The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index; none of the 28 sources its claims cite is checked for support yet.
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
Open accessAbstract
The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption--both intentionally and through widespread cross-contamination--and for the past 60 years it has served a role analogous to that of a model organism. The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%). The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.
Overview
CoChat Summary
Written by AI from the paper’s full text.
TL;DR
The paper reports a haplotype-resolved genome and epigenome of the aneuploid HeLa CCL-2 cancer cell line, using clone dilution pool sequencing to phase variants across full chromosome arms. It finds that HeLa is relatively stable in point variation, maps aneuploidy/LOH and structural rearrangements, and shows haplotype-specific activation of MYC by an integrated HPV-18 genome at chromosome 8q24.21.
Key findings
- HeLa CCL-2 carried 4.1 × 10^6 SNVs, with 90.2% overlapping 1000 Genomes Project variants, similar to control genomes (mean 4.2 × 10^6 SNVs; 87.7% overlap), suggesting no appreciably large accumulation of somatic SNVs relative to inherited variants.
- Copy-number analysis found 61% of the genome at baseline copy number three, only 3% at CN>4 or CN<2, and LOH encompassing 15.7% of the genome, including entire chromosome arms 5p, 6q, Xp, and Xq.
- The study validated 8,165 somatic mutations with an estimated sensitivity of 61.1%, giving a point mutational frequency of 2.16 per Mb, on the lower end of frequencies observed across cancer genomes.
- A highly rearranged HPV-18 integration at chromosome 8q24.21 was reconstructed; the integrated viral genome lacks a functional E2 and is associated with strong, haplotype-specific MYC activation ~500 kb upstream (mean expression ratio 95:1).
Methods
- Haplotype-resolved whole-genome sequencing of HeLa CCL-2 used shotgun sequencing to 88X non-duplicate coverage plus mate-pair, long-read, and clone dilution pool sequencing.
- Phasing used 288 fosmid clone dilution pools, yielding 518,293 non-overlapping clones with a median insert size of 33 kb and 6.3X physical coverage of the haploid reference; haplotype blocks had an N50 of 550 kb and scaffolds covered 1.96 Gb (90.3% of the non-LOH genome) with an N50 of 44.8 Mb.
- Copy number and LOH were mapped with HMM-based read-depth analysis; RNA-Seq and ENCODE datasets were phased against HeLa CCL-2 haplotype and copy-number maps to analyze haplotype-specific expression, chromatin, and transcription factor binding.
Limitations
- The paper states that normal tissue corresponding to HeLa is unavailable, so inherited and somatic variants cannot be fully distinguished; some protein-altering variants could not be excluded as rare inherited variants or passenger mutations.
- The paper states that without estimates for parameters such as the number of doublings during tumorigenesis, cells explanted, and passages in culture, the post-aneuploidy mutational burden cannot be rescaled to a rate per base per division.
- The paper states that further studies are required to resolve the functional relevance of candidate genes and to assess whether they are recurrently altered in HPV+ cervical carcinomas; it also notes that phasing of HeLa S3 ENCODE data relied on CCL-2 maps because the strains are nearly identical, though not identical.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
37 Own result · 12 Check pending · 6 Not checked yet · 5 Own interpretation · 4 Own method · 3 Sources not found · 3 No full text of the sources
In the paper
“The gene-level overlap with the Sanger Cancer Gene Census (SCGC)12 was also comparable (HeLa, n = 4; controls, mean n = 8.7).”
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
What the sources say
- Not matchedcites [12] The Cancer Genome Project. http://www.sanger.ac.uk/genetics/CGP/ (Wellcome Trust Sanger Institute, January 2013)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plainSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Not matched
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Excluding these and sites found in the 11 control genomes, 5,282 sites (mean, 1.32 per haploid Mb) remained at which clones differed in genotype between the two or more amplified copies of the same germline haplotype, with little regional variation in the abundance (Supplementary Fig. 22).”
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
plainSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For example, in non-LOH CN=3 regions that are necessarily 2:1 or 1:2, allelic ratios calculated for each block had distributions centered on 0.32 or 0.65, close to the expected fractions of 1/3 and 2/3 (Supplementary Fig. 14).”
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
plainSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Moreover, on average, each haplotype copy makes a comparable contribution to the transcriptome despite uneven amplification and, in some cases, rearrangement (Figure 3c,e).”
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
plainSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We first calculated the cumulative allelic ratio among shotgun reads for the SNVs residing in each haplotype block, which clustered closely with the underlying haplotype ratio.”
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
plainstates an associationSingle case- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 28
- Probably not a substantial claim. 4
Create a free account to see these claims.
Create a free account to see these assumptions.
36 more claims
Create a free account to see all 70 claims and to verify the 19 references still open.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Generally, various cell lines have revolutionized scientific investigations and have found applications in vaccine development, drug testing for metabolism and toxicity, generating antibodies, exploring gene functions, creating artificial tissues like synthetic skin, and producing biologic substances such as therapeutic proteins [16,19,26].”
From Cell Immortality: In Vitro Effective Techniques to Achieve and Investigate Its Applications and Challenges (2024) · cites this paper as [19]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
“The gene-level overlap with the Sanger Cancer Gene Census (SCGC)12 was also comparable (HeLa, n = 4; controls, mean n = 8.7).”
§ The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line > Abstract
“Canonical tumor suppressors and oncogenes were notably absent among the five SCGC genes with PPA variants in HeLa (BCL11B, EP300, FGFR3, NOTCH1, and PRDM16, Supplementary Tables 3–6).”
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,761
An integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Self-citationLi, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,454
Comprehensive genomic characterization of squamous cell lung cancers
The Cancer Genome Atlas Research Network (2012) · Nature · doi:10.1038/nature11404 · Cited by 3,994
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Self-citationHigh-quality draft assemblies of mammalian genomes from massively parallel sequence data
Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, F. J., Burton, J. N., Walker, B. J., Sharpe, T., Hall, G., Shea, T., Sykes, S. M., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1017351108 · Cited by 1,540
Self-citation
Cited by
Items 201–300 of 364
Yuan, F., Tang, Y., Cao, M., Ren, Y., Li, Y., Yang, G., Ou, Q., Tustumi, F., Sandri, G. B. L., Raissi, D., et al. (2022) · Annals of Translational Medicine · doi:10.21037/atm-22-3147 · Cited by 12
Critical points for an accurate human genome analysis
White, S. J., Laros, J. F. J., Bakker, E., Cambon‐Thomsen, A., Eden, M., Leonard, S., Lochmüller, H., Matthijs, G., Mattocks, C., Patton, S. J., et al. (2017) · Human Mutation · doi:10.1002/humu.23238 · Cited by 12
The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition
Helou, L., Beauclair, L., Dardente, H., Arensburger, P., Buisine, N., Jaszczyszyn, Y., Guillou, F., Lecomte, T., Kentsis, A., & Bigot, Y. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.166805 · Cited by 12
The role of the hepatitis B virus genome and its integration in the hepatocellular carcinoma
Li, W., Wang, S., Jin, Y., Mu, X., Guo, Z., Qiao, S., Jiang, S., Liu, Q., & Cui, X. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1469016 · Cited by 11
Bradbury, N. A. (2017) · Principles of Gender-Specific Medicine · doi:10.1016/b978-0-12-803506-1.00051-6 · Cited by 11
Extracts from Pulsatilla patens target cancer-related signaling pathways in HeLa cells
Łaska, G., Maciejewska‐Turska, M., Sieniawska, E., Świątek, Ł., Pasco, D. S., & Balachandran, P. (2021) · Scientific Reports · doi:10.1038/s41598-021-90136-3 · Cited by 11
In vitro assessment of a computer-designed potential anticancer agent in cervical cancer cells
Visagie, M. H., Jaiswal, S. R., & Joubert, A. M. (2016) · Biological Research · doi:10.1186/s40659-016-0104-5 · Cited by 11
Annonaceae acetogenins: A potential treatment for gynecological and breast cancer
Bravo‐Alfaro, D. A., Montalvo‐González, E., Zapien-Macias, J. M., Sampieri-Morán, J. M., Garcia, H. S., & Luna‐Bárcenas, G. (2024) · Fitoterapia · doi:10.1016/j.fitote.2024.106187 · Cited by 10
Xia, J., Li, J., Wang, X., Li, Y., & Li, J. (2024) · Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy · doi:10.1016/j.saa.2024.125242 · Cited by 10
Cardona-Mendoza, A., Fonseca-Benítez, A. V., Buitrago, D. M., Coy-Barrera, E. D., & Perdomo, S. J. (2023) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2023.117225 · Cited by 10
Multiple HPV integration mode in the cell lines based on long-reads sequencing
Cui, X., Li, Y., Zhang, C., Qi, Y., Sun, Y., & Li, W. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1294146 · Cited by 10
Quantitative control of noise in mammalian gene expression by dynamic histone regulation
Tan, D., Chen, R., Mo, Y., Gu, S. P., Ma, J., Xu, W. Q., Lu, X., He, H., Jiang, F., Fan, W., et al. (2021) · eLife · doi:10.7554/elife.65654 · Cited by 10
Sheard, M. A., Ghent, M. V., Cabral, D. J., Lee, J. C., Khankaldyyan, V., Ji, L., Wu, S., Kang, M. H., Sposto, R., Asgharzadeh, S., et al. (2015) · Experimental Cell Research · doi:10.1016/j.yexcr.2015.03.024 · Cited by 10
Peng, X., Yang, Z., Yang, P., Chai, Y., Liang, W., Li, Z., & Yuan, R. (2020) · Chemical Communications · doi:10.1039/d0cc03858j · Cited by 9
Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs
Gadgil, R. Y., Rider, S. D., Shrestha, R., Alhawach, V., Hitch, D. C., & Leffak, M. (2024) · NAR Cancer · doi:10.1093/narcan/zcae027 · Cited by 9
Hu, Z.-F., Liu, W., Liu, J., Zhou, H., Sun, C., ChaoTian, Guo, X., Zhu, C., Shao, M., Wang, S., et al. (2024) · Antiviral Research · doi:10.1016/j.antiviral.2024.106035 · Cited by 9
Moise, R. K., Jonas, E., Campa, E. M., Clisbee, M., Junior, G. L. L., & Kobetz, E. N. (2021) · Health Education & Behavior · doi:10.1177/1090198121990381 · Cited by 9
High levels of chromosomal instability facilitate the tumor growth and sphere formation
Iemura, K., Anzawa, H., Funayama, R., Iwakami, R., Nakayama, K., Kinoshita, K., & Tanaka, K. (2022) · Cancer Science · doi:10.1111/cas.15457 · Cited by 9
Pulsatilla vulgaris Inhibits Cancer Proliferation in Signaling Pathways of 12 Reporter Genes
Łaska, G., Sieniawska, E., Maciejewska‐Turska, M., Świątek, Ł., Pasco, D. S., & Balachandran, P. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021139 · Cited by 9
Wang, L., Shen, H., Zhu, D., Feng, B., Yu, L., Tian, X., Ren, C., Gao, C., Li, X., Ma, D., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.24080 · Cited by 9
Wu, L. L., Jiang, M., Wang, Y., Zhou, B., Sun, Y., Zhou, K., Xie, J., Zhong, Y., Zhao, Z., Dean, M. C., et al. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.03.008 · Cited by 8
FGFR1 amplification and co-overexpression of c-MYC in oropharyngeal squamous cell carcinoma
Ozretić, L., Wagner, S., Huebbers, C. U., Gattenlöhner, S., Klußmann, J. P., Beutner, D., Zander, T., Buettner, R., & Quaas, A. (2016) · Oral Oncology · doi:10.1016/j.oraloncology.2015.12.006 · Cited by 8
Mügge, F. L. B., & Morlock, G. E. (2022) · Journal of Chromatography A · doi:10.1016/j.chroma.2022.463522 · Cited by 8
Gao, G., & Smith, D. D. (2015) · Viruses · doi:10.3390/v7082831 · Cited by 8
Romana, S. P., Radford‐Weiss, I., Lapierre, J., Doye, V., & Geoffroy, M. (2015) · Chromosoma · doi:10.1007/s00412-015-0567-0 · Cited by 8
Akhtar, M. J., Ahamed, M., Alhadlaq, H. A., & Alrokayan, S. (2021) · ACS Omega · doi:10.1021/acsomega.1c01882 · Cited by 8
Combination of furosemide, gold, and dopamine as a potential therapy for breast cancer
Wang, Z., Mehmood, A., Yao, J., Zhang, H., Wang, L., Al-Shehri, M., Kaushik, A. C., & Wei, D. (2023) · Functional & Integrative Genomics · doi:10.1007/s10142-023-01007-1 · Cited by 8
An integrated valved microfluidic platform for rapid and simultaneous nucleic acid detection
Wang, Z., Yang, F., Zeng, S., Sun, R., Hu, Q. X., & Du, Y. (2025) · Lab on a Chip · doi:10.1039/d5lc01096a · Cited by 7
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences
Pan, W., Zhao, Y., Xu, Y., & Zhou, F. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-164 · Cited by 7
Building Trust in 21st Century Genomics
Szego, M. J., Buchanan, J. A., & Scherer, S. W. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007690 · Cited by 7
Role of the Common Fragile Sites in Cancers with a Human Papillomavirus Etiology
Gao, G., & Smith, D. I. (2016) · Cytogenetic and Genome Research · doi:10.1159/000455287 · Cited by 7
Sima, J., Bartlett, D. A., Gordon, M. R., & Gilbert, D. M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1265 · Cited by 7
AAVS1-Targeted Plasmid Integration in AAV Producer Cell Lines
Luo, Y., Frederick, A., Martin, J. M., Scaria, A., Cheng, S. H., Armentano, D., Wadsworth, S. C., & Vincent, K. A. (2017) · Human Gene Therapy Methods · doi:10.1089/hgtb.2016.158 · Cited by 7
Cancer–drug response prediction via feature aggregation and association graph learning
Xu, K., Wang, M., Zou, X. G., Ji, C., Zhou, H., & Tang, C. (2025) · Engineering Applications of Artificial Intelligence · doi:10.1016/j.engappai.2025.110671 · Cited by 6
Li, K., Huang, F., Zhang, T., Yang, F., Duan, W., Chen, S., Hu, T., & Huang, X. (2025) · BMC Cancer · doi:10.1186/s12885-025-14138-4 · Cited by 6
Wang, L., Shen, H., Feng, B., Zhu, D., Yu, L., Tian, X., Ren, C., Gao, C., Li, X., Ma, D., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0175520 · Cited by 6
Did you forget your cell sex? An update on the inclusion of sex as a variable in AJP-Cell Physiology
Holland, A., & Bradbury, N. A. (2023) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00434.2022 · Cited by 6
Synthetic human gonadal tissues for toxicology
Nishimura, T., & Takebe, T. (2024) · Reproductive Toxicology · doi:10.1016/j.reprotox.2024.108598 · Cited by 6
Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes
Brunette, G. J., Tourdot, R. W., Wang, J., Wangsa, D., Pellman, D. S., & Zhang, C.-Z. (2026) · Cell Systems · doi:10.1016/j.cels.2025.101477 · Cited by 6
NIH director explains HeLa agreement
Callaway, E. (2013) · Nature · doi:10.1038/nature.2013.13521 · Cited by 6
Biology is the root of variability: cautionary tales in Caenorhabditis elegans biology
Pho, K. B., & MacNeil, L. T. (2019) · Biochemical Society Transactions · doi:10.1042/bst20190001 · Cited by 6
Post-identifiability in changing sociotechnological genomic data environments
Akyüz, K., Goisauf, M., Chassang, G., Kozera, Ł., Mežinska, S., Tzortzatou, O., & Mayrhofer, M. T. (2023) · BioSocieties · doi:10.1057/s41292-023-00299-7 · Cited by 6
Carlevaro-Fita, J., Rahim, A., Guigó, R., Vardy, L. A., & Johnson, R. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/013508 · Cited by 6
CENP-A associated lncRNAs influence chromosome segregation in human cellsPreprint
Quénet, D., Sturgill, D. M., Olson, M. K., & Dalal, Y. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/097956 · Cited by 6
Vázquez-Diez, C., & FitzHarris, G. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7780-2_20 · Cited by 5
Sumo-regulatory SENP2 controls the homeostatic squamous mitosis-differentiation checkpoint
Galán-Vidal, J., García-Gaipo, L., Molinuevo, R., Dias, S., Tsoi, L. C., Gómez‐Román, J., Elder, J. T., Hochegger, H., & Gandarillas, A. (2024) · Cell Death and Disease · doi:10.1038/s41419-024-06969-z · Cited by 5
Many Breast Cancer Mutations Parallel Mutations in Known Viral Cancers
Friedenson, B. (2014) · Journal of Genomes and Exomes · doi:10.4137/jge.s18944 · Cited by 5
Building in vitro tools for livestock genomics: chromosomal variation within the PK15 cell line
Johnsson, M., Hickey, J. M., & Jungnickel, M. K. (2024) · BMC Genomics · doi:10.1186/s12864-023-09931-z · Cited by 5
Pabba, M. K., Meyer, J., Celikay, K., Schermelleh, L., Rohr, K., & Cardoso, M. C. (2024) · Histochemistry and Cell Biology · doi:10.1007/s00418-024-02285-x · Cited by 5
A natural product enhances apoptosis via mitochondria/caspase‐mediated pathway in HeLa cells
Fan, Y., Zhang, Y., Liu, Y., Xu, W., Yang, Y., Hao, Y., & Tao, L. (2019) · Journal of Cellular Biochemistry · doi:10.1002/jcb.28939 · Cited by 5
MacKinnon, R. N., Peverall, J., Campbell, L. J., & Wall, M. (2020) · Molecular Cytogenetics · doi:10.1186/s13039-020-00517-y · Cited by 5
Glycome Profiling of Cancer Cell Lines Cultivated in Physiological and Commercial Media
Wang, J., Peng, W., Yu, A., Fokar, M., & Mechref, Y. S. (2022) · Biomolecules · doi:10.3390/biom12060743 · Cited by 5
Kim, S. S.-Y., Kim, E., Kimm, A. K., & Kwak, H. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/836841 · Cited by 5
Reply to: Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes
Liu, Y., Liu, Z., Cao, Z., & Wei, W. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0431-5 · Cited by 5
Expression of HPV oncogenes from a single integration site in cervical cancer cell linesPreprint
Yu, L., Lobanov, A. V., Majerčiak, V., Mirza, S., Band, V., Liu, H., Cam, M., & Zheng, Z. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.25.171959 · Cited by 5
Genomic structures and regulation patterns at HPV integration sites in cervical cancerPreprint
Porter, V., O’Neill, K., MacLennan, S., Corbett, R., Ng, M., Culibrk, L., Hamadeh, Z., Iden, M., Schmidt, R., Tsaih, S., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.04.564800 · Cited by 5
ralphi: A Deep Reinforcement Learning Framework for Haplotype Assembly
Battistella, E., Maheshwari, A., Ekim, B., Berger, B., & Popic, V. (2025) · Lecture notes in computer science · doi:10.1007/978-3-031-90252-9_37 · Cited by 4
Wang, L., Li, X., Ren, C., Liu, L., Yao, J., Wu, M., Shen, H., Zhu, D., Wang, X., Yuan, Z., et al. (2026) · Cell Death and Disease · doi:10.1038/s41419-025-08195-7 · Cited by 4
Xu, X.-S. (2024) · American Journal of Cancer Research · doi:10.62347/kkle8602 · Cited by 4
A new oxygen modification cyclooctaoxygen binds to nucleic acids as sodium crown complex
Kesel, A. J., Day, C. W., Montero, C. M., & Schinazi, R. F. (2016) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2016.01.022 · Cited by 4
Haplotype resolution at the single-cell level
Adey, A. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717798114 · Cited by 4
Self-citationAll cells have a sex: Sex chromosome function at the cellular level
Bradbury, N. A. (2023) · Principles of Gender-Specific Medicine · doi:10.1016/b978-0-323-88534-8.00054-7 · Cited by 4
Ray, D. B., Merrill, G. A., Brenner, F. J., Lytle, L. S., Lam, T., McElhinney, A., Anders, J., Rock, T. T., Lyker, J. K., Barcus, S., et al. (2015) · Experimental Cell Research · doi:10.1016/j.yexcr.2015.07.029 · Cited by 4
Interleukin-1α associates with the tumor suppressor p53 following DNA damage
Novak, J., Zamostna, B., Vopalensky, V., Buryskova, M., Burysek, L., Doleckova, D., & Pospisek, M. (2020) · Scientific Reports · doi:10.1038/s41598-020-63779-x · Cited by 3
Wang, J., Peng, W., Yu, A., Fokar, M., & Mechref, Y. S. (2022) · Biomolecules · doi:10.3390/biom12111575 · Cited by 3
Bourguignon, T., Sharma, P., Hazan‐Halevy, I., & Peer, D. (2026) · Materials Today · doi:10.1016/j.mattod.2026.103436 · Cited by 3
Testing the purity of cell cultures using clinical diagnostic PCR kits
Morozova, A. V., Borchsenius, S. N., Vishnyakov, I. E., & Malinin, A. Y. (2017) · Cell and Tissue Biology · doi:10.1134/s1990519x17030075 · Cited by 3
Fan, W., Yu, M., Wang, X., Xie, W., Tian, R., Cui, Z., Jin, Z., Huang, Z., Das, B. C., Severinov, K., et al. (2021) · Cancer Gene Therapy · doi:10.1038/s41417-021-00355-z · Cited by 3
Genetic privacy and the use of archival human material in genetic studies – current perspectives
Jones, D. G. (2015) · Medicolegal and Bioethics · doi:10.2147/mb.s56057 · Cited by 3
Chroniques génomiques - Henrietta Lacks et les cellules HeLa: Les leçons d’une histoire
Jordan, B. (2013) · médecine/sciences · doi:10.1051/medsci/20132911023 · Cited by 3
Toward Recovering Allele-specific Cancer Genome Graphs
Rajaraman, A., & Ma, J. (2018) · Journal of Computational Biology · doi:10.1089/cmb.2018.0022 · Cited by 3
Towards Recovering Allele-Specific Cancer Genome Graphs
Rajaraman, A., & Ma, J. (2017) · Lecture notes in computer science · doi:10.1007/978-3-319-56970-3_14 · Cited by 2
Furugori, K., Suzuki, H., Abe, R., Horiuchi, K., Akiyama, T., Hirose, T., Toyoda, A., & Takahashi, H. (2024) · Genes to Cells · doi:10.1111/gtc.13121 · Cited by 2
Andersen, K. Y., Salachan, P. V., Borre, M., Ulhøi, B. P., Stougaard, M., Sørensen, K. D., & Steiniche, T. (2024) · Infectious Agents and Cancer · doi:10.1186/s13027-024-00619-x · Cited by 2
ADARB1 inhibits glycolysis and progression of cervical cancer through the HMGB1/PFKFB3 axis
Liu, X., Wang, A., Su, M., Liang, Z., Ren, H., Yao, S., Wan, S., Gao, Y., Wang, H., & Cai, H. (2026) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2026.168191 · Cited by 2
viroCapt: A Bioinformatics Pipeline for Identifying Viral Insertion in Human Host Genome
Wack, M., Veyer, D. L., Péneau, C., Lameiras, S., Digan, W. E., Nicolas, A. G., Zucman‐Rossi, J., Imbeaud, S., Burgun, A., Péré, H., et al. (2022) · Studies in health technology and informatics · doi:10.3233/shti220602 · Cited by 2
Who Can Use Your Cells Or Tissues For Scientific Research?
Beers, J. L., Geffert, R. M., Latham, B. D., & Jackson, K. D. (2024) · Frontiers for Young Minds · doi:10.3389/frym.2024.1233752 · Cited by 2
Progress in genomics according to bingo: 2013 edition
Karczewski, K. J. (2013) · Genome biology · doi:10.1186/gb4148 · Cited by 2
NCMHap: a novel method for haplotype reconstruction based on Neutrosophic c-means clustering
Zamani, F., Olyaee, M. H., & Khanteymoori, A. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03775-0 · Cited by 2
Ma, H. T. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1538-6_23 · Cited by 2
Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges
Chan, A. P.-Y., Choi, Y., Rangan, A., Zhang, G., Podder, A., Berens, M. E., Sharma, S. K., Pirrotte, P., Byron, S. A., Duggan, D., et al. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2819-5_1 · Cited by 2
Haplotype-Phased Common Marmoset Embryonic Stem Cells for Genome Editing Using CRISPR/Cas9Preprint
Zhou, B., Ho, S. S., Leung, L. C., Ward, T. R., Ho, M., Plastini, M. J., Vermilyea, S. C., Emborg, M. E., Golos, T. G., Albertelli, M. A., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3299433 · Cited by 2
Graph-based deep reinforcement learning for haplotype assembly with RalphiPreprint
Battistella, E., Maheshwari, A., Ekim, B., Berger, B., & Popic, V. (2025) · Genome Research · doi:10.1101/gr.280569.125 · Cited by 2
lncRNA PCED1B-AS1 facilitates cervical cancer progression via targeting miR-361-3p
Wang, S., Wang, J., & Wang, K. (2025) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770.2025.2537150 · Cited by 1
Mohamed, H. R. H., Elhaggan, S. O., Hekal, R. S., Fahmy, C. W. H., Noure, Z., Ahmed, N., Diab, A., & Safwat, G. (2026) · Scientific Reports · doi:10.1038/s41598-026-45693-w · Cited by 1
Comparison of the experimental methods in haplotype sequencing via next generation sequencing
Tu, J., Lü, N., Duan, M., Ju, A., Sun, X. S., & Lu, Z. (2016) · Quantitative Biology · doi:10.1007/s40484-016-0068-z · Cited by 1
Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B)
Loiseau, V., Cordaux, R., Giraud, I., Beby‐Defaux, A., Lévêque, N., & Gilbert, C. (2020) · Scientific Reports · doi:10.1038/s41598-020-73169-y · Cited by 1
HiCancer: accurate and complete cancer genome phasing with Hi-C reads
Pan, W., Gong, D., Sun, D., & Luo, H. (2021) · Scientific Reports · doi:10.1038/s41598-021-86104-6 · Cited by 1
Giannelli, G. (2009) · CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) · Cited by 1
Münger, K. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.98745-2 · Cited by 1
Cell rounding causes genomic instability by dissociation of single-stranded DNA-binding proteinsPreprint
Guo, Q., Liao, X., Wang, X.-W., Liu, L., & Song, B. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/463653 · Cited by 1
HPV Virology: Cellular Targets of HPV Oncogenes and Transformation
Smith, E. A., Matrka, M. C., & Wells, S. I. (2015) · Springer eBooks · doi:10.1007/978-3-319-21100-8_4
Identificação de RNAs longos não-codificadores de proteínas regulados por micro-RNAs
Amaral, M. S. (2013) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.46.2013.tde-22102014-102412
Maretty, L., Sibbesen, J. A., & Krogh, A. (2014)
Does family always matter? Public genomes and their effect on relatives
Quake, S. R. (2013)
Engineered Nucleases and Trinucleotide Repeat Diseases
Wilson, J. H., Moye, C., & Mittelman, D. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-3509-3_9
Odkrycie komórek HeLa początkiem rewolucji w badaniach in vitro
Harańczyk, N. A., & Pocheć, E. (2016) · Jagiellonian University Repository (Jagiellonian University)
Detection of HBV integration in plasma and paired tumor samples
Cui, X., Huo, Q., Yan, W., & Li, W. (2017) · Biomedical Research-tokyo
The Cellular and Molecular Axis of Muscle Regeneration
Ieronimakis, N. M. (2014) · ResearchWorks at the University of Washington (University of Washington)
Metadata
- Authors
- Adey, A., Burton, J. N., Kitzman, J. O., Hiatt, J. B., Lewis, A. P., Martin, B. K., Qiu, R., Lee, C., & Shendure, J.
- Affiliations
- University of Washington (US)
- Corresponding author
- Adey, Andrew
- Shendure, Jay
- ORCID
- Venue
- Nature
- Published
- 2013-08-07
- Volume
- 500
- Issue
- 7461
- Pages
- 207-211
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3740412
- OpenAlex
- W1972616856
- Cited by
- 362
- References
- 43
- Citations by year
- 2026: 16 · 2025: 12 · 2024: 33 · 2023: 24 · 2022: 21 · 2021: 36 · 2020: 26 · 2019: 28 · 2018: 27 · 2017: 30 · 2016: 33 · 2015: 31 · 2014: 28 · 2013: 15
- FWCI
- 16.82
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Institute on Aging (F30AG039173)
- National Human Genome Research Institute (R01HG006283, T32HG000035)
- National Cancer Institute (R21CA160080)
- National Institute of General Medical Sciences (T32GM007266)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Health Sciences › Medicine › Epidemiology › Cervical Cancer and HPV Research
- Keywords
- haplotype-resolved genome, aneuploidy, copy number variation, loss of heterozygosity, MYC activation, somatic mutation rate, epigenome, DNA methylation, histone modifications, cell line stability
- MeSH terms
- Proto-Oncogene Mas, Aneuploidy, Uterine Cervical Neoplasms, Female, Haplotypes, HeLa Cells, Humans, Molecular Sequence Data, Mutation, Transcriptional Activation, Genome, Human, Genes, myc, Sequence Analysis, DNA, Human papillomavirus 18, DNA Copy Number Variations, Epigenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-11-12, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-12 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
