Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA

Authors: Liu, Minetta C., Oxnard, Geoffrey R., Klein, Eric A., Smith, David, Richards, Donald, Yeatman, Timothy J., Cohn, Allen L., Lapham, Rosanna, Clement, Jessica, Parker, Alexander S., Tummala, Mohan K., McIntyre, Kristi, Sekeres, Mikkael A., Bryce, Alan H., Siegel, Robert, Wang, Xuezhong, Cosgrove, David P., Abu-Rustum, Nadeem R., Trent, Jonathan, Thiel, David D., Becerra, Carlos, Agrawal, Manish, Garbo, Lawrence E., Giguere, Jeffrey K., Michels, Ross M., Harris, Ronald P., Richey, Stephen L., McCarthy, Timothy A., Waterhouse, David M., Couch, Fergus J., Wilks, Sharon T., Krie, Amy K., Balaraman, Rama, Restrepo, Alvaro, Meshad, Michael W., Rieger-Christ, Kimberly, Sullivan, Travis, Lee, Christine M., Greenwald, Daniel R., Oh, William, Tsao, Che-Kai, Fleshner, Neil, Kennecke, Hagen F., Khalil, Maged F., Spigel, David R., Manhas, Atisha P., Ulrich, Brian K., Kovoor, Philip A., Stokoe, Christopher, Courtright, Jay G., Yimer, Habte A., Larson, Timothy G., Swanton, Charles, Seiden, Michael V., Cummings, Steven R., Absalan, Farnaz, Alexander, Gregory, Allen, Brian, Amini, Hamed, Aravanis, Alexander M., Bagaria, Siddhartha, Bazargan, Leila, Beausang, John F., Berman, Jennifer, Betts, Craig, Blocker, Alexander, Bredno, Joerg, Calef, Robert, Cann, Gordon, Carter, Jeremy, Chang, Christopher, Chawla, Hemanshi, Chen, Xiaoji, Chien, Tom C., Civello, Daniel, Davydov, Konstantin, Demas, Vasiliki, Desai, Mohini, Dong, Zhao, Fayzullina, Saniya, Fields, Alexander P., Filippova, Darya, Freese, Peter, Fung, Eric T., Gnerre, Sante, Gross, Samuel, Halks-Miller, Meredith, Hall, Megan P., Hartman, Anne-Renee, Hou, Chenlu, Hubbell, Earl, Hunkapiller, Nathan, Jagadeesh, Karthik, Jamshidi, Arash, Jiang, Roger, Jung, Byoungsok, Kim, TaeHyung, Klausner, Richard D., Kurtzman, Kathryn N., Lee, Mark, Lin, Wendy, Lipson, Jafi, Liu, Hai, Liu, Qinwen, Lopatin, Margarita, Maddala, Tara, Maher, M. Cyrus, Melton, Collin, Mich, Andrea, Nautiyal, Shivani, Newman, Jonathan, Newman, Joshua, Nicula, Virgil, Nicolaou, Cosmos, Nikolic, Ongjen, Pan, Wenying, Patel, Shilpen, Prins, Sarah A., Rava, Richard, Ronaghi, Neda, Sakarya, Onur, Satya, Ravi Vijaya, Schellenberger, Jan, Scott, Eric, Sehnert, Amy J., Shaknovich, Rita, Shanmugam, Avinash, Shashidhar, K.C., Shen, Ling, Shenoy, Archana, Shojaee, Seyedmehdi, Singh, Pranav, Steffen, Kristan K., Tang, Susan, Toung, Jonathan M., Valouev, Anton, Venn, Oliver, Williams, Richard T., Wu, Tony, Xu, Hui H., Yakym, Christopher, Yang, Xiao, Yecies, Jessica, Yip, Alexander S., Youngren, Jack, Yue, Jeanne, Zhang, Jingyang, Zhang, Lily, Zhang, Lori (Quan), Zhang, Nan, Curtis, Christina, Berry, Donald A., Liu, M.C., Oxnard, G.R., Klein, E.A., Swanton, C., Seiden, M.V.

Source: In Annals of Oncology June 2020 31(6):745-759

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

Authors: Birgmeier, Johannes, Deisseroth, Cole A., Hayward, Laura E., Galhardo, Luisa M.T., Tierno, Andrew P., Jagadeesh, Karthik A., Stenson, Peter D., Cooper, David N., Bernstein, Jonathan A., Haeussler, Maximilian, Bejerano, Gill ^*

Source: In Genetics in Medicine February 2020 22(2):362-370

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Authors: Smillie, Christopher S., Biton, Moshe, Ordovas-Montanes, Jose, Sullivan, Keri M., Burgin, Grace, Graham, Daniel B., Herbst, Rebecca H., Rogel, Noga, Slyper, Michal, Waldman, Julia, Sud, Malika, Andrews, Elizabeth, Velonias, Gabriella, Haber, Adam L., Jagadeesh, Karthik, Vickovic, Sanja, Yao, Junmei, Stevens, Christine, Dionne, Danielle, Nguyen, Lan T., Villani, Alexandra-Chloé, Hofree, Matan, Creasey, Elizabeth A., Huang, Hailiang, Rozenblatt-Rosen, Orit, Garber, John J., Khalili, Hamed, Desch, A. Nicole, Daly, Mark J., Ananthakrishnan, Ashwin N., Shalek, Alex K., Xavier, Ramnik J., Regev, Aviv

Source: In Cell 25 July 2019 178(3):714-730

CRISPR/Cas9 Genome Engineering in Engraftable Human Brain-Derived Neural Stem Cells

Authors: Dever, Daniel P., Scharenberg, Samantha G., Camarena, Joab, Kildebeck, Eric J., Clark, Joseph T., Martin, Renata M., Bak, Rasmus O., Tang, Yuming, Dohse, Monika, Birgmeier, Johannes A., Jagadeesh, Karthik A., Bejerano, Gill, Tsukamoto, Ann, Gomez-Ospina, Natalia, Uchida, Nobuko, Porteus, Matthew H.

Source: In iScience 31 May 2019 15:524-535

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization

Authors: Jagadeesh, Karthik A., Birgmeier, Johannes, Guturu, Harendra, Deisseroth, Cole A., Wenger, Aaron M., Bernstein, Jonathan A., Bejerano, Gill

Source: In Genetics in Medicine February 2019 21(2):464-470

Deriving genomic diagnoses without revealing patient genomes

Authors: Jagadeesh, Karthik A., Wu, David J., Birgmeier, Johannes A., Boneh, Dan, Bejerano, Gill

Source: Science, 2017 Aug . 357(6352), 692-695.

Access URL: https://www.jstor.org/stable/26399652

Spatial multiomic landscape of the human placenta at molecular resolution

Authors: Ounadjela, Johain R., Zhang, Ke, Kobayashi-Kirschvink, Koseki J., Jin, Kang, J. C. Russell, Andrew, Lackner, Andreas I., Callahan, Claire, Viggiani, Francesca, Dey, Kushal K., Jagadeesh, Karthik, Maxian, Theresa, Prandstetter, Anna-Maria, Nadaf, Naeem, Gong, Qiyu, Raichur, Ruth, Zvezdov, Morgan L., Hui, Mingyang, Simpson, Mattew, Liu, Xinwen, Min, Wei, Knöfler, Martin, Chen, Fei, Haider, Sandra, Shu, Jian

Source: Ounadjela, Johain R., Ke Zhang, Koseki J. Kobayashi-Kirschvink, Kang Jin, Andrew J. C. Russell, Andreas I. Lackner, Claire Callahan et al. "Spatial multiomic landscape of the human placenta at molecular resolution." Nat Med 30, no. 12 (2024): 3495-3508. DOI: 10.1038/s41591-024-03073-9

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Relation: Nature Medicine; Nat Med

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37380390

Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types.

Authors: Kim, Samuel S., Truong, Buu, Jagadeesh, Karthik, Dey, Kushal K., Shen, Amber Z., Raychaudhuri, Soumya, Kellis, Manolis, Price, Alkes L.

Source: Nature Communications; 1/20/2024, Vol. 15 Issue 1, p1-11, 11p

Subject Terms: GENOME-wide association studies, ETIOLOGY of diseases, GENETIC variation, RNA sequencing, GENE expression

Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance

Authors: Dorans, Elizabeth, Jagadeesh, Karthik, Dey, Kushal, Price, Alkes

Source: Dorans, Elizabeth, Karthik Jagadeesh, Kushal Dey, Alkes Price. "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance." No Journal No Volume. DOI: 10.1101/2024.05.24.24307813

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Relation: Nature Genetics

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37380376

Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles

Authors: Sakaue, Saori, Weinand, Kathryn, Isaac, Shakson, Dey, Kushal K., Jagadeesh, Karthik, Kanai, Masahiro, Watts, Gerald F. M., Zhu, Zhu, Albrecht, Jennifer, Anolik, Jennifer H., Apruzzese, William, Banda, Nirmal, Barnas, Jennifer L., Bathon, Joan M., Ben-Artzi, Ami, Boyce, Brendan F., Boyle, David L., Bridges, S. Louis, Bykerk, Vivian P., Campbell, Debbie, Carr, Hayley L., Ceponis, Arnold, Chicoine, Adam, Cordle, Andrew, Curtis, Michelle, Deane, Kevin D., DiCarlo, Edward, Dunn, Patrick, Filer, Andrew, Firestein, Gary S., Forbess, Lindsy, Geraldino-Pardilla, Laura, Goodman, Susan M., Gravallese, Ellen M., Gregersen, Peter K., Guthridge, Joel M., Gutierrez-Arcelus, Maria, Gurajala, Siddarth, Michael Holers, V., Horowitz, Diane, Hughes, Laura B., Ishigaki, Kazuyoshi, Ivashkiv, Lionel B., James, Judith A., Jonsson, Anna Helena, Kang, Joyce B., Keras, Gregory, Korsunsky, Ilya, Lakhanpal, Amit, Lederer, James A., Li, Zhihan J., Li, Yuhong, Liao, Katherine P., Mandelin, Arthur M., Mantel, Ian, Maybury, Mark, Mears, Joseph, Meednu, Nida, Millard, Nghia, Moreland, Larry W., Nathan, Aparna, Nerviani, Alessandra, Orange, Dana E., Perlman, Harris, Pitzalis, Costantino, Rangel-Moreno, Javier, Rao, Deepak A., Raza, Karim, Reshef, Yakir, Ritchlin, Christopher, Rivellese, Felice, Robinson, William H., Rumker, Laurie, Sahbudin, Ilfita, Seifert, Jennifer A., Slowikowski, Kamil, Smith, Melanie H., Tabechian, Darren, Scheel-Toellner, Dagmar, Utz, Paul J., Weisenfeld, Dana, Weisman, Michael H., Xiao, Qian, Zhang, Fan, Brenner, Michael B., McDavid, Andrew, Donlin, Laura T., Wei, Kevin, Price, Alkes L., Raychaudhuri, Soumya

Source: Sakaue, Saori, Kathryn Weinand, Shakson Isaac, Kushal K. Dey, Karthik Jagadeesh, Masahiro Kanai, Gerald F. M. Watts et al. "Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles." Nat Genet 56, no. 4 (2024): 615-626. DOI: 10.1038/s41588-024-01682-1

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Relation: Nature Genetics; Nat Genet

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37379190

Transgenic ferret models define pulmonary ionocyte diversity and function.

Authors: Yuan, Feng, Gasser, Grace N., Lemire, Evan, Montoro, Daniel T., Jagadeesh, Karthik, Zhang, Yan, Duan, Yifan, Ievlev, Vitaly, Wells, Kristen L., Rotti, Pavana G., Shahin, Weam, Winter, Michael, Rosen, Bradley H., Evans, Idil, Cai, Qian, Yu, Miao, Walsh, Susan A., Acevedo, Michael R., Pandya, Darpan N., Akurathi, Vamsidhar

Source: Nature; Sep2023, Vol. 621 Issue 7980, p857-867, 11p

Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution

Authors: Kang, Joyce B., Shen, Amber Z., Gurajala, Saisriram, Nathan, Aparna, Rumker, Laurie, Aguiar, Vitor R. C., Valencia, Cristian, Lagattuta, Kaitlyn A., Zhang, Fan, Jonsson, Anna Helena, Yazar, Seyhan, Alquicira-Hernandez, Jose, Khalili, Hamed, Ananthakrishnan, Ashwin N., Jagadeesh, Karthik, Dey, Kushal, Albrecht, Jennifer, Apruzzese, William, Banda, Nirmal, Barnas, Jennifer L., Bathon, Joan M., Ben-Artzi, Ami, Boyce, Brendan F., Boyle, David L., Bridges, S. Louis, Bykerk, Vivian P., Campbell, Debbie, Carr, Hayley L., Ceponis, Arnold, Chicoine, Adam, Cordle, Andrew, Curtis, Michelle, Deane, Kevin D., DiCarlo, Edward, Dunn, Patrick, Filer, Andrew, Firestein, Gary S., Forbess, Lindsy, Geraldino-Pardilla, Laura, Goodman, Susan M., Gravallese, Ellen M., Gregersen, Peter K., Guthridge, Joel M., Holers, V. Michael, Horowitz, Diane, Hughes, Laura B., Ishigaki, Kazuyoshi, Ivashkiv, Lionel B., James, Judith A., Keras, Gregory, Korsunsky, Ilya, Lakhanpal, Amit, Lederer, James A., Lewis, Myles, Li, Zhihan J., Li, Yuhong, Liao, Katherine P., Mandelin, Arthur M., Mantel, Ian, Marks, Kathryne E., Maybury, Mark, McDavid, Andrew, McGeachy, Mandy J., Mears, Joseph, Meednu, Nida, Millard, Nghia, Moreland, Larry W., Nayar, Saba, Nerviani, Alessandra, Orange, Dana E., Perlman, Harris, Pitzalis, Costantino, Rangel-Moreno, Javier, Raza, Karim, Reshef, Yakir, Ritchlin, Christopher, Rivellese, Felice, Robinson, William H., Sahbudin, Ilfita, Singaraju, Anvita, Seifert, Jennifer A., Slowikowski, Kamil, Smith, Melanie H., Tabechian, Darren, Scheel-Toellner, Dagmar, Utz, Paul J., Watts, Gerald F. M., Wei, Kevin, Weinand, Kathryn, Weisenfeld, Dana, Weisman, Michael H., Wyse, Aaron, Xiao, Qian, Zhu, Zhu, Daly, Mark J., Xavier, Ramnik J., Donlin, Laura T., Anolik, Jennifer H., Powell, Joseph E., Rao, Deepak A., Brenner, Michael B., Gutierrez-Arcelus, Maria, Luo, Yang, Sakaue, Saori, Raychaudhuri, Soumya

Source: Kang, Joyce B., Amber Z. Shen, Saisriram Gurajala, Aparna Nathan, Laurie Rumker, Vitor R. C. Aguiar, Cristian Valencia et al. "Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution." Nat Genet 55, no. 12 (2023): 2255-2268. DOI: 10.1038/s41588-023-01586-6

Subject Terms: Genetics

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Relation: Nature Genetics; Nat Genet

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37377786

Polygenic architecture of rare coding variation across 394,783 exomes.

Authors: Weiner, Daniel J., Nadig, Ajay, Jagadeesh, Karthik A., Dey, Kushal K., Neale, Benjamin M., Robinson, Elise B., Karczewski, Konrad J., O’Connor, Luke J.

Source: Nature; Feb2023, Vol. 614 Issue 7948, p492-499, 8p

Treatment-associated remodeling of the pancreatic cancer endothelium at singlecell resolution.

Authors: Shiau, Carina, Su, Jennifer, Guo, Jimmy A., Hong, Theodore S., Wo, Jennifer Y., Jagadeesh, Karthik A., Hwang, William L.

Source: Frontiers in Oncology; 9/16/2022, Vol. 12, p1-10, 10p

Subject Terms: PANCREATIC cancer, NEOADJUVANT chemotherapy, PROTON therapy, ENDOTHELIUM, PANCREATIC duct

Severe autoinflammation in 4 patients with C-terminal variants in cell division control protein 42 homolog (CDC42) successfully treated with IL-1β inhibition

Authors: Gernez, Yael, de Jesus, Adriana A., Alsaleem, Hanouf, Macaubas, Claudia, Roy, Amitava, Lovell, Daniel, Jagadeesh, Karthik A., Alehashemi, Sara, Erdman, Laura, Grimley, Michael, Talarico, Susanna, Bacchetta, Rosa, Lewis, David B., Canna, Scott W., Laxer, Ron M., Mellins, Elizabeth D., Goldbach-Mansky, Raphaela, Weinacht, Katja G.

Source: In The Journal of Allergy and Clinical Immunology October 2019 144(4):1122-1125

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.

Authors: Delorey, Toni M., Ziegler, Carly G. K., Heimberg, Graham, Normand, Rachelly, Yang, Yiming, Segerstolpe, Åsa, Abbondanza, Domenic, Fleming, Stephen J., Subramanian, Ayshwarya, Montoro, Daniel T., Jagadeesh, Karthik A., Dey, Kushal K., Sen, Pritha, Slyper, Michal, Pita-Juárez, Yered H., Phillips, Devan, Biermann, Jana, Bloom-Ackermann, Zohar, Barkas, Nikolaos, Ganna, Andrea

Source: Nature; 7/1/2021, Vol. 595 Issue 7865, p107-113, 7p

Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity

Authors: Gazal, Steven, Weissbrod, Omer, Hormozdiari, Farhad, Dey, Kushal, Nasser, Joseph, Jagadeesh, Karthik, Weiner, Daniel, Shi, Huwenbo, Fulco, Charles, O’Connor, Luke, Pasaniuc, Bogdan, Engreitz, Jesse M., Price, Alkes L.

Source: Gazal, Steven, Omer Weissbrod, Farhad Hormozdiari, Kushal Dey, Joseph Nasser, Karthik Jagadeesh, Daniel Weiner et al. "Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity." Nat Genet 54, no. 6 (2022): 827-836. DOI: 10.1038/s41588-022-01087-y

Subject Terms: Genetics

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Relation: Nature Genetics; Nat Genet

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37376879

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Authors: Zhang, Jinye, Hou, Kangcheng, Dey, Kushal, Sakaue, Saori, Jagadeesh, Karthik, Weinand, Kathryn, Taychameekiatchai, Aris, Rao, Poorvi, Pisco, Angela, Zou, James, Wang, Bruce, Gandal, Michael, Raychaudhuri, Soumya, Pasaniuc, Bogdan, Price, Alkes

Source: Zhang, Jinye, Kangcheng Hou, Kushal Dey, Saori Sakaue, Karthik Jagadeesh, Kathryn Weinand, Aris Taychameekiatchai et al. "Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data." No Journal No Volume. DOI: 10.21203/rs.3.rs-933790/v1

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Relation: Nature Genetics

Access URL: https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37376808

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