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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules. | Cheng AP, Rusinek I, Sossin A, Widman AJ, Meiri E, Krieger G, Hirschberg O, Tov DS, Gilad S, Jaimovich A, Barad O, Avaylon S, Rajagopalan S, Potenski C, Prieto T, Yuan DJ, Furatero R, Runnels A, Costa BM, Shoag JE, Assaad MA, Sigouros M, Manohar J, King A, Wilkes D, Otilano J, Malbari MS, Elemento O, Mosquera JM, Altorki NK, Saxena A, Callahan MK, Robine N, Germer S, Evrony GD, Faltas BM, Landau DA | bioRxiv : the preprint server for biology | 40832334 | bioRxiv | 2025 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/40832334 |
| Comprehensive benchmarking of somatic mutation detection by the SMaHT Network. | Somatic Mosaicism across Human Tissues Network, Abyzov A | bioRxiv : the preprint server for biology | 41279200 | bioRxiv | 2025 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/41279200 |
| The Somatic Mosaicism across Human Tissues Network. | Coorens THH, Oh JW, Choi YA, Lim NS, Zhao B, Voshall A, Abyzov A, Antonacci-Fulton L, Aparicio S, Ardlie KG, Bell TJ, Bennett JT, Bernstein BE, Blanchard TG, Boyle AP, Buenrostro JD, Burns KH, Chen F, Chen R, Choudhury S, Doddapaneni HV, Eichler EE, Evrony GD, Faith MA, Fazzio TG, Fulton RS, Garber M, Gehlenborg N, Germer S, Getz G, Gibbs RA, Hernandez RG, Jin F, Korbel JO, Landau DA, Lawson HA, Lennon NJ, Li H, Li Y, Loh PR, Marth G, McConnell MJ, Mills RE, Montgomery SB, Natarajan P, Park PJ, Satija R, Sedlazeck FJ, Shao DD, Shen H, Stergachis AB, Underhill HR, Urban AE, VonDran MW, Walsh CA, Wang T, Wu TP, Zong C, Lee EA, Vaccarino FM, Somatic Mosaicism across Human Tissues Network | Nature | 40604182 | Nature | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40604182 |
| A comprehensive view of somatic mosaicism by single-cell DNA analysis. | Luquette LJ, Coorens THH, Natu A, Suvakov M, Caplin A, Jun MS, Mo A, Pelt J, Anderson L, Berselli M, Bhamidipati S, Blanchard T, Brew J, Chun HE, Chun H, Dehankar MK, Feng WC, Furatero R, Grochowski CM, Ho E, Jang Y, Kottapalli K, Leonard MK, Lim NS, Lindsay T, Nicholson S, Raimondi I, Runnels A, Scharlee C, Shin J, Veit AD, VonDran M, Wang Y, Yuan DJ, Zhao Y, SMaHT Single Cell Focus Group, Bell TJ, Ardlie K, Doddapaneni H, Fulton R, Germer S, Landau D, Oh JW, Park PJ, Vaccarino FM, Walsh C, Abyzov A | bioRxiv : the preprint server for biology | 41279272 | bioRxiv | 2025 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/41279272 |
| Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data. | Jiny Ha YJ, Maziec D, Markowski J, Georges SJ, Parmalee NL, Berselli M, Coorens THH, Dong S, Gardiner S, Kalra D, Li D, Miao B, Musunuri R, Xue L, Yu Z, Walker K, Anderson L, Au NYT, Cibulskis C, Doddapaneni H, Grochowski CM, Jensen DM, Lindsay T, Loy K, Narayan A, Narzisi G, Ou J, Pham MM, Runnels AM, Stergachis AB, Sutherlin LM, Wang T, Jin H, Feng WC, Zhang Y, Veit AD, TaeHee Kim C, Chun HE, SMaHT Network Single Nucleotide Variant (SNV) Working Group, Ardlie K, Fulton RS, Germer S, Gibbs R, Marth GT, Bennett JT, Park PJ | bioRxiv : the preprint server for biology | 41278982 | bioRxiv | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/41278982 |
| A telomere-to-telomere map of somatic mutation burden and functional impact in cancer. | Sohn MH, Dubocanin D, Vollger MR, Kwon Y, Minkina A, Munson KM, Hart SF, Ranchalis JE, Parmalee NL, Sedeño-Cortés AE, Ou J, Au NY, Bohaczuk S, Carroll B, Frazar CD, Harvey WT, Hoekzema K, Huang MF, Jacques CN, Jensen DM, Kolar JT, Lee R, Lin J, Loy K, Mack T, Mao Y, Pham MM, Ryke E, Smith JD, Sutherlin L, Swanson EG, Weiss JM, Wg SA, Carvalho C, Coorens TH, Harris K, Wei CL, Eichler EE, Altemose N, Bennett JT, Stergachis AB | bioRxiv : the preprint server for biology | 41279560 | bioRxiv | 2025 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/41279560 |
| Protamine lacunae preserve the paternal chromatin landscape in sperm. | Tullius TW, Heuer RA, Bohaczuk SC, Mallory B, Dubocanin D, Ranchalis J, Ayaz A, Mason CE, Seli E, Phillippy AM, Stergachis AB, Lesch BJ | bioRxiv : the preprint server for biology | 41256633 | bioRxiv | 2025 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/41256633 |
| Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes. | Zhang Y, Viswanadham VV, Andreopoulos M, Glodzik D, Liu R, Luquette LJ, Jo SY, Narayan A, Niu M, Anderson L, Brew JA, Chao H, Cibulskis C, Dong G, Evani US, Feng WC, Grońska-Pęski M, Helland A, Hilal N, Jabara NT, Jin H, Li N, Manam MD, Mallett SL, Runnels A, Scharlee C, Smith C, SMaHT Duplex Sequencing Focus Group, Shao D, Walsh CA, Adalsteinsson VA, Lee EA, Park PJ, Ardlie KG, Germer S, Gibbs RA, Choudhury S, Doddapaneni HV, Evrony GD, Zong C, Coorens THH | bioRxiv : the preprint server for biology | 41446189 | bioRxiv | 2025 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/41446189 |
| Genetic variation across and within individuals. | Yu Z, Coorens THH, Uddin MM, Ardlie KG, Lennon N, Natarajan P | Nature reviews. Genetics | 38548833 | Nat Rev Genet | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38548833 |
| Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions. | Zhang Y, English AC, Paulin LF, Grochowski CM, Maheshwari S, Mack T, Berselli M, Veit AD, Fu Y, SMaHT SV working group, Park PJ, Sedlazeck FJ | bioRxiv : the preprint server for biology | 41000761 | bioRxiv | 2025 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/41000761 |
| Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes. | Ganz J, Luquette LJ, Bizzotto S, Miller MB, Zhou Z, Bohrson CL, Jin H, Tran AV, Viswanadham VV, McDonough G, Brown K, Chahine Y, Chhouk B, Galor A, Park PJ, Walsh CA | Cell | 38503282 | Cell | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38503282 |
| Patterns and drivers of 43,617 mosaic chromosomal alterations in blood. | Tang D, Kamitaki N, Mukamel RE, Rubinacci S, Loh PR | medRxiv : the preprint server for health sciences | 40766159 | medRxiv | 2025 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/40766159 |
| Diploid donor-specific assembly enhances somatic structural variant detection in cancer genomes. | Zhang Y, Qu H, Qin Q, Li H, Park PJ | bioRxiv : the preprint server for biology | 41280039 | bioRxiv | 2025 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/41280039 |
| Efficient near-telomere-to-telomere assembly of nanopore simplex reads. | Cheng H, Qu H, McKenzie S, Lawrence KR, Windsor R, Vella M, Park PJ, Li H | Nature | 41639459 | Nature | 2026 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/41639459 |
| Multi-platform framework for mapping somatic retrotransposition in human tissues. | Wang S, Bae M, Wang J, Zhao B, Nguyen K, Mallett S, Switzenberg JA, Losh SJ, Sexton CE, Miao B, Dong S, Zeng X, Wang Z, McDonald TL, Mumm C, Gadde RK, Tariq AM, Chen Z, Feng WC, Burn A, Park J, Chu C, Shen H, Wang T, Urban AE, Zhu X, Li H, Burns KH, Chun HE, Park PJ, SMaHT MEI Working Group, Boyle AP, Mills RE, Zhou W, Lee EA | bioRxiv : the preprint server for biology | 41278868 | bioRxiv | 2025 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/41278868 |
| Efficient near telomere-to-telomere assembly of Nanopore Simplex reads. | Cheng H, Qu H, McKenzie S, Lawrence KR, Windsor R, Vella M, Park PJ, Li H | bioRxiv : the preprint server for biology | 41332538 | bioRxiv | 2025 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/41332538 |
| Computational analysis of DNA methylation from long-read sequencing. | Fu Y, Timp W, Sedlazeck FJ | Nature reviews. Genetics | 40155770 | Nat Rev Genet | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40155770 |
| From high-throughput transcriptome characterization of individual synaptosomes to constructing the whole-brain connectome. | Niu M, Zong C | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 37550440 | Neuropsychopharmacology | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37550440 |
| Validation of Single-Nucleotide Mosaic Variants Through Droplet Digital PCR. | Grochowski CM, Gibbs RA, Doddapaneni H | Current protocols | 38774978 | Curr Protoc | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38774978 |
| Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T. | Paulin LF, Fan J, O'Neill K, Pleasance E, Porter VL, Jones SJM, Sedlazeck FJ | Genome research | 40097200 | Genome Res | 2025 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/40097200 |
| The benefit of a complete reference genome for cancer structural variant analysis. | Paulin LF, Fan J, O'Neill K, Pleasance E, Porter VL, Jones SJM, Sedlazeck FJ | medRxiv : the preprint server for health sciences | 38562786 | medRxiv | 2024 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/38562786 |
| Characterization of Cancer Evolution Landscape Based on Accurate Detection of Somatic Mutations in Single Tumor Cells. | Niu M, Zhang Y, Luo J, Sinson JC, Thompson AM, Zong C | bioRxiv : the preprint server for biology | 37873375 | bioRxiv | 2023 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/37873375 |
| A complete diploid human genome benchmark for personalized genomics. | Hansen NF, Dwarshuis N, Ji HJ, Rhie A, Loucks H, Logsdon GA, Vollger MR, Storer JM, Kim J, Adam E, Altemose N, Antipov D, Asri M, Barreira S, Bohaczuk SC, Bzikadze AV, Carioscia SA, Carroll A, Chao KH, Chu Y, Das A, Ebert P, English A, Fleharty M, Fleming LE, Formenti G, Guarracino A, Hartley GA, Jenike K, Kalleberg J, Kang Y, King R, Lipovac J, Mastoras M, Mitchell MW, Negi S, Olson ND, Oshima KK, Paulin LF, Pickett BD, Porubsky D, Ranchalis J, Ranjan D, Rautiainen M, Riethman H, Schnabel RD, Sedlazeck FJ, Shafin K, Sikic M, Solar SJ, Sweeten AP, Timp W, Wagner J, Yoo D, Zhou Y, Garrison E, Eichler EE, Schatz MC, Stergachis AB, O'Neill RJ, Miga KH, Salzberg SL, Koren S, Zook JM, Phillippy AM | bioRxiv : the preprint server for biology | 41000953 | bioRxiv | 2025 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/41000953 |
| Scalable and comprehensive mosaic variant calling using DRAGEN. | Behera S, Rossi M, Wang Y, Izydorczyk MB, Tran D, Dalgard CL, Kalef-Ezra E, Kottapalli K, Mehta H, Parnaby G, Risse-Adams OS, Scholz SW, Shen H, Nelson TM, Visvanath A, Zheng X, Doddapaneni H, Garcia T, Mason CE, Proukakis C, Han J, Mehio R, Catreux S, Sedlazeck FJ | medRxiv : the preprint server for health sciences | 41674597 | medRxiv | 2026 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/41674597 |
| Integrating Single-Molecule Sequencing and Deep Learning to Predict Haplotype-Specific 3D Chromatin Organization in a Mendelian Condition. | Dubocanin D, Kalygina A, Franklin JM, Chittenden C, Vollger MR, Neph S, Stergachis AB, Altemose N | bioRxiv : the preprint server for biology | 40166185 | bioRxiv | 2025 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/40166185 |
| The regulatory potential of transposable elements in maize. | Bubb KL, Hamm MO, Tullius TW, Min JK, Ramirez-Corona B, Mueth NA, Ranchalis J, Mao Y, Bergstrom EJ, Vollger MR, Trapnell C, Cuperus JT, Stergachis AB, Queitsch C | bioRxiv : the preprint server for biology | 39026747 | bioRxiv | 2025 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/39026747 |
| Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. | Bohaczuk SC, Amador ZJ, Li C, Mallory BJ, Swanson EG, Ranchalis J, Vollger MR, Munson KM, Walsh T, Hamm MO, Mao Y, Lieber A, Stergachis AB | Genome research | 39653420 | Genome Res | 2024 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/39653420 |
| A haplotype-resolved view of human gene regulation. | Vollger MR, Swanson EG, Neph SJ, Ranchalis J, Munson KM, Ho CH, Cheng YHH, Sedeño-Cortés AE, Fondrie WE, Bohaczuk SC, Dippel MA, Mao Y, Parmalee NL, Mallory BJ, Harvey WT, Kwon Y, Garcia GH, Hoekzema K, Meyer JG, Cicek M, Eichler EE, Noble WS, Witten DM, Bennett JT, Ray JP, Stergachis AB | bioRxiv : the preprint server for biology | 40501892 | bioRxiv | 2025 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/40501892 |
| DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools. | Jha A, Bohaczuk SC, Mao Y, Ranchalis J, Mallory BJ, Min AT, Hamm MO, Swanson E, Dubocanin D, Finkbeiner C, Li T, Whittington D, Noble WS, Stergachis AB, Vollger MR | Genome research | 38849157 | Genome Res | 2024 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/38849157 |
| Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. | Bohaczuk SC, Amador ZJ, Li C, Mallory BJ, Swanson EG, Ranchalis J, Vollger MR, Munson KM, Walsh T, Hamm MO, Mao Y, Lieber A, Stergachis AB | bioRxiv : the preprint server for biology | 39026856 | bioRxiv | 2024 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/39026856 |
| The regulatory potential of transposable elements in maize. | Bubb KL, Hamm MO, Tullius TW, Min JK, Ramirez-Corona B, Mueth NA, Ranchalis J, Mao Y, Bergstrom EJ, Vollger MR, Trapnell C, Cuperus JT, Stergachis AB, Queitsch C | Nature plants | 40360747 | Nat Plants | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40360747 |
| Mapping single-cell diploid chromatin fiber architectures using DAF-seq. | Swanson EG, Mao Y, Mallory BJ, Vollger MR, Bohaczuk SC, Oliveira CB, Lyon DB, Ranchalis J, Parmalee NL, Cohen BA, Bennett JT, Stergachis AB | Nature biotechnology | 41339527 | Nat Biotechnol | 2025 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/41339527 |
| Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation. | Foltz JA, Tran J, Wong P, Fan C, Schmidt E, Fisk B, Becker-Hapak M, Russler-Germain DA, Johnson J, Marin ND, Cubitt CC, Pence P, Rueve J, Pureti S, Hwang K, Gao F, Zhou AY, Foster M, Schappe T, Marsala L, Berrien-Elliott MM, Cashen AF, Bednarski JJ, Fertig E, Griffith OL, Griffith M, Wang T, Petti AA, Fehniger TA | Science immunology | 38941480 | Sci Immunol | 2024 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/38941480 |
| Modbed track: Visualization of modified bases in single-molecule sequencing. | Li D, Zhuo X, Harrison JK, Liu S, Wang T | Cell genomics | 38116122 | Cell Genom | 2023 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/38116122 |
| Tranquillyzer: A Flexible Neural Network Framework for Structural Annotation and Demultiplexing of Long-Read Transcriptomes. | Semwal A, Morrison J, Beddows I, Palmer T, Majewski MF, Jang HJ, Johnson BK, Shen H | bioRxiv : the preprint server for biology | 40766630 | bioRxiv | 2025 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/40766630 |
| Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline. | Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino FM, Abyzov A | Nature communications | 39438473 | Nat Commun | 2024 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/39438473 |
| Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline. | Jang Y, Tomasini L, Bae T, Szekely A, Vaccarino FM, Abyzov A | bioRxiv : the preprint server for biology | 38948757 | bioRxiv | 2024 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/38948757 |
| Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells. | Grimes K, Jeong H, Amoah A, Xu N, Niemann J, Raeder B, Hasenfeld P, Stober C, Rausch T, Benito E, Jann JC, Nowak D, Emini R, Hoenicka M, Liebold A, Ho A, Shuai S, Geiger H, Sanders AD, Korbel JO | Nature genetics | 38806714 | Nat Genet | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38806714 |
| Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. | Zhou B, Arthur JG, Guo H, Kim T, Huang Y, Pattni R, Wang T, Kundu S, Luo JXJ, Lee H, Nachun DC, Purmann C, Monte EM, Weimer AK, Qu PP, Shi M, Jiang L, Yang X, Fullard JF, Bendl J, Girdhar K, Kim M, Chen X, PsychENCODE Consortium, Greenleaf WJ, Duncan L, Ji HP, Zhu X, Song G, Montgomery SB, Palejev D, Zu Dohna H, Roussos P, Kundaje A, Hallmayer JF, Snyder MP, Wong WH, Urban AE | Cell | 39353437 | Cell | 2024 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/39353437 |
| Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex. | Viswanadham VV, Kim SN, Caglayan E, Doan RN, Dou Y, Bizzotto S, Khoshkhoo S, Huang AY, Yeh R, Chhouk BH, Truong A, Chappell KM, Beaudin M, Barton A, Akula SK, Zhao Y, Rento L, Lodato M, Szeto RA, Ganz J, Li P, Tsai JW, Hill RS, Park PJ, Walsh CA | Cell reports | 41240340 | Cell Rep | 2025 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/41240340 |
| Activating Ras-MAPK pathway variants drive hippocampal clonal competition in human epilepsy. | Khoshkhoo S, Bae M, Wang Y, Tillett A, Ramirez RB, Finander B, Egan ED, Marx L, Patel D, Zhou Z, Chahine Y, Chhouk B, Zoullas SM, Lai A, Coras R, Bielle F, Navarro V, Mathon B, Valiante TA, Moradi Chameh H, Gao AF, Krings T, Gooley S, Hildebrand MS, Bulluss K, Clark J, Morokoff AP, King JA, Todaro M, Kwan P, O'Brien TJ, Berkovic SF, Scheffer IE, Perucca P, Lapinskas E, Rolston JD, Cosgrove GR, Sarkis RA, D'Gama AM, Alexadrescu S, Yang E, Poduri A, Richardson RM, Erson-Omay EZ, DeLanerolle N, Spencer DD, Brown KS, Miller MB, Roberts AE, Santos LN, Kontaridis MI, Bien CG, Blacklow SC, Kahle KT, Blümcke I, Huang AY, Lee EA, Walsh CA | bioRxiv : the preprint server for biology | 41659639 | bioRxiv | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41659639 |
| ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia. | Lai J, Demirbas D, Kim J, Jeffries AM, Tolles A, Park J, Chittenden TW, Buckley PG, Yu TW, Lodato MA, Lee EA | Cell reports | 38159274 | Cell Rep | 2024 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/38159274 |
| Contributions of Germline and Somatic Mosaic Genetics to Thoracic Aortic Aneurysms in Nonsyndromic Individuals. | Chen MH, Deng ES, Yamada JM, Choudhury S, Scotellaro J, Kelley L, Isselbacher E, Lindsay ME, Walsh CA, Doan RN | Journal of the American Heart Association | 38958128 | J Am Heart Assoc | 2024 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/38958128 |
| Somatic Genomic and Transcriptomic Changes in Single Ischemic Human Heart Cardiomyocytes. | Hilal N, An Z, Prondzynski M, Matsui E, Sahu D, Mao S, Jung YL, Yang Y, Epstein S, Chen MH, Pu W, Monte FD, Huang AY, Choudhury S | Research square | 39975917 | Res Sq | 2025 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/39975917 |
| L1 insertion intermediates recombine with one another or with DNA breaks to form genome rearrangements. | Mendez-Dorantes C, Kalinowski JC, Law CT, Schofield P, Burn A, Burns KH | bioRxiv : the preprint server for biology | 41000934 | bioRxiv | 2025 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/41000934 |
| High-quality nuclei isolation from postmortem human heart muscle tissues for single-cell studies. | Araten S, Mathieu R, Jetly A, Shin H, Hilal N, Zhang B, Morillo K, Nandan D, Sivankutty I, Chen MH, Choudhury S | Journal of molecular and cellular cardiology | 36977444 | J Mol Cell Cardiol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36977444 |
| Single-Cell Genomics and Somatic Variation in Circulating and Cardiac Resident Cells. | Hilal N, Arava M, Choudhury S | Circulation research | 41481681 | Circ Res | 2026 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/41481681 |
| Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart. | Choudhury S, Sivankutty I, Jung Y, Huang A, Araten S, Kenny C, An Z, Doan R, Foijer F, Matsu E, Rosen I, Marciano J, Jain A, Sun L, Hilal N, Lee E, Walsh C, Chen M | Research square | 38853931 | Res Sq | 2024 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/38853931 |
| Cell-type-informed genotyping of mosaic focal epilepsies reveals cell-autonomous and non-cell-autonomous disease-associated transcriptional programs. | Bizzotto S, Talukdar M, Stronge EA, Ramirez RB, Yang Y, Huang AY, Hu Q, Hou Y, Hylton NK, Finander B, Tillett A, Zhou Z, Chhouk BH, D'Gama AM, Yang E, Green TE, Reutens DC, Mullen SA, Scheffer IE, Hildebrand MS, Buono RJ, Blümcke I, Poduri AH, Khoshkhoo S, Walsh CA | Proceedings of the National Academy of Sciences of the United States of America | 40674414 | Proc Natl Acad Sci U S A | 2025 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/40674414 |
| Defining heritability, plasticity, and transition dynamics of cellular phenotypes in somatic evolution. | Schiffman JS, D'Avino AR, Prieto T, Pang Y, Fan Y, Rajagopalan S, Potenski C, Hara T, Suvà ML, Gawad C, Landau DA | Nature genetics | 39317739 | Nat Genet | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39317739 |
| Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. | Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F, Landau DA | Cell stem cell | 37582363 | Cell Stem Cell | 2023 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/37582363 |
| Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. | Yuan DJ, Zinno J, Botella T, Dhingra D, Wang S, Hawkins A, Swett A, Sotelo J, Raviram R, Hughes C, Potenski C, Yokoyama A, Kakiuchi N, Ogawa S, Landau DA | bioRxiv : the preprint server for biology | 38826366 | bioRxiv | 2024 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/38826366 |
| The future of rapid and automated single-cell data analysis using reference mapping. | Lotfollahi M, Yuhan Hao, Theis FJ, Satija R | Cell | 38729109 | Cell | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38729109 |
| CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. | Kowalski MH, Wessels HH, Linder J, Choudhary S, Hartman A, Hao Y, Mascio I, Dalgarno C, Kundaje A, Satija R | bioRxiv : the preprint server for biology | 36798324 | bioRxiv | 2023 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/36798324 |
| Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens. | Jiang L, Dalgarno C, Papalexi E, Mascio I, Wessels HH, Yun H, Iremadze N, Lithwick-Yanai G, Lipson D, Satija R | Nature cell biology | 40011560 | Nat Cell Biol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40011560 |
| Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus. | Prieto T, Yuan DJ, Zinno J, Hughes C, Midler N, Kao S, Huuhtanen J, Raviram R, Fotopoulou F, Ruthen N, Rajagopalan S, Schiffman JS, D'Avino AR, Yoon SH, Sotelo J, Omans ND, Wheeler N, Garces A, Pradhan B, Cheng AP, Robine N, Potenski C, Godfrey K, Kakiuchi N, Yokoyama A, Ogawa S, Abrams J, Raimondi I, Landau DA | bioRxiv : the preprint server for biology | 41279007 | bioRxiv | 2025 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/41279007 |
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