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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 |
|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| Validation of Single-Nucleotide Mosaic Variants Through Droplet Digital PCR. | Grochowski CM, Gibbs RA, Doddapaneni H | Current protocols | 38774978 | Curr Protoc | 2024 May |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Mapping genotypes to chromatin accessibility profiles in single cells. | Izzo F, Myers RM, Ganesan S, Mekerishvili L, Kottapalli S, Prieto T, Eton EO, Botella T, Dunbar AJ, Bowman RL, Sotelo J, Potenski C, Mimitou EP, Stahl M, El Ghaity-Beckley S, Arandela J, Raviram R, Choi DC, Hoffman R, Chaligné R, Abdel-Wahab O, Smibert P, Ghobrial IM, Scandura JM, Marcellino B, Levine RL, Landau DA | Nature | 38720070 | Nature | 2024 May |
| 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 |
| 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 |
| GoT-Splice protocol for multi-omics profiling of gene expression, cell-surface proteins, mutational status, and RNA splicing in human cells. | Ganesan S, Cortés-López M, Swett AD, Dai X, Hickey S, Chamely P, Hawkins AG, Juul S, Landau DA, Gaiti F | STAR protocols | 38512867 | STAR Protoc | 2024 Jun 21 |
| Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms. | Dunbar AJ, Bowman RL, Park YC, O'Connor K, Izzo F, Myers RM, Karzai A, Zaroogian Z, Kim WJ, Fernández-Maestre I, Waarts MR, Nazir A, Xiao W, Codilupi T, Brodsky M, Farina M, Cai L, Cai SF, Wang B, An W, Yang JL, Mowla S, Eisman SE, Hanasoge Somasundara AV, Glass JL, Mishra T, Houston R, Guzzardi E, Martinez Benitez AR, Viny AD, Koche RP, Meyer SC, Landau DA, Levine RL | Cancer discovery | 38230747 | Cancer Discov | 2024 May 1 |
| 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 |
| Single-cell mapping of regulatory DNA:Protein interactions. | Chi WY, Yoon SH, Mekerishvili L, Ganesan S, Potenski C, Izzo F, Landau D, Raimondi I | bioRxiv : the preprint server for biology | 39803441 | bioRxiv | 2025 Jan 2 |
| 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 |
| Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell AJC, Weir JA, Nadaf NM, Shabet M, Kumar V, Kambhampati S, Raichur R, Marrero GJ, Liu S, Balderrama KS, Vanderburg CR, Shanmugam V, Tian L, Iorgulescu JB, Yoon CH, Wu CJ, Macosko EZ, Chen F | Nature | 38093010 | Nature | 2024 Jan |
| Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas. | Underhill HR, Karsy M, Davidson CJ, Hellwig S, Stevenson S, Goold EA, Vincenti S, Sellers DL, Dean C, Harrison BE, Bronner MP, Colman H, Jensen RL | Cancer research | 38270917 | Cancer Res | 2024 Apr 1 |
| Single-cell total-RNA profiling unveils regulatory hubs of transcription factors. | Niu Y, Luo J, Zong C | Nature communications | 39009595 | Nat Commun | 2024 Jul 15 |
| Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. | Panda A, Suvakov M, Thorvaldsdottir H, Mesirov JP, Robinson JT, Abyzov A | Bioinformatics (Oxford, England) | 39018173 | Bioinformatics | 2024 Aug 2 |
| Chromosomal rearrangements and instability caused by the LINE-1 retrotransposon. | Mendez-Dorantes C, Zeng X, Karlow JA, Schofield P, Turner S, Kalinowski J, Denisko D, Lee EA, Burns KH, Zhang CZ | bioRxiv : the preprint server for biology | 39764018 | bioRxiv | 2024 Dec 17 |
| LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. | Mendez-Dorantes C, Burns KH | Genes & development | 38092519 | Genes Dev | 2023 Dec 26 |
| Comparative Genomics Reveals LINE-1 Recombination with Diverse RNAs. | Law CT, Burns KH | bioRxiv : the preprint server for biology | 39975348 | bioRxiv | 2025 Feb 3 |
| Detection of mosaic and population-level structural variants with Sniffles2. | Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ | Nature biotechnology | 38168980 | Nat Biotechnol | 2024 Oct |
| High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation. | Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson ZB, Storz SHR, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CRDR), Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE | Genome research | 39358015 | Genome Res | 2024 Nov 20 |
| Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. | Kalef-Ezra E, Turan ZG, Perez-Rodriguez D, Bomann I, Behera S, Morley C, Scholz SW, Jaunmuktane Z, Demeulemeester J, Sedlazeck FJ, Proukakis C | bioRxiv : the preprint server for biology | 37609320 | bioRxiv | 2023 Nov 21 |
| Characterization and visualization of tandem repeats at genome scale. | Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA | Nature biotechnology | 38168995 | Nat Biotechnol | 2024 Oct |
| Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. | Kalef-Ezra E, Turan ZG, Perez-Rodriguez D, Bomann I, Behera S, Morley C, Scholz SW, Jaunmuktane Z, Demeulemeester J, Sedlazeck FJ, Proukakis C | Communications biology | 39384904 | Commun Biol | 2024 Oct 9 |
| Comprehensive genome analysis and variant detection at scale using DRAGEN. | Behera S, Catreux S, Rossi M, Truong S, Huang Z, Ruehle M, Visvanath A, Parnaby G, Roddey C, Onuchic V, Finocchio A, Cameron DL, English A, Mehtalia S, Han J, Mehio R, Sedlazeck FJ | Nature biotechnology | 39455800 | Nat Biotechnol | 2024 Oct 25 |
| Single cell long read whole genome sequencing reveals somatic transposon activity in human brain. | Izydorczyk MB, Kalef-Ezra E, Horner DW, Zheng X, Holmes N, Toffoli M, Sahin ZG, Han Y, Mehta HH, Muzny DM, Ameur A, Sedlazeck FJ, Proukakis C | medRxiv : the preprint server for health sciences | 39606404 | medRxiv | 2024 Nov 11 |
| Analysis and benchmarking of small and large genomic variants across tandem repeats. | English AC, Dolzhenko E, Ziaei Jam H, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ | Nature biotechnology | 38671154 | Nat Biotechnol | 2025 Mar |
| Publisher Correction: Detection of mosaic and population-level structural variants with Sniffles2. | Smolka M, Paulin LF, Grochowski CM, Horner DW, Mahmoud M, Behera S, Kalef-Ezra E, Gandhi M, Hong K, Pehlivan D, Scholz SW, Carvalho CMB, Proukakis C, Sedlazeck FJ | Nature biotechnology | 38253882 | Nat Biotechnol | 2024 Oct |
| Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. | Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, Anderson Z, Storz SH, Ward SA, Sinha M, Gonzaga-Jauregui C, Clarke WE, Basile AO, Corvelo A, Reeves C, Helland A, Musunuri RL, Revsine M, Patterson KE, Paschal CR, Zakarian C, Goodwin S, Jensen TD, Robb E, 1000 Genomes ONT Sequencing Consortium, University of Washington Center for Rare Disease Research (UW-CRDR), Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium, McCombie WR, Sedlazeck FJ, Zook JM, Montgomery SB, Garrison E, Kolmogorov M, Schatz MC, McLaughlin RN Jr, Dashnow H, Zody MC, Loose M, Jain M, Eichler EE, Miller DE | medRxiv : the preprint server for health sciences | 38496498 | medRxiv | 2024 Mar 7 |
| A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex. | Zhou W, Mumm C, Gan Y, Switzenberg JA, Wang J, De Oliveira P, Kathuria K, Losh SJ, McDonald TL, Bessell B, Van Deynze K, McConnell MJ, Boyle AP, Mills RE | bioRxiv : the preprint server for biology | 39763954 | bioRxiv | 2024 Dec 21 |
| Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly. | Fu C, Ngo J, Zhang S, Lu L, Miron A, Schafer S, Gage FH, Jin F, Schumacher FR, Wynshaw-Boris A | Human molecular genetics | 36519762 | Hum Mol Genet | 2023 May 5 |
| magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. | Guo Z, Duan D, Tang W, Zhu J, Bush WS, Zhang L, Zhu X, Jin F, Feng H | PLoS computational biology | 38346081 | PLoS Comput Biol | 2024 Feb |
| Genome-wide meta-analyses of cross substance use disorders in European, African, and Latino ancestry populations. | Lai D, Zhang M, Green N, Abreu M, Schwantes-An TH, Parker C, Zhang S, Jin F, Sun A, Zhang P, Edenberg H, Liu Y, Foroud T | Research square | 39070649 | Res Sq | 2024 Jul 16 |
| Easy Hi-C: A Low-Input Method for Capturing Genome Organization. | Lu L, Jin F | Methods in molecular biology (Clifton, N.J.) | 36427146 | Methods Mol Biol | 2023 |
| STAG2 mutations regulate 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme. | Xu W, Kim JS, Yang T, Ya A, Sadzewicz L, Tallon L, Harris BT, Sarkaria J, Jin F, Waldman T | The Journal of biological chemistry | 38705393 | J Biol Chem | 2024 Jun |
| Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. | Weng C, Gu A, Zhang S, Lu L, Ke L, Gao P, Liu X, Wang Y, Hu P, Plummer D, MacDonald E, Zhang S, Xi J, Lai S, Leskov K, Yuan K, Jin F, Li Y | Nature communications | 37669939 | Nat Commun | 2023 Sep 5 |
| Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry. | Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Qiao M, Vardarajan BN, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Alzheimer's Disease Genetics Consortium, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Xu W, Jin F, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C | Alzheimer's & dementia : the journal of the Alzheimer's Association | 38958117 | Alzheimers Dement | 2024 Aug |
| Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk. | Celis K, Moreno MDMM, Rajabli F, Whitehead P, Hamilton-Nelson K, Dykxhoorn DM, Nuytemans K, Wang L, Flanagan M, Weintraub S, Geula C, Gearing M, Dalgard CL, Jin F, Bennett DA, Schuck T, Pericak-Vance MA, Griswold AJ, Young JI, Vance JM | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37037656 | Alzheimers Dement | 2023 Sep |
| DNA mismatch and damage patterns revealed by single-molecule sequencing. | Liu MH, Costa BM, Bianchini EC, Choi U, Bandler RC, Lassen E, Grońska-Pęski M, Schwing A, Murphy ZR, Rosenkjær D, Picciotto S, Bianchi V, Stengs L, Edwards M, Nunes NM, Loh CA, Truong TK, Brand RE, Pastinen T, Wagner JR, Skytte AB, Tabori U, Shoag JE, Evrony GD | Nature | 38867045 | Nature | 2024 Jun |
| methylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing. | Zhang W, Macias-Velasco JF, Zhuo X, Belter EA Jr, Tomlinson C, Garza J, Tekkey N, Li D, Wang T | Nucleic acids research | 39868538 | Nucleic Acids Res | 2025 Jan 24 |
| Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution. | Chen Y, Hou Y, Zeng Q, Wang I, Shang M, Shin K, Hemauer C, Xing X, Kang J, Zhao G, Wang T | Genome research | 39809530 | Genome Res | 2025 Jan 22 |
