. Gigascience. 2026. PMID: 41543303 Free PMC article.

44

Harnessing artificial intelligence for genomic variant prediction: advances, challenges, and future directions.

Pakpahan I, Sihombing M, Liu H, Wang M, Su Z, Fang M. Pakpahan I, et al. Gigascience. 2026 Jan 21;15:giag004. doi: 10.1093/gigascience/giag004. Gigascience. 2026. PMID: 41518203 Free PMC article. Review.

45

deMEM: a novel divide-and-conquer framework based on de Bruijn graph for scalable multiple sequence alignment.

Wei Y, Huang Z, Zhang P, Wang Y, Li Y, Yu L, Zou Q. Wei Y, et al. Gigascience. 2026 Jan 21;15:giaf163. doi: 10.1093/gigascience/giaf163. Gigascience. 2026. PMID: 41489486 Free PMC article.

46

Genome Assembly of Three Shrub Mangroves in the Genus Acanthus Reveals Two Polyploidy Events and Expansion of Genes Linked to Root Adaptation in Coastal Habitats.

Nawae W, Naktang C, Paenpong P, Sangsrakru D, Yoocha T, U-Thoomporn S, Kongkachana W, Wanthongchai P, Yamprasai S, Samart C, Tangphatsornruang S, Pootakham W. Nawae W, et al. Gigascience. 2026 Jan 21;15:giaf162. doi: 10.1093/gigascience/giaf162. Gigascience. 2026. PMID: 41481123 Free PMC article.

47

Charting immune variation through genetics and single-cell genomics.

Powell JE. Powell JE. Gigascience. 2026 Jan 21;15:giaf161. doi: 10.1093/gigascience/giaf161. Gigascience. 2026. PMID: 41467452 Free PMC article.

48

An evaluation of computational methods for reconstruction of human viral DNA genomes.

Sousa MJP, Toppinen M, Pyöriä L, Hedman K, Sajantila A, Perdomo MF, Pratas D. Sousa MJP, et al. Gigascience. 2026 Jan 21;15:giaf159. doi: 10.1093/gigascience/giaf159. Gigascience. 2026. PMID: 41453206 Free PMC article.

49

Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids.

Martin SLF, La Torre R, Danneels B, Tooming-Klunderud A, Skage M, Kollias S, Tørresen OK, Anbaran MF, Stur E, Jakobsen KS, Martin MD, Ekrem T. Martin SLF, et al. Gigascience. 2026 Jan 21;15:giaf160. doi: 10.1093/gigascience/giaf160. Gigascience. 2026. PMID: 41427890 Free PMC article.

50

Open RGB imaging workflow for morphological and morphometric analysis of fruits using deep learning: a case study on almonds.

Mas-Gómez J, Rubio M, Dicenta F, Martínez-García PJ. Mas-Gómez J, et al. Gigascience. 2026 Jan 21;15:giaf157. doi: 10.1093/gigascience/giaf157. Gigascience. 2026. PMID: 41416705 Free PMC article.

51

The genomes of 5 mantises provide insights into sex chromosome evolution and Mantodea phylogeny clarification.

Liu H, Lei L, Jiang F, Zhang B, Wang H, Zhang Y, Zhao H, Wang G, Fan W. Liu H, et al. Gigascience. 2026 Jan 21;15:giaf158. doi: 10.1093/gigascience/giaf158. Gigascience. 2026. PMID: 41410494 Free PMC article.

52

LinkML: an open data modeling framework.

Moxon SAT, Solbrig H, Harris NL, Kalita P, Miller MA, Patil S, Schaper K, Bizon C, Caufield JH, Cuesta SC, Cox C, Dekervel F, Dooley DM, Duncan WD, Fliss T, Gehrke S, Graefe ASL, Hegde H, Ireland AJ, Jacobsen JOB, Krishnamurthy M, Kroll C, Linke D, Ly R, Matentzoglu N, Overton JA, Saunders JL, Unni DR, Vaidya G, Vierdag WAM; LinkML Community Contributors; Ruebel O, Chute CG, Brush MH, Haendel MA, Mungall CJ. Moxon SAT, et al. Gigascience. 2026 Jan 21;15:giaf152. doi: 10.1093/gigascience/giaf152. Gigascience. 2026. PMID: 41384800 Free PMC article.

53

Improved reference assembly and core collection resequencing to facilitate exploration of important agronomical traits for the improvement of oilseed crop, Carthamus tinctorius L.

Sharma M, Bhardwaj V, Oraon PK, Choudhary S, Ambreen H, Shukla RN, Jamedar HR, Vijjeswarapu A, Jaiswal V, Kadirvel P, Jagannath A, Goel S. Sharma M, et al. Gigascience. 2026 Jan 21;15:giaf151. doi: 10.1093/gigascience/giaf151. Gigascience. 2026. PMID: 41378979 Free PMC article.

54

An integrative multiomics random forest framework for robust biomarker discovery.

Zhang W, Huang H, Wang L, Lehmann BD, Chen XS. Zhang W, et al. Gigascience. 2026 Jan 21;15:giaf148. doi: 10.1093/gigascience/giaf148. Gigascience. 2026. PMID: 41363728 Free PMC article.

55

Giant chromosomes of a tiny plant-the complete telomere-to-telomere genome assembly of the simple thalloid liverwort Apopellia endiviifolia (Jungermanniopsida, Marchantiophyta).

Szablińska-Piernik J, Sulima P, Sawicki J. Szablińska-Piernik J, et al. Gigascience. 2026 Jan 21;15:giaf145. doi: 10.1093/gigascience/giaf145. Gigascience. 2026. PMID: 41316987 Free PMC article.

56

pyRootHair: Machine learning accelerated software for high-throughput phenotyping of plant root hair traits.

Tsang I, Percival-Alwyn L, Rawsthorne S, Cockram J, Leigh F, Atkinson JA. Tsang I, et al. Gigascience. 2026 Jan 21;15:giaf141. doi: 10.1093/gigascience/giaf141. Gigascience. 2026. PMID: 41231584 Free PMC article.

57

RNA-SeqEZPZ: a point-and-click pipeline for comprehensive transcriptomics analysis with interactive visualizations.

Taslim C, Zhang Y, Rask G, Kendall GC, Theisen ER. Taslim C, et al. Gigascience. 2026 Jan 21;15:giaf133. doi: 10.1093/gigascience/giaf133. Gigascience. 2026. PMID: 41222189 Free PMC article.

58

A preregistered, open pipeline for early cerebral palsy risk assessment from Infant Videos.

Segado M, Prosser LA, Duncan AF, Johnson MJ, Kording KP. Segado M, et al. Gigascience. 2026 Jan 20:giag003. doi: 10.1093/gigascience/giag003. Online ahead of print. Gigascience. 2026. PMID: 41556563 Free article.

59

Challenges in structural variant calling in low-complexity regions.

Qin Q, Li H. Qin Q, et al. Gigascience. 2025 Jan 6;14:giaf154. doi: 10.1093/gigascience/giaf154. Gigascience. 2025. PMID: 41384802 Free PMC article.

60

A sulfatide-centered ultra-high-resolution magnetic resonance MALDI imaging benchmark dataset for MS1-based lipid annotation tools.

Gruber L, Schmidt S, Enzlein T, Hopf C. Gruber L, et al. Gigascience. 2025 Jan 6;14:giaf150. doi: 10.1093/gigascience/giaf150. Gigascience. 2025. PMID: 41363756 Free PMC article.

61

Translating short-form Python exercises to other programming languages using diverse prompting strategies.

Piccolo SR, Stevens HP. Piccolo SR, et al. Gigascience. 2025 Jan 6;14:giaf149. doi: 10.1093/gigascience/giaf149. Gigascience. 2025. PMID: 41358832 Free PMC article.

62

Multi-omics and high-spatial-resolution omics: deciphering complexity in neurological disorders.

Liu X, Li F, Czosnyka M, Czosnyka Z, Yu H, Tong X, Xing Y, Li H, Pu K, Feng K, Zhang K, Pang M, Ming D. Liu X, et al. Gigascience. 2025 Jan 6;14:giaf137. doi: 10.1093/gigascience/giaf137. Gigascience. 2025. PMID: 41348969 Free PMC article.

63

Endometrial whole-slide images dataset for detection of malignancy in endometrial biopsies.

Mohammadi M, Fell C, Bell S, Bryson G, Syed S, Konanahalli P, Harris-Birtill D, Arandjelovic O, Orange C, Shahi P, Um IH, Blackwood JD, Harrison DJ. Mohammadi M, et al. Gigascience. 2025 Jan 6;14:giaf147. doi: 10.1093/gigascience/giaf147. Gigascience. 2025. PMID: 41348968 Free PMC article.

64

Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.

Kopalli V, Arslan K, Morales-Díaz N, Zanini SF, Golicz AA. Kopalli V, et al. Gigascience. 2025 Jan 6;14:giaf121. doi: 10.1093/gigascience/giaf121. Gigascience. 2025. PMID: 41342577 Free PMC article.

65

Cervical whole-slide images dataset for multiclass classification.

Mohammadi M, Fell C, Morrison D, Bell S, Bryson G, Syed S, Konanahalli P, Harris-Birtill D, Arandjelovic O, Orange C, Shahi P, Um IH, Blackwood JD, Harrison DJ. Mohammadi M, et al. Gigascience. 2025 Jan 6;14:giaf144. doi: 10.1093/gigascience/giaf144. Gigascience. 2025. PMID: 41317151 Free PMC article.

66

Segmentation-based quality control of structural MRI using the CAT12 toolbox.

Dahnke R, Kalc P, Ziegler G, Grosskreutz J, Gaser C. Dahnke R, et al. Gigascience. 2025 Jan 6;14:giaf146. doi: 10.1093/gigascience/giaf146. Gigascience. 2025. PMID: 41316989 Free PMC article.

67

A high-quality chromosome-level genome assembly of the oligophagous fruit fly Bactrocera tsuneonis (Diptera: Tephritidae) and insights into its host specificity.

Guo T, Li W, Zhang Y, Yang W, Li Z, Qin Y. Guo T, et al. Gigascience. 2025 Jan 6;14:giaf143. doi: 10.1093/gigascience/giaf143. Gigascience. 2025. PMID: 41263491 Free PMC article.

68

Chromosome-level assemblies of two hexaploid bamboos, Thyrsostachys oliveri and Thyrsostachys siamensis, provide a foundation for functional and comparative genomics studies.

Naktang C, Khanbo S, Phadphon P, U-Thoomporn S, Sangsakru D, Sonthirod C, Waiyamitra P, Sungkaew S, Tangphatsornruang S, Pootakham W. Naktang C, et al. Gigascience. 2025 Jan 6;14:giaf142. doi: 10.1093/gigascience/giaf142. Gigascience. 2025. PMID: 41247287 Free PMC article.

69

NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing data.

Woller F, Arend L, Fuchsberger C, List M, Blumenthal DB. Woller F, et al. Gigascience. 2025 Jan 6;14:giaf140. doi: 10.1093/gigascience/giaf140. Gigascience. 2025. PMID: 41206544 Free PMC article.

70

Complete end-to-end learning from protein feature representation to protein interactome inference.

Chen YH, Liu CF, Leu JY, Tsai HK. Chen YH, et al. Gigascience. 2025 Jan 6;14:giaf122. doi: 10.1093/gigascience/giaf122. Gigascience. 2025. PMID: 41206398 Free PMC article.

71

Population-level allelic dispersion modeling by maelstRom yields genome-wide maps of allele-specific dysregulation during early carcinogenesis.

Stroobandt C, Coussement L, Goovaerts T, De Graeve F, Galle J, Van Criekinge W, De Meyer T. Stroobandt C, et al. Gigascience. 2025 Jan 6;14:giaf125. doi: 10.1093/gigascience/giaf125. Gigascience. 2025. PMID: 41188181 Free PMC article.

72

Quantitative detection of DNA methylation from nanopore sequencing data without raw signals.

Feng Z, Zhang C, Jin S, Niu J, Feng H. Feng Z, et al. Gigascience. 2025 Jan 6;14:giaf113. doi: 10.1093/gigascience/giaf113. Gigascience. 2025. PMID: 41170607 Free PMC article.

73

The effects of bioinformatics preprocessing on cell-free DNA fragment analysis.

Ivanković I, Balázs Z, Gitchev T, Trottet C, Moldovan N, Bahce I, Mouliere F, Krauthammer M. Ivanković I, et al. Gigascience. 2025 Jan 6;14:giaf139. doi: 10.1093/gigascience/giaf139. Gigascience. 2025. PMID: 41165721 Free PMC article.

74

GTestimate: improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator.

Fahrenberger M, Esk C, Knoblich JA, von Haeseler A. Fahrenberger M, et al. Gigascience. 2025 Jan 6;14:giaf084. doi: 10.1093/gigascience/giaf084. Gigascience. 2025. PMID: 41159548 Free PMC article.

75

TinkerHap-a novel read-based phasing algorithm with integrated multimethod support for enhanced accuracy.

Hartmann U, Shaham E, Nathan D, Blech I, Zeevi D. Hartmann U, et al. Gigascience. 2025 Jan 6;14:giaf138. doi: 10.1093/gigascience/giaf138. Gigascience. 2025. PMID: 41147705 Free PMC article.

76

EssSubgraph improves performance and generalizability of mammalian essential gene prediction with large networks.

Wen H, Carpenter S, McGinnis K, Nelson A, Smith K, Hong T. Wen H, et al. Gigascience. 2025 Jan 6;14:giaf136. doi: 10.1093/gigascience/giaf136. Gigascience. 2025. PMID: 41134033 Free PMC article.

77

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes.

Bağcı C, Negri T, Buena-Atienza E, Gross C, Ossowski S, Ziemert N. Bağcı C, et al. Gigascience. 2025 Jan 6;14:giaf135. doi: 10.1093/gigascience/giaf135. Gigascience. 2025. PMID: 41133998 Free PMC article.

78

On the path to reference genomes for all biodiversity: laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life.

Howard C, Denton A, Jackson BW, Bates A, Jay J, Yatsenko H, Raman PS, Thomas A, Oatley G, do Amaral RV, Göktan ZE, Gómez JPN, Clayton Lucey I, Sinclair E, Quail MA, Blaxter M, Howe K, Lawniczak MKN. Howard C, et al. Gigascience. 2025 Jan 6;14:giaf119. doi: 10.1093/gigascience/giaf119. Gigascience. 2025. PMID: 41129326 Free PMC article.

79

GFFx: A Rust-based suite of utilities for ultra-fast genomic feature extraction.

Chen B, Wu D, Zhang G. Chen B, et al. Gigascience. 2025 Jan 6;14:giaf124. doi: 10.1093/gigascience/giaf124. Gigascience. 2025. PMID: 41129325 Free PMC article.

80

SurGen: 1020 H&E-stained whole-slide images with survival and genetic markers.

Myles C, Um IH, Marshall C, Harris-Birtill D, Harrison DJ. Myles C, et al. Gigascience. 2025 Jan 6;14:giaf086. doi: 10.1093/gigascience/giaf086. Gigascience. 2025. PMID: 41128428 Free PMC article.

81

Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test.

Forer L, Schönherr S. Forer L, et al. Gigascience. 2025 Jan 6;14:giaf130. doi: 10.1093/gigascience/giaf130. Gigascience. 2025. PMID: 41124057 Free PMC article.

82

Datagraphy: toward a systematic approach to dataset discovery.

Petit P, Vuillerme N. Petit P, et al. Gigascience. 2025 Jan 6;14:giaf134. doi: 10.1093/gigascience/giaf134. Gigascience. 2025. PMID: 41124051 Free PMC article.

83

MRanalysis: a comprehensive online platform for integrated, multimethod Mendelian randomization and associated post-GWAS analyses.

Xing A, Cai T, Du H, Li Z, Ng H, Li J, Jiang G, Chen L, Li K. Xing A, et al. Gigascience. 2025 Jan 6;14:giaf131. doi: 10.1093/gigascience/giaf131. Gigascience. 2025. PMID: 41124022 Free PMC article.

84

CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology.

Xu Q, Wu L, Rebelo M, Feng S, Yu X, Farheen F, Kihara D, Zhou ZH. Xu Q, et al. Gigascience. 2025 Jan 6;14:giaf127. doi: 10.1093/gigascience/giaf127. Gigascience. 2025. PMID: 41124016 Free PMC article.

85

Genos: a human-centric genomic foundation model.

Lin A, Xie B, Ye C, Wang C, Chen D, Wang E, Lu F, Xue G, Zhang H, Zhan J, Zhang J, Pang J, Liang J, Lin J, Ma J, Hu J, Ma J, Dong J, Li J, Liu J, Chen J, Li J, Ding K, Deng K, Chen K, Wang L, Liu L, Guo L, Xiong L, Yang L, Cheng M, Chen N, Chen R, Sun S, Li S, Chen S, Liu S, Xie S, Liu S, Zhou T, Tang W, Zhang W, Jiang X, Qi X, Jin X, Tan X, Hu X, Xu X, Feng X, Lu Y, Gao Y, Shang Y, He Y, Yuan Y, Wang Y, Liu Y, Xiao Z, Meng Z, Li Z, Zhao Z, Yang Z, Wang Z. Lin A, et al. Gigascience. 2025 Jan 6;14:giaf132. doi: 10.1093/gigascience/giaf132. Gigascience. 2025. PMID: 41122975 Free PMC article.

86

Reproducible processing of TCGA regulatory networks.

Fanfani V, Shutta KH, Mandros P, Fischer J, Saha E, Micheletti S, Chen C, Ben Guebila M, Lopes-Ramos CM, Quackenbush J. Fanfani V, et al. Gigascience. 2025 Jan 6;14:giaf126. doi: 10.1093/gigascience/giaf126. Gigascience. 2025. PMID: 41114645 Free PMC article.

87

Cross-modal contrastive learning decodes developmental regulatory features through chromatin potential analysis.

Yang Y, Xie C, He Q, Yang M. Yang Y, et al. Gigascience. 2025 Jan 6;14:giaf053. doi: 10.1093/gigascience/giaf053. Gigascience. 2025. PMID: 41105015 Free PMC article.

88

PanGIA: A universal framework for identifying association between ncRNAs and diseases.

Liu X, Lü X, Chen Q, Sun J, Zhao T, Zhu Y. Liu X, et al. Gigascience. 2025 Jan 6;14:giaf123. doi: 10.1093/gigascience/giaf123. Gigascience. 2025. PMID: 41105014 Free PMC article.

89

ColoPola: A polarimetric imaging dataset for colorectal cancer detection.

Pham TT, Vo QH, Nguyen TV, Nguyen TH, Phan QH, Le TH. Pham TT, et al. Gigascience. 2025 Jan 6;14:giaf120. doi: 10.1093/gigascience/giaf120. Gigascience. 2025. PMID: 41100285 Free PMC article.

90

The enduring advantages of the SLOW5 file format for raw nanopore sequencing data.

Gamaarachchi H, Jenner S, Samarakoon H, Ferguson JM, Deveson IW. Gamaarachchi H, et al. Gigascience. 2025 Jan 6;14:giaf118. doi: 10.1093/gigascience/giaf118. Gigascience. 2025. PMID: 41100284 Free PMC article.

91

SeedGerm-VIG: an open and comprehensive pipeline to quantify seed vigor in wheat and other cereal crops using deep learning-powered dynamic phenotypic analysis.

Dai J, Wen Z, Ali M, Huang J, Liu S, Zhao J, Pinheiro F, Yang C, Wang B, Ye L, Guan X, Zhou J. Dai J, et al. Gigascience. 2025 Jan 6;14:giaf129. doi: 10.1093/gigascience/giaf129. Gigascience. 2025. PMID: 41100176 Free PMC article.

92

Emerging AI approaches for cancer spatial omics.

Noorbakhsh J, Foroughi Pour A, Chuang J. Noorbakhsh J, et al. Gigascience. 2025 Jan 6;14:giaf128. doi: 10.1093/gigascience/giaf128. Gigascience. 2025. PMID: 41100170 Free PMC article. Review.

93

DUNE: a versatile neuroimaging encoder captures brain complexity across 3 major diseases: cancer, dementia, and schizophrenia.

Barba T, Bagley BA, Steyaert S, Carrillo-Perez F, Sadée C, Iv M, Gevaert O. Barba T, et al. Gigascience. 2025 Jan 6;14:giaf116. doi: 10.1093/gigascience/giaf116. Gigascience. 2025. PMID: 41092455 Free PMC article.

94

Comparative genomics and multiomics analyses reveal the evolution and physiological basis of rubber biosynthesis in Hevea species.

Lau NS, Okubo-Kurihara E, Makita Y, Oktavia F, Kuriyama T, Kurihara Y, Hamasaki H, Nakamura Y, Kadota M, Nishimura O, Kuraku S, Othman AS, Matsui M. Lau NS, et al. Gigascience. 2025 Jan 6;14:giaf115. doi: 10.1093/gigascience/giaf115. Gigascience. 2025. PMID: 41070844 Free PMC article.

95

Unsupervised multiscale clustering of single-cell transcriptomes to identify hierarchical structures of cell subtypes.

Song WM, Ming C, Forst CV, Zhang B. Song WM, et al. Gigascience. 2025 Jan 6;14:giaf111. doi: 10.1093/gigascience/giaf111. Gigascience. 2025. PMID: 41066207 Free PMC article.

96

The Great Genotyper: a graph-based method for population genotyping of small and structural variants.

Shokrof M, Abuelanin M, Brown CT, Mansour TA. Shokrof M, et al. Gigascience. 2025 Jan 6;14:giaf112. doi: 10.1093/gigascience/giaf112. Gigascience. 2025. PMID: 41041811 Free PMC article.

97

Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.

Oskolkov N, Jin C, Clinton SL, Guinet B, Wijnands F, Johnson E, Kutschera VE, Kinsella CM, Heintzman PD, van der Valk T. Oskolkov N, et al. Gigascience. 2025 Jan 6;14:giaf108. doi: 10.1093/gigascience/giaf108. Gigascience. 2025. PMID: 41041810 Free PMC article.

98

The complete genome assembly of Astragalus membranaceus: enabling more accurate genetic research.

Qin H, Li A, Zhong S, Wang H, Tian H. Qin H, et al. Gigascience. 2025 Jan 6;14:giaf117. doi: 10.1093/gigascience/giaf117. Gigascience. 2025. PMID: 41032019 Free PMC article.

99

MGMA-PPIS: Predicting the protein-protein interaction site with multiview graph embedding and multiscale attention fusion.

Han Y, Zhang SW, Zhang QQ, Shi MH. Han Y, et al. Gigascience. 2025 Jan 6;14:giaf114. doi: 10.1093/gigascience/giaf114. Gigascience. 2025. PMID: 41032018 Free PMC article.

100

Foundation model of electronic medical records for adaptive risk estimation.

Renc P, Grzeszczyk MK, Oufattole N, Goode D, Jia Y, Bieganski S, McDermott MBA, Was J, Samir AE, Cunningham JW, Bates DW, Sitek A. Renc P, et al. Gigascience. 2025 Jan 6;14:giaf107. doi: 10.1093/gigascience/giaf107. Gigascience. 2025. PMID: 41026508 Free PMC article.

101

PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking.

Nasr E, Henger A, Grüning B, Zierep P, Batut B. Nasr E, et al. Gigascience. 2025 Jan 6;14:giaf017. doi: 10.1093/gigascience/giaf017. Gigascience. 2025. PMID: 41004266 Free PMC article.

102

AEnet: a practical tool to construct the splicing-associated phenotype atlas at a single cell level.

Liu S, Chen X, Huang X, Wang Y, Huang W, Qin P, Li R, Zou X, Pang W, Huang X, Liu S, Bai Y, Wu L. Liu S, et al. Gigascience. 2025 Jan 6;14:giaf110. doi: 10.1093/gigascience/giaf110. Gigascience. 2025. PMID: 40990037 Free PMC article.

103

A high-quality reference genome for the Ural Owl (Strix uralensis) enables investigations of cell cultures as a genomic resource for endangered species.

Chrysostomakis I, Mozer A, Di-Nizo CB, Fischer D, Sargheini N, von der Mark L, Huettel B, Astrin JJ, Töpfer T, Böhne A. Chrysostomakis I, et al. Gigascience. 2025 Jan 6;14:giaf106. doi: 10.1093/gigascience/giaf106. Gigascience. 2025. PMID: 40986362 Free PMC article.

104

First chromosome-level genome assembly of the colonial chordate model Botryllus schlosseri (Tunicata).

De Thier O, Lebel M, Tawfeeq MM, Faure R, Dru P, Blanchoud S, Alié A, Brown FD, Flot JF, Tiozzo S. De Thier O, et al. Gigascience. 2025 Jan 6;14:giaf097. doi: 10.1093/gigascience/giaf097. Gigascience. 2025. PMID: 40971594 Free PMC article.

105

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence.

Arantes LS, Brown T, De Panis D, Whiting SD, Young EJ, LaCasella EL, Carvajal GA, Kennedy A, Edmunds D, Bentley BP, Balacco J, Whelan C, Jain N, Tilley T, O'Toole B, Traore P, Jarvis ED, Berry O, Dutton PH, Komoroske LM, Mazzoni CJ. Arantes LS, et al. Gigascience. 2025 Jan 6;14:giaf105. doi: 10.1093/gigascience/giaf105. Gigascience. 2025. PMID: 40971593 Free PMC article.

106

A retrieval-augmented knowledge mining method with deep thinking LLMs for biomedical research and clinical support.

Feng Y, Wang J, He R, Zhou L, Li Y. Feng Y, et al. Gigascience. 2025 Jan 6;14:giaf109. doi: 10.1093/gigascience/giaf109. Gigascience. 2025. PMID: 40971592 Free PMC article.

107

CNSistent integration and feature extraction from somatic copy number profiles.

Streck A, Schwarz RF. Streck A, et al. Gigascience. 2025 Jan 6;14:giaf104. doi: 10.1093/gigascience/giaf104. Gigascience. 2025. PMID: 40971591 Free PMC article.

108

The Earth Hologenome Initiative: Data Release 1.

Gaun N, Pietroni C, Martin-Bideguren G, Lauritsen J, Aizpurua O, Fernandes JM, Ferreira E, Aubret F, Sarraude T, Perry C, Wauters L, Romeo C, Spada M, Tranquillo C, Sutton AO, Griesser M, Warrington MH, Pérez I de Lanuza G, Abalos J, Aguilar P, de la Cruz F, Juste J, Alonso-Alonso P, Groombridge J, Louch R, Ruhomaun K, Henshaw S, Cabido C, Barrio IG, Šunje E, Hosner P, Prates I, While GM, García-Roa R, Uller T, Feiner N, Bonaccorso E, Klein-Ipsen P, Rotovnik RM, Alberdi A, Eisenhofer R. Gaun N, et al. Gigascience. 2025 Jan 6;14:giaf102. doi: 10.1093/gigascience/giaf102. Gigascience. 2025. PMID: 40910796 Free PMC article.

109

A framework to mine laser microdissection-based omics data and uncover regulators of pancreatic cancer heterogeneity.

Chiaro PD, Diaferia GR, Natoli G, Barozzi I. Chiaro PD, et al. Gigascience. 2025 Jan 6;14:giaf101. doi: 10.1093/gigascience/giaf101. Gigascience. 2025. PMID: 40910795 Free PMC article.

110

Finding easy regions for short-read variant calling from pangenome data.

Li H. Li H. Gigascience. 2025 Jan 6;14:giaf103. doi: 10.1093/gigascience/giaf103. Gigascience. 2025. PMID: 40905373 Free PMC article.

111

High-precision machine learning identifies a reproducible functional connectivity signature of autism spectrum diagnosis in a subset of individuals.

Clarke N, Urchs S, Nguyen HD, Moreau C, Dansereau C, Tam A, Evans AC, Bellec L. Clarke N, et al. Gigascience. 2025 Jan 6;14:giaf091. doi: 10.1093/gigascience/giaf091. Gigascience. 2025. PMID: 40899917 Free PMC article.

112

Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing.

Chang JJ, Yang X, Teng H, Zhang J, Reames B, Zhang S, Corbin V, Coin LJM. Chang JJ, et al. Gigascience. 2025 Jan 6;14:giaf098. doi: 10.1093/gigascience/giaf098. Gigascience. 2025. PMID: 40899916 Free PMC article.

113

Nanopore- and AI-empowered microbial viability inference.

Ürel H, Benassou S, Marti H, Reska T, Sauerborn E, Pinheiro Alves De Souza Y, Perlas A, Rayo E, Biggel M, Kesselheim S, Borel N, Martin EJ, Venegas CB, Schloter M, Schröder K, Mittelstrass J, Prospero S, Ferguson JM, Urban L. Ürel H, et al. Gigascience. 2025 Jan 6;14:giaf100. doi: 10.1093/gigascience/giaf100. Gigascience. 2025. PMID: 40899150 Free PMC article.

114

Exploring the role of normalization and feature selection in microbiome disease classification pipelines.

Garach Vélez I, Ortuño Guzmán FM, Rojas Ruiz I, Herrera Maldonado LJ. Garach Vélez I, et al. Gigascience. 2025 Jan 6;14:giaf096. doi: 10.1093/gigascience/giaf096. Gigascience. 2025. PMID: 40891529 Free PMC article.

115

The Open Pediatric Cancer Project.

Geng Z, Wafula E, Corbett RJ, Zhang Y, Jin R, Gaonkar KS, Shukla S, Rathi KS, Hill D, Lahiri A, Miller DP, Sickler A, Keith K, Blackden C, Chroni A, Brown MA, Kraya AA, Clark KL, Rood BR, Resnick AC, Van Kuren N, Maris JM, Farrel A, Koptyra MP, Trooskin GR, Coleman N, Zhu Y, Stefankiewicz S, Abdullaev Z, Chinwalla AT, Santi M, Naqvi AS, Mason JL, Koschmann CJ, Huang X, Diskin SJ, Aldape K, Farrow BK, Ma W, Zhang B, Ennis BM, Tasian S, Phul S, Lueder MR, Zhong C, Dybas JM, Wang P, Taylor D, Rokita JL. Geng Z, et al. Gigascience. 2025 Jan 6;14:giaf093. doi: 10.1093/gigascience/giaf093. Gigascience. 2025. PMID: 40891528 Free PMC article.

116

A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.

Arshad F, Jayaraman S, Talenti A, Owen R, Mohsin M, Mansoor S, Asif M, Prendergast J. Arshad F, et al. Gigascience. 2025 Jan 6;14:giaf099. doi: 10.1093/gigascience/giaf099. Gigascience. 2025. PMID: 40884803 Free PMC article.

117

BVSim: A benchmarking variation simulator mimicking human variation spectrum.

Luo Y, Zhang Z, Wang S, Shi J, Hao J, Lian S, Hu T, Ishibashi T, Wang D, Yu W, Fan X. Luo Y, et al. Gigascience. 2025 Jan 6;14:giaf095. doi: 10.1093/gigascience/giaf095. Gigascience. 2025. PMID: 40884802 Free PMC article.

118

Group-specific discriminant analysis enhances detection of sex differences in brain functional network lateralization.

Zhou S, Luo J, Jiang Y, Wang H, Lu H, Gong G. Zhou S, et al. Gigascience. 2025 Jan 6;14:giaf082. doi: 10.1093/gigascience/giaf082. Gigascience. 2025. PMID: 40884801 Free PMC article.

119

SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis.

Li X, Pechuan-Jorge X, Risom T, Foo C, Prilipko A, Zubkov A, Chan C, Chang P, Peale F, Ziai J, Rost S, Hibar D, McGinnis L, Tabatsky E, Ye X, Bravo HC, Shi Z, Nowicka M, Scherdin J, Cowan J, Giltnane J, Orlova D, Jesudason R. Li X, et al. Gigascience. 2025 Jan 6;14:giaf090. doi: 10.1093/gigascience/giaf090. Gigascience. 2025. PMID: 40880135 Free PMC article.

120

A telomere-to-telomere genome assembly of koi carp (Cyprinus carpio) using long reads and Hi-C technology.

Yuan J, Li J, Yong J, Liao X, Guo H, Niu Y. Yuan J, et al. Gigascience. 2025 Jan 6;14:giaf087. doi: 10.1093/gigascience/giaf087. Gigascience. 2025. PMID: 40880134 Free PMC article.

121

WaveSeekerNet: accurate prediction of influenza A virus subtypes and host source using attention-based deep learning.

Nguyen HH, Rudar J, Lesperance N, Vernygora O, Taylor GW, Laing C, Lapen D, Leung CK, Lung O. Nguyen HH, et al. Gigascience. 2025 Jan 6;14:giaf089. doi: 10.1093/gigascience/giaf089. Gigascience. 2025. PMID: 40880133 Free PMC article.

122

Comparing linear and nonlinear finite element models of vertebral strength across the thoracolumbar spine: a benchmark from density-calibrated computed tomography.

Walle M, Matheson BE, Boyd SK. Walle M, et al. Gigascience. 2025 Jan 6;14:giaf094. doi: 10.1093/gigascience/giaf094. Gigascience. 2025. PMID: 40880132 Free PMC article.

123

DeepAnnotation: A novel interpretable deep learning-based genomic selection model that integrates comprehensive functional annotations.

Ma W, Zheng W, Qin S, Wang C, Lei B, Liu Y. Ma W, et al. Gigascience. 2025 Jan 6;14:giaf083. doi: 10.1093/gigascience/giaf083. Gigascience. 2025. PMID: 40874866 Free PMC article.

124

HeteroMRI: Robust white matter abnormality classification across multi-scanner MRI data.

Abedi M, Shekarchizadeh N, Bazin PL, Scherf N, Lier J, Bergner CC; Alzheimer’s Disease Neuroimaging Initiative; Köhler W, Kirsten T. Abedi M, et al. Gigascience. 2025 Jan 6;14:giaf092. doi: 10.1093/gigascience/giaf092. Gigascience. 2025. PMID: 40844084 Free PMC article.

125

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes.

Guo Q, Pan Y, Dai W, Guo F, Zeng T, Chen W, Mi Y, Zhang Y, Shi S, Jiang W, Cai H, Wu B, Zhou Y, Wang Y, Yang C, Shi X, Yan X, Chen J, Cai C, Yang J, Xu X, Gu Y, Dong Y, Li Q. Guo Q, et al. Gigascience. 2025 Jan 6;14:giaf079. doi: 10.1093/gigascience/giaf079. Gigascience. 2025. PMID: 40825570 Free PMC article.

126

A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps.

Patel HR, Alreja K, Reis ALM, Chang JK, Chew ZA, Jung H, Hammond JM, Deveson IW, Ruiz-Herrera A, Marin-Gual L, Holleley CE, Zhang X, Lister NC, Whiteley S, Xiong L, Dissanayake DSB, Waters PD, Georges A. Patel HR, et al. Gigascience. 2025 Jan 6;14:giaf085. doi: 10.1093/gigascience/giaf085. Gigascience. 2025. PMID: 40825569 Free PMC article.

127

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation.

Guang X, Yang J, Zhang S, Guo F, Li L, Lian X, Zeng T, Cai C, Liu F, Li Z, Hu Y, Fang D, He W, Sahu SK, Li W, Lu H, Li Y, Liu H, Xu X, Gu Y, Hu F, Dong Y, Wei T. Guang X, et al. Gigascience. 2025 Jan 6;14:giaf074. doi: 10.1093/gigascience/giaf074. Gigascience. 2025. PMID: 40825568 Free PMC article.

128

SynProtX: a large-scale proteomics-based deep learning model for predicting synergistic anticancer drug combinations.

Boonyarit B, Kositchutima M, Phattalung TN, Yamprasert N, Thuwajit C, Rungrotmongkol T, Nutanong S. Boonyarit B, et al. Gigascience. 2025 Jan 6;14:giaf080. doi: 10.1093/gigascience/giaf080. Gigascience. 2025. PMID: 40796376 Free PMC article.

129

PeptideMiner-neuropeptide discovery across the animal kingdom.

Mendel HC, Hopping G, Undheim EAB, Zuegg J, Lewis RJ, Forbes BE, Kaas Q, Muttenthaler M. Mendel HC, et al. Gigascience. 2025 Jan 6;14:giaf078. doi: 10.1093/gigascience/giaf078. Gigascience. 2025. PMID: 40796375 Free PMC article.

130

A holistic genome dataset of bacteria and archaea of mangrove sediments.

Pan S, Du H, Zheng R, Zhang C, Pan J, Yang X, Wang C, Lin X, Li J, Liu W, Zhou H, Yu X, Mo S, Zhang G, Zhao G, He Z, Tian Y, Jiang C, Qu W, Liu Y, Li M. Pan S, et al. Gigascience. 2025 Jan 6;14:giaf081. doi: 10.1093/gigascience/giaf081. Gigascience. 2025. PMID: 40796374 Free PMC article.

131

MetaboSERV-a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access.

Tucholski T, Maennel A, Njipouombe Nsangou YA, Schuchardt S, Gruber M, Kellermeier F, Dettmer K, Oefner PJ, Gronwald W, Altenbuchinger M, Dönitz J, Zacharias HU. Tucholski T, et al. Gigascience. 2025 Jan 6;14:giaf075. doi: 10.1093/gigascience/giaf075. Gigascience. 2025. PMID: 40748655 Free PMC article.

132

Telomere-to-telomere chromosome-scale genome assemblies of black and golden koi carp variants support construction of an ancient karyotype of Cypriniformes.

Bian C, Huan R, Shi Q. Bian C, et al. Gigascience. 2025 Jan 6;14:giaf073. doi: 10.1093/gigascience/giaf073. Gigascience. 2025. PMID: 40720841 Free article.

133

Reducing skin microbiome exposure impacts through swine farm biosecurity.

Slizovskiy IB, Gaire TN, Ferm PM, Odland CA, Dee SA, Nerem J, Bravo JE, Kimball AD, Boucher C, Noyes NR. Slizovskiy IB, et al. Gigascience. 2025 Jan 6;14:giaf062. doi: 10.1093/gigascience/giaf062. Gigascience. 2025. PMID: 40720840 Free PMC article.

134

Retraction and replacement of: Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis.

[No authors listed] [No authors listed] Gigascience. 2025 Jan 6;14:giaf066. doi: 10.1093/gigascience/giaf066. Gigascience. 2025. PMID: 40669867 Free PMC article. No abstract available.

135

Telomere-to-telomere genome and resequencing of 231 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis.

Zhou Y, Wang C, Wang B, Xu D, Zhang X, Ge Y, Jiang S, Tang F, Chen C, Li X, Jian J, You Y. Zhou Y, et al. Gigascience. 2025 Jan 6;14:giaf067. doi: 10.1093/gigascience/giaf067. Gigascience. 2025. PMID: 40669866 Free PMC article.

136

Correction to: The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement.

[No authors listed] [No authors listed] Gigascience. 2025 Jan 6;14:giaf088. doi: 10.1093/gigascience/giaf088. Gigascience. 2025. PMID: 40665468 Free PMC article. No abstract available.

137

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot.

Aramburu O, Gómez-Pardo B, Rodríguez-Villamayor P, Blanco-Hortas A, Lamas J, Dewari P, Perojil-Morata D, Boudinot P, Macqueen DJ, Bouza C, Martínez P. Aramburu O, et al. Gigascience. 2025 Jan 6;14:giaf077. doi: 10.1093/gigascience/giaf077. Gigascience. 2025. PMID: 40665467 Free PMC article.

138

The telomere-to-telomere gap-free reference genome and taxonomic reassessment of Siniperca roulei.

Jiang M, Zhao C, Ma F, Yin D, Wang C, Jian J, Liu K. Jiang M, et al. Gigascience. 2025 Jan 6;14:giaf068. doi: 10.1093/gigascience/giaf068. Gigascience. 2025. PMID: 40665466 Free PMC article.

139

SeuratExtend: streamlining single-cell RNA-seq analysis through an integrated and intuitive framework.

Hua Y, Weng L, Zhao F, Rambow F. Hua Y, et al. Gigascience. 2025 Jan 6;14:giaf076. doi: 10.1093/gigascience/giaf076. Gigascience. 2025. PMID: 40627366 Free PMC article.

140

eNRSA: a faster and more powerful approach for nascent transcriptome analysis.

Wang J, Chen HC, Hiebert SW, Sheng Q, Tansey WP, Shyr Y, Liu Q. Wang J, et al. Gigascience. 2025 Jan 6;14:giaf071. doi: 10.1093/gigascience/giaf071. Gigascience. 2025. PMID: 40613436 Free PMC article.

141

A telomere-to-telomere gapless genome reveals SlPRR1 control of circadian rhythm and photoperiodic flowering in tomato.

Liu H, Zhang JQ, Tao JP, Chen C, Su LY, Xiong JS, Xiong AS. Liu H, et al. Gigascience. 2025 Jan 6;14:giaf058. doi: 10.1093/gigascience/giaf058. Gigascience. 2025. PMID: 40601421 Free PMC article.

142

The genome of Hippophae salicifolia provides new insights into the sexual differentiation of sea buckthorn.

Chen M, Yang X, Xun L, Qu Z, Yang S, Yang Y, Yang Y. Chen M, et al. Gigascience. 2025 Jan 6;14:giaf046. doi: 10.1093/gigascience/giaf046. Gigascience. 2025. PMID: 40601420 Free PMC article.

143

Integrating comparative genomics and risk classification by assessing virulence, antimicrobial resistance, and plasmid spread in microbial communities with gSpreadComp.

Kasmanas JC, Magnúsdóttir S, Zhang J, Smalla K, Schloter M, Stadler PF, de Leon Ferreira de Carvalho ACP, Rocha U. Kasmanas JC, et al. Gigascience. 2025 Jan 6;14:giaf072. doi: 10.1093/gigascience/giaf072. Gigascience. 2025. PMID: 40569694 Free PMC article.

144

CellBinDB: a large-scale multimodal annotated dataset for cell segmentation with benchmarking of universal models.

Shi C, Fan J, Deng Z, Liu H, Kang Q, Li Y, Guo J, Wang J, Gong J, Liao S, Chen A, Zhang Y, Li M. Shi C, et al. Gigascience. 2025 Jan 6;14:giaf069. doi: 10.1093/gigascience/giaf069. Gigascience. 2025. PMID: 40552981 Free PMC article.

145

PVGA: a precise viral genome assembler using an iterative alignment graph.

Song Z, Cai D, Sun Y, Wang L. Song Z, et al. Gigascience. 2025 Jan 6;14:giaf063. doi: 10.1093/gigascience/giaf063. Gigascience. 2025. PMID: 40552980 Free PMC article.

146

CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome.

Barbosa MC, Marques da Silva JF, Alves LC, Finn RD, Paschoal AR. Barbosa MC, et al. Gigascience. 2025 Jan 6;14:giaf055. doi: 10.1093/gigascience/giaf055. Gigascience. 2025. PMID: 40549543 Free PMC article.

147

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database.

Ikeda S, Zou Z, Bono H, Moriya Y, Kawashima S, Katayama T, Oki S, Ohta T. Ikeda S, et al. Gigascience. 2025 Jan 6;14:giaf070. doi: 10.1093/gigascience/giaf070. Gigascience. 2025. PMID: 40549542 Free PMC article.

148

The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement.

Liu F, Li Y, Wang G, Zhang D, Yang X, Zhou C, Zhou R, Liu H. Liu F, et al. Gigascience. 2025 Jan 6;14:giaf059. doi: 10.1093/gigascience/giaf059. Gigascience. 2025. PMID: 40531666 Free PMC article.

149

PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer counting.

Xu Z, Nie F, Wang J. Xu Z, et al. Gigascience. 2025 Jan 6;14:giaf061. doi: 10.1093/gigascience/giaf061. Gigascience. 2025. PMID: 40526493 Free PMC article.

150

Identifying candidate genetic variants for egg number by analyzing over 1,000 fully sequenced layers.

Ni A, Bovenhuis H, Calus MPL, Li Y, Yuan J, Sun Y, Chen J. Ni A, et al. Gigascience. 2025 Jan 6;14:giaf064. doi: 10.1093/gigascience/giaf064. Gigascience. 2025. PMID: 40526492 Free PMC article.

151

SpatialSNV: A novel method for identifying and analyzing spatially resolved SNVs in tumor microenvironments.

Liu Y, Zhu F, Li X, Guan X, Hou Y, Feng Y, Dong X, Li Y. Liu Y, et al. Gigascience. 2025 Jan 6;14:giaf065. doi: 10.1093/gigascience/giaf065. Gigascience. 2025. PMID: 40515555 Free PMC article.

152

Artificial intelligence: the human response to approach the complexity of big data in biology.

Melandri G, R-Radohery G, Beaumont C, de Cripan SM, Muller C, Piras L, Pereira MA, Salvador AF, Domingo-Almenara X, Bolger M, Colombié S, Prigent S, Arechederra BG, Canela NC, Pétriacq P. Melandri G, et al. Gigascience. 2025 Jan 6;14:giaf057. doi: 10.1093/gigascience/giaf057. Gigascience. 2025. PMID: 40504538 Free PMC article. Review.

153

The FIP 1.0 Data Set: Highly resolved annotated image time series of 4,000 wheat plots grown in 6 years.

Roth L, Boss M, Kirchgessner N, Aasen H, Aguirre-Cuellar BP, Akiina PPA, Anderegg J, Castillo JG, Chen X, Corrado S, Cybulski K, Keller B, Göbel Kortstee S, Kronenberg L, Liebisch F, Nousi P, Oppliger C, Perich G, Pfeifer J, Yu K, Storni N, Tschurr F, Treier S, Volpi M, Zellweger H, Zumsteg O, Hund A, Walter A. Roth L, et al. Gigascience. 2025 Jan 6;14:giaf051. doi: 10.1093/gigascience/giaf051. Gigascience. 2025. PMID: 40498535 Free PMC article.

154

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii).

Mochales-Riaño G, Hirst SR, Talavera A, Burriel-Carranza B, Pagone V, Estarellas M, Busschau T, Boissinot S, Hogan MP, Tena-Garcés J, Pla D, Calvete JJ, Els J, Margres MJ, Carranza S. Mochales-Riaño G, et al. Gigascience. 2025 Jan 6;14:giaf030. doi: 10.1093/gigascience/giaf030. Gigascience. 2025. PMID: 40478730 Free PMC article.

155

Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles.

Yen EC, Gilbert JD, Balard A, Taxonera A, Fairweather K, Ford HL, Thorburn DJ, Rossiter SJ, Martín-Durán JM, Eizaguirre C. Yen EC, et al. Gigascience. 2025 Jan 6;14:giaf054. doi: 10.1093/gigascience/giaf054. Gigascience. 2025. PMID: 40478729 Free PMC article.

156

Health Data Nexus: an open data platform for AI research and education in medicine.

Adams J, Cymerys R, Szuster K, Hekman D, Salo Z, Solanki R, Mamdani M, Johnson A, Ryniak K, Pollard T, Rotenberg D, Haibe-Kains B. Adams J, et al. Gigascience. 2025 Jan 6;14:giaf050. doi: 10.1093/gigascience/giaf050. Gigascience. 2025. PMID: 40459424 Free PMC article.

157

Analysis-ready VCF at Biobank scale using Zarr.

Czech E, Tyler W, White T, Jeffery B, Millar TR, Elsworth B, Guez J, Hancox J, Karczewski KJ, Miles A, Tallman S, Unneberg P, Wojdyla R, Zabad S, Hammerbacher J, Kelleher J. Czech E, et al. Gigascience. 2025 Jan 6;14:giaf049. doi: 10.1093/gigascience/giaf049. Gigascience. 2025. PMID: 40451243 Free PMC article.

158

Chromosome-level genome assembly of Pinus massoniana provides insights into conifer adaptive evolution.

Chen H, Qin X, Chen Y, Zhang H, Feng Y, Tan J, Chen X, Hu L, Xie J, Xie J, Yang Z. Chen H, et al. Gigascience. 2025 Jan 6;14:giaf056. doi: 10.1093/gigascience/giaf056. Gigascience. 2025. PMID: 40443099 Free PMC article.

159

Lifting the curse from high-dimensional data: automated projection pursuit clustering for a variety of biological data modalities.

Simpson C, Tabatsky E, Rahil Z, Eddins DJ, Tkachev S, Georgescauld F, Papalegis D, Culka M, Levy T, Gregoretti I, Meehan C, Schiller C, Bestak K, Schapiro D, Chernyshev A, Walther G, Ghosn EEB, Orlova D. Simpson C, et al. Gigascience. 2025 Jan 6;14:giaf052. doi: 10.1093/gigascience/giaf052. Gigascience. 2025. PMID: 40440093 Free PMC article.

160

Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.

Lawniczak MKN, Kocot KM, Astrin JJ, Blaxter M, Sotero-Caio CG, Barker KB, Childers AK, Coddington J, Davis P, Howe K, Johnson WE, McKenna DD, Wideman JG, Pettersson OV, Ras V, Santos BF; Earth BioGenome Project Samples and Processing Subcommittee. Lawniczak MKN, et al. Gigascience. 2025 Jan 6;14:giaf041. doi: 10.1093/gigascience/giaf041. Gigascience. 2025. PMID: 40440092 Free PMC article.

161

A Case for estradiol: younger brains in women with earlier menarche and later menopause.

Luders E, Poromaa IS, Barth C, Gaser C. Luders E, et al. Gigascience. 2025 Jan 6;14:giaf060. doi: 10.1093/gigascience/giaf060. Gigascience. 2025. PMID: 40407124 Free PMC article.

162

M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications.

Zhang Y, Tang L, Zhi S, Hu B, Zuo Z, Ren J, Xie Y, Luo X. Zhang Y, et al. Gigascience. 2025 Jan 6;14:giaf040. doi: 10.1093/gigascience/giaf040. Gigascience. 2025. PMID: 40388309 Free PMC article.

163

Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.

Wang S, Kong F, Dai D, Li C, Hao Y, Wang E, Cao Z, Wang Y, Wang W, Li S. Wang S, et al. Gigascience. 2025 Jan 6;14:giaf042. doi: 10.1093/gigascience/giaf042. Gigascience. 2025. PMID: 40388308 Free PMC article.

164

Multiomics analysis of umbilical cord hematopoietic stem cells from a multiethnic cohort of Hawaii reveals the intergenerational effect of maternal prepregnancy obesity and risks for cancers.

Du Y, Benny PA, Shao Y, Schlueter RJ, Gurary A, Lum-Jones A, Lassiter CB, AlAkwaa FM, Tiirikainen M, Towner D, Ward WS, Garmire LX. Du Y, et al. Gigascience. 2025 Jan 6;14:giaf039. doi: 10.1093/gigascience/giaf039. Gigascience. 2025. PMID: 40388307 Free PMC article.

165

Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.

Wang ZF, Yu EP, Fu L, Deng HG, Zhu WG, Xu FX, Cao HL. Wang ZF, et al. Gigascience. 2025 Jan 6;14:giaf047. doi: 10.1093/gigascience/giaf047. Gigascience. 2025. PMID: 40378137 Free PMC article.

166

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.

Bolleman J, Emonet V, Altenhoff A, Bairoch A, Blatter MC, Bridge A, Duvaud S, Gasteiger E, Kuznetsov D, Moretti S, Michel PA, Morgat A, Pagni M, Redaschi N, Zahn-Zabal M, de Farias TM, Sima AC. Bolleman J, et al. Gigascience. 2025 Jan 6;14:giaf045. doi: 10.1093/gigascience/giaf045. Gigascience. 2025. PMID: 40378136 Free PMC article.

167

A near telomere-to-telomere genome assembly of the Jinhua pig: enabling more accurate genetic research.

Cao C, Miao J, Xie Q, Sun J, Cheng H, Zhang Z, Wu F, Liu S, Ye X, Gong H, Zhang Z, Wang Q, Pan Y, Wang Z. Cao C, et al. Gigascience. 2025 Jan 6;14:giaf048. doi: 10.1093/gigascience/giaf048. Gigascience. 2025. PMID: 40372724 Free PMC article.

168

HVSeeker: a deep-learning-based method for identification of host and viral DNA sequences.

Al-Najim A, Hauns S, Tran VD, Backofen R, Alkhnbashi OS. Al-Najim A, et al. Gigascience. 2025 Jan 6;14:giaf037. doi: 10.1093/gigascience/giaf037. Gigascience. 2025. PMID: 40372723 Free PMC article.

169

Spatial integration of multi-omics data from serial sections using the novel Multi-Omics Imaging Integration Toolset.

Wess M, Andersen MK, Midtbust E, Guillem JCC, Viset T, Størkersen Ø, Krossa S, Rye MB, Tessem MB. Wess M, et al. Gigascience. 2025 Jan 6;14:giaf035. doi: 10.1093/gigascience/giaf035. Gigascience. 2025. PMID: 40366868 Free PMC article.

170

External validation of machine learning models-registered models and adaptive sample splitting.

Gallitto G, Englert R, Kincses B, Kotikalapudi R, Li J, Hoffschlag K, Bingel U, Spisak T. Gallitto G, et al. Gigascience. 2025 Jan 6;14:giaf036. doi: 10.1093/gigascience/giaf036. Gigascience. 2025. PMID: 40366867 Free PMC article.

171

Telomere-to-telomere genome of common bean (Phaseolus vulgaris L., YP4).

Wang Y, Hao X, Chen C, Wang H, Gao P, Yang X, Dong X, Qin H, Li M, Hou S, Jian J, Chang J, Wu J, Mu Z. Wang Y, et al. Gigascience. 2025 Jan 6;14:giaf001. doi: 10.1093/gigascience/giaf001. Gigascience. 2025. PMID: 40366866 Free PMC article.

172

New implementation of data standards for AI in oncology: Experience from the EuCanImage project.

García-Lezana T, Bobowicz M, Frid S, Rutherford M, Recuero M, Riklund K, Cabrelles A, Rygusik M, Fromont L, Francischello R, Neri E, Capella S, Navarro A, Prior F, Bona J, Nicolas P, Starmans MPA, Lekadir K, Rambla J. García-Lezana T, et al. Gigascience. 2025 Jan 6;14:giae101. doi: 10.1093/gigascience/giae101. Gigascience. 2025. PMID: 40359998 Free PMC article.

173

Image segmentation of treated and untreated tumor spheroids by fully convolutional networks.

Streller M, Michlíková S, Ciecior W, Lönnecke K, Kunz-Schughart LA, Lange S, Voss-Böhme A. Streller M, et al. Gigascience. 2025 Jan 6;14:giaf027. doi: 10.1093/gigascience/giaf027. Gigascience. 2025. PMID: 40331344 Free PMC article.

174

The haplotype-resolved T2T genome for Bauhinia × blakeana sheds light on the genetic basis of flower heterosis.

Mu W, Darian JC, Sung WK, Guo X, Yang T, Tang MWM, Chen Z, Tong SKH, Chik IWS, Davidson RL, Edmunds SC, Wei T, Tsui SK. Mu W, et al. Gigascience. 2025 Jan 6;14:giaf044. doi: 10.1093/gigascience/giaf044. Gigascience. 2025. PMID: 40276955 Free PMC article.

175

RWRtoolkit: multi-omic network analysis using random walks on multiplex networks in any species.

Kainer D, Lane M, Sullivan KA, Miller JI, Cashman M, Morgan M, Cliff A, Romero J, Walker A, Dakota Blair D, Chhetri H, Wang Y, Pavicic M, Furches A, Noshay J, Drake M, Ireland AJ, Missaoui A, Kang Y, Sedbrook JC, Dehal P, Canon S, Jacobson D. Kainer D, et al. Gigascience. 2025 Jan 6;14:giaf028. doi: 10.1093/gigascience/giaf028. Gigascience. 2025. PMID: 40272882 Free PMC article.

176

Overture: an open-source genomics data platform.

Shiell M, Bajari R, Andric D, Eubank J, Chan BF, Richardsson AJ, Ali A, Allabadi B, Alturmessov Y, Baker J, Catton A, Cullion K, DeMaria D, Dos Santos P, Feher H, Gerthoffert F, Ha M, Haw RA, Kachru A, Lepsa A, Li A, Mistry RN, Nahal-Bose HK, Pejovic A, Rich S, Rivera L, Schütte C, Su E, Tisma R, Uddin J, Wang C, Wilmer AN, Xiang L, Zhang J, Stein LD, Ferretti V, Courtot M, Yung CK. Shiell M, et al. Gigascience. 2025 Jan 6;14:giaf038. doi: 10.1093/gigascience/giaf038. Gigascience. 2025. PMID: 40272881 Free PMC article.

177

Interspecific hybridization in Brassica species leads to changes in agronomic traits through the regulation of gene expression by chromatin accessibility and DNA methylation.

Quan C, Zhang Q, Zhang X, Chai K, Cheng G, Ma C, Dai C. Quan C, et al. Gigascience. 2025 Jan 6;14:giaf029. doi: 10.1093/gigascience/giaf029. Gigascience. 2025. PMID: 40272880 Free PMC article.

178

GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

Marino GB, Olaiya S, Evangelista JE, Clarke DJB, Ma'ayan A. Marino GB, et al. Gigascience. 2025 Jan 6;14:giaf025. doi: 10.1093/gigascience/giaf025. Gigascience. 2025. PMID: 40208796 Free PMC article.

179

Network-based anomaly detection algorithm reveals proteins with major roles in human tissues.

Kagan D, Jubran J, Yeger-Lotem E, Fire M. Kagan D, et al. Gigascience. 2025 Jan 6;14:giaf034. doi: 10.1093/gigascience/giaf034. Gigascience. 2025. PMID: 40197822 Free PMC article.

180

Phased high-quality genome of the gymnosperm Himalayan Yew assists in paclitaxel pathway exploration.

Li Z, Zong H, Liu X, Wang X, Liu S, Jiao X, Chen X, Wu H, Liu Z, Wang Z, Wang Y, Liu Y, Zhou B, Li Z, Du Q, Li J, Cheng J, Bai J, Zhu X, Yang Y, Liu G, Zhang L, Jiang H, Wang W. Li Z, et al. Gigascience. 2025 Jan 6;14:giaf026. doi: 10.1093/gigascience/giaf026. Gigascience. 2025. PMID: 40184434 Free PMC article.

181

VCF2Dis: an ultra-fast and efficient tool to calculate pairwise genetic distance and construct population phylogeny from VCF files.

Xu L, He W, Tai S, Huang X, Qin M, Liao X, Jing Y, Yang J, Fang X, Shi J, Jin N. Xu L, et al. Gigascience. 2025 Jan 6;14:giaf032. doi: 10.1093/gigascience/giaf032. Gigascience. 2025. PMID: 40184433 Free PMC article.

182

Defining the limits of plant chemical space: challenges and estimations.

Hart CE, Gadiya Y, Kind T, Krettler CA, Gaetz M, Misra BB, Healey D, Allen A, Colluru V, Domingo-Fernández D. Hart CE, et al. Gigascience. 2025 Jan 6;14:giaf033. doi: 10.1093/gigascience/giaf033. Gigascience. 2025. PMID: 40184432 Free PMC article.

183

Telomere-to-telomere genome assembly of Electrophorus electricus provides insights into the evolution of electric eels.

Qi Z, Liu Q, Li H, Zhang Y, Yu Z, Luo W, Wang K, Zhang Y, Pan S, Wang C, Jiang H, Qiu Q, Wang W, Fan G, Li Y. Qi Z, et al. Gigascience. 2025 Jan 6;14:giaf024. doi: 10.1093/gigascience/giaf024. Gigascience. 2025. PMID: 40167991 Free PMC article.

184

The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses.

Liang Y, Xu K, Li J, Shi J, Wei J, Zheng X, He W, Zhang X. Liang Y, et al. Gigascience. 2025 Jan 6;14:giaf031. doi: 10.1093/gigascience/giaf031. Gigascience. 2025. PMID: 40167990 Free PMC article.

185

Correction to: "UDE DIATOMS in the Wild 2024": a new image dataset of freshwater diatoms for training deep learning models.

[No authors listed] [No authors listed] Gigascience. 2025 Jan 6;14:giaf043. doi: 10.1093/gigascience/giaf043. Gigascience. 2025. PMID: 40139910 Free PMC article. No abstract available.

186

High-fidelity wheat plant reconstruction using 3D Gaussian splatting and neural radiance fields.

Stuart LAG, Wells DM, Atkinson JA, Castle-Green S, Walker J, Pound MP. Stuart LAG, et al. Gigascience. 2025 Jan 6;14:giaf022. doi: 10.1093/gigascience/giaf022. Gigascience. 2025. PMID: 40139909 Free PMC article.

187

EnrichDO: a global weighted model for Disease Ontology enrichment analysis.

Yang H, Fu H, Zhang M, Liu Y, He YO, Wang C, Cheng L. Yang H, et al. Gigascience. 2025 Jan 6;14:giaf021. doi: 10.1093/gigascience/giaf021. Gigascience. 2025. PMID: 40139908 Free PMC article.

188

Observational, causal relationship and shared genetic basis between cholelithiasis and gastroesophageal reflux disease: evidence from a cohort study and comprehensive genetic analysis.

Lyu Y, Tong S, Huang W, Ma Y, Zeng R, Jiang R, Luo R, Leung FW, Lian Q, Sha W, Chen H. Lyu Y, et al. Gigascience. 2025 Jan 6;14:giaf023. doi: 10.1093/gigascience/giaf023. Gigascience. 2025. PMID: 40139907 Free PMC article.

189

Genomic and transcriptomic analyses of Heteropoda venatoria reveal the expansion of P450 family for starvation resistance in spiders.

Zhang G, Wang Y, Jiang H, Wang Y. Zhang G, et al. Gigascience. 2025 Jan 6;14:giaf019. doi: 10.1093/gigascience/giaf019. Gigascience. 2025. PMID: 40117180 Free PMC article.

190

How to select predictive models for decision-making or causal inference.

Doutreligne M, Varoquaux G. Doutreligne M, et al. Gigascience. 2025 Jan 6;14:giaf016. doi: 10.1093/gigascience/giaf016. Gigascience. 2025. PMID: 40117179 Free PMC article.

191

Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants.

Lee H, Seo PJ. Lee H, et al. Gigascience. 2025 Jan 6;14:giaf020. doi: 10.1093/gigascience/giaf020. Gigascience. 2025. PMID: 40117178 Free PMC article.

192

Characteristics and filtering of low-frequency artificial short deletion variations based on nanopore sequencing.

Ye F, Zhu J, Zhang X, Zhang J, Xie Z, Yang T, Han Y, Yang X, Ren Z, Ni M. Ye F, et al. Gigascience. 2025 Jan 6;14:giaf018. doi: 10.1093/gigascience/giaf018. Gigascience. 2025. PMID: 40117177 Free PMC article.

193

Healthy microbiome-moving towards functional interpretation.

Zielińska K, Udekwu KI, Rudnicki W, Frolova A, Łabaj PP. Zielińska K, et al. Gigascience. 2025 Jan 6;14:giaf015. doi: 10.1093/gigascience/giaf015. Gigascience. 2025. PMID: 40117176 Free PMC article.

194

NanoMnT: an STR analysis tool for Oxford Nanopore sequencing data driven by a comprehensive analysis of error profile in STR regions.

Park G, An H, Luo H, Park J. Park G, et al. Gigascience. 2025 Jan 6;14:giaf013. doi: 10.1093/gigascience/giaf013. Gigascience. 2025. PMID: 40094553 Free PMC article.

195

Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa).

Starcevic A, Figueredo RTA, Naldoni J, Corrêa LL, Okamura B, Adriano EA, Long PF. Starcevic A, et al. Gigascience. 2025 Jan 6;14:giaf014. doi: 10.1093/gigascience/giaf014. Gigascience. 2025. PMID: 40080648 Free PMC article.

196

Cerebellocerebral connectivity predicts body mass index: a new open-source Python-based framework for connectome-based predictive modeling.

Bachmann T, Mueller K, Kusnezow SNA, Schroeter ML, Piaggi P, Weise CM. Bachmann T, et al. Gigascience. 2025 Jan 6;14:giaf010. doi: 10.1093/gigascience/giaf010. Gigascience. 2025. PMID: 40072905 Free PMC article.

197

A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance.

Han H, Salinas N, Barbey CR, Jang YJ, Fan Z, Verma S, Whitaker VM, Lee S. Han H, et al. Gigascience. 2025 Jan 6;14:giaf005. doi: 10.1093/gigascience/giaf005. Gigascience. 2025. PMID: 40072904 Free PMC article.

198

An analysis of performance bottlenecks in MRI preprocessing.

Dugré M, Chatelain Y, Glatard T. Dugré M, et al. Gigascience. 2025 Jan 6;14:giae098. doi: 10.1093/gigascience/giae098. Gigascience. 2025. PMID: 40072903 Free PMC article.

199

Correction to: Habitat suitability maps for Australian flora and fauna under CMIP6 climate scenarios.

[No authors listed] [No authors listed] Gigascience. 2025 Jan 6;14:giae031. doi: 10.1093/gigascience/giae031. Gigascience. 2025. PMID: 40040458 Free PMC article. No abstract available.

200

Benchmarking short-read metagenomics tools for removing host contamination.

Gao Y, Luo H, Lyu H, Yang H, Yousuf S, Huang S, Liu YX. Gao Y, et al. Gigascience. 2025 Jan 6;14:giaf004. doi: 10.1093/gigascience/giaf004. Gigascience. 2025. PMID: 40036691 Free PMC article.

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