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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 | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing. | Guo, Zhenxing; Duan, Daoyu; Tang, Wen; Zhu, Julia; Bush, William S; Zhang, Liangliang; Zhu, Xiaofeng; Jin, Fulai; Feng, Hao | PLoS computational biology | 38346081 | 2024 Feb |
| Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell, Andrew J C; Weir, Jackson A; Nadaf, Naeem M; Shabet, Matthew; Kumar, Vipin; Kambhampati, Sandeep; Raichur, Ruth; Marrero, Giovanni J; Liu, Sophia; Balderrama, Karol S; Vanderburg, Charles R; Shanmugam, Vignesh; Tian, Luyi; Iorgulescu, J Bryan; Yoon, Charles H; Wu, Catherine J; Macosko, Evan Z; Chen, Fei | Nature | 38093010 | 2024 Jan |
| Subclonal Cancer Driver Mutations Are Prevalent in the Unresected Peritumoral Edema of Adult Diffuse Gliomas. | Underhill, Hunter R; Karsy, Michael; Davidson, Christian J; Hellwig, Sabine; Stevenson, Samuel; Goold, Eric A; Vincenti, Sydney; Sellers, Drew L; Dean, Charlie; Harrison, Brion E; Bronner, Mary P; Colman, Howard; Jensen, Randy L | Cancer research | 38270917 | 2024 Apr 01 |
| DNA mismatch and damage patterns revealed by single-molecule sequencing. | Liu, Mei Hong; Costa, Benjamin M; Bianchini, Emilia C; Choi, Una; Bandler, Rachel C; Lassen, Emilie; Grońska-Pęski, Marta; Schwing, Adam; Murphy, Zachary R; Rosenkjær, Daniel; Picciotto, Shany; Bianchi, Vanessa; Stengs, Lucie; Edwards, Melissa; Nunes, Nuno Miguel; Loh, Caitlin A; Truong, Tina K; Brand, Randall E; Pastinen, Tomi; Wagner, J Richard; Skytte, Anne-Bine; Tabori, Uri; Shoag, Jonathan E; Evrony, Gilad D | Nature | 38867045 | 2024 Jun |
| Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline. | Jang, Yeongjun; Tomasini, Livia; Bae, Taejeong; Szekely, Anna; Vaccarino, Flora M; Abyzov, Alexej | bioRxiv : the preprint server for biology | 38948757 | 2024 Jun 22 |
| Genome-wide analysis and visualization of copy number with CNVpytor in igv.js. | Panda, Arijit; Suvakov, Milovan; Thorvaldsdottir, Helga; Mesirov, Jill P; Robinson, James T; Abyzov, Alexej | Bioinformatics (Oxford, England) | 39018173 | 2024 Aug 02 |
| Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. | Bohaczuk, Stephanie C; Amador, Zachary J; Li, Chang; Mallory, Benjamin J; Swanson, Elliott G; Ranchalis, Jane; Vollger, Mitchell R; Munson, Katherine M; Walsh, Tom; Hamm, Morgan O; Mao, Yizi; Lieber, Andre; Stergachis, Andrew B | bioRxiv : the preprint server for biology | 39026856 | 2024 Jul 13 |
| STAG2 mutations regulate 3D genome organization, chromatin loops, and Polycomb signaling in glioblastoma multiforme. | Xu, Wanying; Kim, Jung-Sik; Yang, Tianyi; Ya, Alvin; Sadzewicz, Lisa; Tallon, Luke; Harris, Brent T; Sarkaria, Jann; Jin, Fulai; Waldman, Todd | The Journal of biological chemistry | 38705393 | 2024 Jun |
| Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. | Yuan, Dennis J; Zinno, John; Botella, Theo; Dhingra, Dalia; Wang, Shu; Hawkins, Allegra; Swett, Ariel; Sotelo, Jesus; Raviram, Ramya; Hughes, Clayton; Potenski, Catherine; Yokoyama, Akira; Kakiuchi, Nobuyuki; Ogawa, Seishi; Landau, Dan A | bioRxiv : the preprint server for biology | 38826366 | 2024 May 23 |
| Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart. | Choudhury, Sangita; Sivankutty, Indu; Jung, Youngsook; Huang, August; Araten, Sarah; Kenny, Connor; An, Zheming; Doan, Ryan; Foijer, Floris; Matsu, Erica; Rosen, Ila; Marciano, Jack; Jain, Asish; Sun, Liang; Hilal, Nazia; Lee, Eunjung; Walsh, Christopher; Chen, Ming | Research square | 38853931 | 2024 May 30 |
| Detection of mosaic and population-level structural variants with Sniffles2. | Smolka, Moritz; Paulin, Luis F; Grochowski, Christopher M; Horner, Dominic W; Mahmoud, Medhat; Behera, Sairam; Kalef-Ezra, Ester; Gandhi, Mira; Hong, Karl; Pehlivan, Davut; Scholz, Sonja W; Carvalho, Claudia M B; Proukakis, Christos; Sedlazeck, Fritz J | Nature biotechnology | 38168980 | 2024 Jan 02 |
| The benefit of a complete reference genome for cancer structural variant analysis. | Paulin, Luis F; Fan, Jeremy; O'Neill, Kieran; Pleasance, Erin; Porter, Vanessa L; Jones, Steven J M; Sedlazeck, Fritz J | medRxiv : the preprint server for health sciences | 38562786 | 2024 Mar 18 |
| Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. | Gustafson, Jonas A; Gibson, Sophia B; Damaraju, Nikhita; Zalusky, Miranda Pg; Hoekzema, Kendra; Twesigomwe, David; Yang, Lei; Snead, Anthony A; Richmond, Phillip A; De Coster, Wouter; Olson, Nathan D; Guarracino, Andrea; Li, Qiuhui; Miller, Angela L; Goffena, Joy; Anderson, Zachery; Storz, Sophie Hr; Ward, Sydney A; Sinha, Maisha; Gonzaga-Jauregui, Claudia; Clarke, Wayne E; Basile, Anna O; Corvelo, André; Reeves, Catherine; Helland, Adrienne; Musunuri, Rajeeva Lochan; Revsine, Mahler; Patterson, Karynne E; Paschal, Cate R; Zakarian, Christina; Goodwin, Sara; Jensen, Tanner D; Robb, Esther; 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, W Richard; Sedlazeck, Fritz J; Zook, Justin M; Montgomery, Stephen B; Garrison, Erik; Kolmogorov, Mikhail; Schatz, Michael C; McLaughlin Jr, Richard N; Dashnow, Harriet; Zody, Michael C; Loose, Matt; Jain, Miten; Eichler, Evan E; Miller, Danny E | medRxiv : the preprint server for health sciences | 38496498 | 2024 Mar 07 |
| Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes. | Ganz, Javier; Luquette, Lovelace J; Bizzotto, Sara; Miller, Michael B; Zhou, Zinan; Bohrson, Craig L; Jin, Hu; Tran, Antuan V; Viswanadham, Vinayak V; McDonough, Gannon; Brown, Katherine; Chahine, Yasmine; Chhouk, Brian; Galor, Alon; Park, Peter J; Walsh, Christopher A | Cell | 38503282 | 2024 Apr 11 |
| ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia. | Lai, Jenny; Demirbas, Didem; Kim, Junho; Jeffries, Ailsa M; Tolles, Allie; Park, Junseok; Chittenden, Thomas W; Buckley, Patrick G; Yu, Timothy W; Lodato, Michael A; Lee, Eunjung Alice | Cell reports | 38159274 | 2024 Jan 23 |
| Jak2V617F Reversible Activation Shows Its Essential Requirement in Myeloproliferative Neoplasms. | Dunbar, Andrew J; Bowman, Robert L; Park, Young C; O'Connor, Kavi; Izzo, Franco; Myers, Robert M; Karzai, Abdul; Zaroogian, Zachary; Kim, Won Jun; Fernández-Maestre, Inés; Waarts, Michael R; Nazir, Abbas; Xiao, Wenbin; Codilupi, Tamara; Brodsky, Max; Farina, Mirko; Cai, Louise; Cai, Sheng F; Wang, Benjamin; An, Wenbin; Yang, Julie L; Mowla, Shoron; Eisman, Shira E; Hanasoge Somasundara, Amritha Varshini; Glass, Jacob L; Mishra, Tanmay; Houston, Remie; Guzzardi, Emily; Martinez Benitez, Anthony R; Viny, Aaron D; Koche, Richard P; Meyer, Sara C; Landau, Dan A; Levine, Ross L | Cancer discovery | 38230747 | 2024 May 01 |
| Validation of Single-Nucleotide Mosaic Variants Through Droplet Digital PCR. | Grochowski, Christopher M; Gibbs, Richard A; Doddapaneni, Harsha | Current protocols | 38774978 | 2024 May |
| The future of rapid and automated single-cell data analysis using reference mapping. | Lotfollahi, Mohammad; Yuhan Hao; Theis, Fabian J; Satija, Rahul | Cell | 38729109 | 2024 May 09 |
| Single-cell total-RNA profiling unveils regulatory hubs of transcription factors. | Niu, Yichi; Luo, Jiayi; Zong, Chenghang | Nature communications | 39009595 | 2024 Jul 15 |
| The regulatory potential of transposable elements in maize. | Bubb, Kerry L; Hamm, Morgan O; Min, Joseph K; Ramirez-Corona, Bryan; Mueth, Nicholas A; Ranchalis, Jane; Vollger, Mitchell R; Trapnell, Cole; Cuperus, Josh T; Queitsch, Christine; Stergachis, Andrew B | bioRxiv : the preprint server for biology | 39026747 | 2024 Jul 14 |
| Publisher Correction: Detection of mosaic and population-level structural variants with Sniffles2. | Smolka, Moritz; Paulin, Luis F; Grochowski, Christopher M; Horner, Dominic W; Mahmoud, Medhat; Behera, Sairam; Kalef-Ezra, Ester; Gandhi, Mira; Hong, Karl; Pehlivan, Davut; Scholz, Sonja W; Carvalho, Claudia M B; Proukakis, Christos; Sedlazeck, Fritz J | Nature biotechnology | 38253882 | 2024 Jan 22 |
| Mapping genotypes to chromatin accessibility profiles in single cells. | Izzo, Franco; Myers, Robert M; Ganesan, Saravanan; Mekerishvili, Levan; Kottapalli, Sanjay; Prieto, Tamara; Eton, Elliot O; Botella, Theo; Dunbar, Andrew J; Bowman, Robert L; Sotelo, Jesus; Potenski, Catherine; Mimitou, Eleni P; Stahl, Maximilian; El Ghaity-Beckley, Sebastian; Arandela, JoAnn; Raviram, Ramya; Choi, Daniel C; Hoffman, Ronald; Chaligné, Ronan; Abdel-Wahab, Omar; Smibert, Peter; Ghobrial, Irene M; Scandura, Joseph M; Marcellino, Bridget; Levine, Ross L; Landau, Dan A | Nature | 38720070 | 2024 May |
| Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells. | Grimes, Karen; Jeong, Hyobin; Amoah, Amanda; Xu, Nuo; Niemann, Julian; Raeder, Benjamin; Hasenfeld, Patrick; Stober, Catherine; Rausch, Tobias; Benito, Eva; Jann, Johann-Christoph; Nowak, Daniel; Emini, Ramiz; Hoenicka, Markus; Liebold, Andreas; Ho, Anthony; Shuai, Shimin; Geiger, Hartmut; Sanders, Ashley D; Korbel, Jan O | Nature genetics | 38806714 | 2024 Jun |
| Easy Hi-C: A Low-Input Method for Capturing Genome Organization. | Lu, Leina; Jin, Fulai | Methods in molecular biology (Clifton, N.J.) | 36427146 | 2023 |
| Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly. | Fu, Chen; Ngo, Justine; Zhang, Shanshan; Lu, Leina; Miron, Alexander; Schafer, Simon; Gage, Fred H; Jin, Fulai; Schumacher, Fredrick R; Wynshaw-Boris, Anthony | Human molecular genetics | 36519762 | 2023 May 05 |
| High-quality nuclei isolation from postmortem human heart muscle tissues for single-cell studies. | Araten, Sarah; Mathieu, Ronald; Jetly, Anushka; Shin, Hoon; Hilal, Nazia; Zhang, Bo; Morillo, Katherine; Nandan, Deepa; Sivankutty, Indu; Chen, Ming Hui; Choudhury, Sangita | Journal of molecular and cellular cardiology | 36977444 | 2023 Jun |
| Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk. | Celis, Katrina; Moreno, Maria D M Muniz; Rajabli, Farid; Whitehead, Patrice; Hamilton-Nelson, Kara; Dykxhoorn, Derek M; Nuytemans, Karen; Wang, Liyong; Flanagan, Margaret; Weintraub, Sandra; Geula, Changiz; Gearing, Marla; Dalgard, Clifton L; Jin, Fulai; Bennett, David A; Schuck, Theresa; Pericak-Vance, Margaret A; Griswold, Anthony J; Young, Juan I; Vance, Jeffery M | Alzheimer's & dementia : the journal of the Alzheimer's Association | 37037656 | 2023 Sep |
| Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. | Cortés-López, Mariela; Chamely, Paulina; Hawkins, Allegra G; Stanley, Robert F; Swett, Ariel D; Ganesan, Saravanan; Mouhieddine, Tarek H; Dai, Xiaoguang; Kluegel, Lloyd; Chen, Celine; Batta, Kiran; Furer, Nili; Vedula, Rahul S; Beaulaurier, John; Drong, Alexander W; Hickey, Scott; Dusaj, Neville; Mullokandov, Gavriel; Stasiw, Adam M; Su, Jiayu; Chaligné, Ronan; Juul, Sissel; Harrington, Eoghan; Knowles, David A; Potenski, Catherine J; Wiseman, Daniel H; Tanay, Amos; Shlush, Liran; Lindsley, Robert C; Ghobrial, Irene M; Taylor, Justin; Abdel-Wahab, Omar; Gaiti, Federico; Landau, Dan A | Cell stem cell | 37582363 | 2023 Sep 07 |
| Single-cell somatic copy number variants in brain using different amplification methods and reference genomes. | Kalef-Ezra, Ester; Turan, Zeliha Gozde; Perez-Rodriguez, Diego; Bomann, Ida; Behera, Sairam; Morley, Caoimhe; Scholz, Sonja W; Jaunmuktane, Zane; Demeulemeester, Jonas; Sedlazeck, Fritz J; Proukakis, Christos | bioRxiv : the preprint server for biology | 37609320 | 2023 Nov 21 |
| Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. | Weng, Chen; Gu, Anniya; Zhang, Shanshan; Lu, Leina; Ke, Luxin; Gao, Peidong; Liu, Xiaoxiao; Wang, Yuntong; Hu, Peinan; Plummer, Dylan; MacDonald, Elise; Zhang, Saixian; Xi, Jiajia; Lai, Sisi; Leskov, Konstantin; Yuan, Kyle; Jin, Fulai; Li, Yan | Nature communications | 37669939 | 2023 Sep 05 |
| LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. | Mendez-Dorantes, Carlos; Burns, Kathleen H | Genes & development | 38092519 | 2023 Dec 26 |
| Modbed track: Visualization of modified bases in single-molecule sequencing. | Li, Daofeng; Zhuo, Xiaoyu; Harrison, Jessica K; Liu, Shane; Wang, Ting | Cell genomics | 38116122 | 2023 Dec 13 |
