pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection

Authors: Xia, Huiming, Hoang, My, Schmidt, Evelyn, Kiwala, Susanna, McMichael, Joshua, Skidmore, Zachary L., Fisk, Bryan, Song, Jonathan J., Hundal, Jasreet, Mooney, Thomas, Walker, Jason R., Goedegebuure, S. Peter, Miller, Christopher A., Gillanders, William E., Griffith, Obi L., Griffith, Malachi

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2406.06985

The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway

Authors: Chen, Hao ^{1, 2}, Ferguson, Cole J. ^{2, 3}, Mitchell, Dylan C. ⁴, Risch, Isabel ⁵, Titus, Amanda ⁶, Paulo, Joao A. ⁴, Hwang, Andrew ¹, Beck, Loren K. ¹, Lin, Tsen-Hsuan ⁷, Gu, Wei ⁸, Song, Sheng-Kwei ⁷, Yuede, Carla M. ⁶, Yano, Hiroko ^{1, 9, 10}, Griffith, Obi L. ⁵, Griffith, Malachi ⁵, Gygi, Steven P. ⁴, Bonni, Azad ^{2, 11, ∗}, Kim, Albert H. ^{1, 9, 10, 12, 13, ∗∗}

Source: In Cell Reports 25 February 2025 44(2)

Single-Cell Transcriptomic Analysis of Kaposi Sarcoma.

Authors: Rauch, Daniel A.^1,2, Ramos, Paula Valiño^1,2, Khanfar, Mariam^1,3, Harding, John^1,2, Joseph, Ancy^1,2, Fahad, Anam⁴, Simonson, Paul⁴, Risch, Isabel^1,3, Griffith, Obi^1,3, Griffith, Malachi^1,3, Ratner, Lee^1,2, lratner@wustl.edu

Source: PLoS Pathogens; 4/1/2025, Vol. 21 Issue 4, p1-27, 27p

Bam-readcount -- rapid generation of basepair-resolution sequence metrics

Authors: Khanna, Ajay, Larson, David E., Srivatsan, Sridhar Nonavinkere, Mosior, Matthew, Abbott, Travis E., Kiwala, Susanna, Ley, Timothy J., Duncavage, Eric J., Walter, Matthew J., Walker, Jason R., Griffith, Obi L., Griffith, Malachi, Miller, Christopher A.

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/2107.12817

Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma

Authors: Ramirez, Cody A., Becker-Hapak, Michelle, Singhal, Kartik, Russler-Germain, David A., Frenkel, Felix, Barnell, Erica K., McClain, Ethan D., Desai, Sweta, Schappe, Timothy, Onyeador, Onyinyechi C., Kudryashova, Olga, Belousov, Vladislav, Bagaev, Alexander, Ocheredko, Elena, Kiwala, Susanna, Hundal, Jasreet, Skidmore, Zachary L., Watkins, Marcus P., Mooney, Thomas B., Walker, Jason R., Krysiak, Kilannin, Gomez, Felicia, Fronick, Catrina C., Fulton, Robert S., Schreiber, Robert D., Mehta-Shah, Neha, Cashen, Amanda F., Kahl, Brad S., Ataullakhanov, Ravshan, Bartlett, Nancy L., Griffith, Malachi, Griffith, Obi L., Fehniger, Todd A.

Source: In Blood Advances 13 August 2024 8(15):4035-4049

Whole-genome sequences reveal zygotic composition in chimeric twins

Authors: Yoon, Christopher J., Nam, Chang Hyun, Kim, Taewoo, Lee, Jeong Seok, Kim, Ryul, Yi, Kijong, Koh, June-Young, Kim, Jiye, Won, Hyein, Oh, Ji Won, Griffith, Obi L., Griffith, Malachi, Sung, Joohon, Kim, Tae Yeul, Cho, Duck, Choi, Ji Seon, Ju, Young Seok

Source: In Human Genetics and Genomics Advances 18 July 2024 5(3)

Endothelial cells are a key target of IFN-g during response to combined PD-1/CTLA-4 ICB treatment in a mouse model of bladder cancer

Authors: Freshour, Sharon L. ¹, Chen, Timothy H.-P. ¹, Fisk, Bryan ^{1, 2}, Shen, Haolin ¹, Mosior, Matthew ^{1, 2}, Skidmore, Zachary L. ^{1, 2}, Fronick, Catrina ², Bolzenius, Jennifer K. ^{1, 3}, Griffith, Obi L. ^{1, 2, 3, 4, ∗}, Arora, Vivek K. ^{1, 3, ∗∗}, Griffith, Malachi ^{1, 2, 3, 4, 5, ∗∗∗}

Source: In iScience 20 October 2023 26(10)

Mutations associated with progression in follicular lymphoma predict inferior outcomes at diagnosis: Alliance A151303

Authors: Russler-Germain, David A., Krysiak, Kilannin, Ramirez, Cody, Mosior, Matthew, Watkins, Marcus P., Gomez, Felicia, Skidmore, Zachary L., Trani, Lee, Gao, Feng, Geyer, Susan, Cashen, Amanda F., Mehta-Shah, Neha, Kahl, Brad S., Bartlett, Nancy L., Alderuccio, Juan P., Lossos, Izidore S., Ondrejka, Sarah L., Hsi, Eric D., Martin, Peter, Leonard, John P., Griffith, Malachi, Griffith, Obi L., Fehniger, Todd A.

Source: In Blood Advances 26 September 2023 7(18):5524-5539

Distinct clonal identities of B-ALLs arising after lenolidomide therapy for multiple myeloma

Authors: Barnell, Erica K., Skidmore, Zachary L., Newcomer, Kenneth F., Chavez, Monique, Campbell, Katie M., Cotto, Kelsy C., Spies, Nicholas C., Ruzinova, Marianna B., Wang, Tianjiao, Abro, Brooj, Kreisel, Friederike, Parikh, Bijal A., Duncavage, Eric J., Frater, John L., Lee, Yi-Shan, Hassan, Anjum, King, Justin A., Kohnen, Daniel R., Fiala, Mark A., Welch, John S., Uy, Geoffrey L., Vij, Kiran, Vij, Ravi, Griffith, Malachi, Griffith, Obi L., Wartman, Lukas D. ^∗∗

Source: In Blood Advances 24 January 2023 7(2):236-245

Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers

Authors: Skidmore, Zachary L, Kunisaki, Jason, Lin, Yiing, Cotto, Kelsy C, Barnell, Erica K, Hundal, Jasreet, Krysiak, Kilannin, Magrini, Vincent, Trani, Lee, Walker, Jason R, Fulton, Robert, Brunt, Elizabeth M, Miller, Christopher A, Wilson, Richard K, Mardis, Elaine R, Griffith, Malachi, Chapman, William, Griffith, Obi L

Source: In Cancer Genetics June 2022 264-265:90-99

Standardized evidence-based approach for assessment of oncogenic and clinical significance of NTRK fusions

Authors: Saliba, Jason, Church, Alanna J., Rao, Shruti, Danos, Arpad, Furtado, Larissa V., Laetsch, Theodore, Zhang, Liying, Nardi, Valentina, Lin, Wan-Hsin, Ritter, Deborah I., Madhavan, Subha, Li, Marilyn M., Griffith, Obi L., Griffith, Malachi, Raca, Gordana, Roy, Angshumoy

Source: In Cancer Genetics June 2022 264-265:50-59

Integrative genomic analysis reveals low T-cell infiltration as the primary feature of tobacco use in HPV-positive oropharyngeal cancer

Authors: Wahle, Benjamin M. ¹, Zolkind, Paul ¹, Ramirez, Ricardo J. ¹, Skidmore, Zachary L. ², Anderson, Sydney R. ², Mazul, Angela ¹, Hayes, D. Neil ³, Sandulache, Vlad C. ^{4, 7, 8}, Thorstad, Wade L. ⁵, Adkins, Douglas ⁶, Griffith, Obi L. ^{2, 6, 9}, Griffith, Malachi ^{2, 6, 9}, Zevallos, Jose P. ^{1, 10, ∗}

Source: In iScience 20 May 2022 25(5)

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)

Authors: Horak, Peter, Griffith, Malachi, Danos, Arpad M., Pitel, Beth A., Madhavan, Subha, Liu, Xuelu, Chow, Cynthia, Williams, Heather, Carmody, Leigh, Barrow-Laing, Lisa, Rieke, Damian, Kreutzfeldt, Simon, Stenzinger, Albrecht, Tamborero, David, Benary, Manuela, Rajagopal, Padma Sheila, Ida, Cristiane M., Lesmana, Harry, Satgunaseelan, Laveniya, Merker, Jason D., Tolstorukov, Michael Y., Campregher, Paulo Vidal, Warner, Jeremy L., Rao, Shruti, Natesan, Maya, Shen, Haolin, Venstrom, Jeffrey, Roy, Somak, Tao, Kayoko, Kanagal-Shamanna, Rashmi, Xu, Xinjie, Ritter, Deborah I., Pagel, Kym, Krysiak, Kilannin, Dubuc, Adrian, Akkari, Yassmine M., Li, Xuan Shirley, Lee, Jennifer, King, Ian, Raca, Gordana, Wagner, Alex H., Li, Marylin M., Plon, Sharon E., Kulkarni, Shashikant, Griffith, Obi L., Chakravarty, Debyani, Sonkin, Dmitriy

Source: In Genetics in Medicine May 2022 24(5):986-998

Phase 1/dose expansion trial of brentuximab vedotin and lenalidomide in relapsed or refractory diffuse large B-cell lymphoma

Authors: Ward, Jeffrey P. ^*, Berrien-Elliott, Melissa M., Gomez, Felicia, Luo, Jingqin, Becker-Hapak, Michelle, Cashen, Amanda F., Wagner-Johnston, Nina D., Maddocks, Kami, Mosior, Matthew, Foster, Mark, Krysiak, Kilannin, Schmidt, Alina, Skidmore, Zachary L., Desai, Sweta, Watkins, Marcus P., Fischer, Anne, Griffith, Malachi, Griffith, Obi L., Fehniger, Todd A. ^*, Bartlett, Nancy L. ^*

Source: In Blood 31 March 2022 139(13):1999-2010

Donor memory-like NK cells persist and induce remissions in pediatric patients with relapsed AML after transplant

Authors: Bednarski, Jeffrey J. ^*, Zimmerman, Clare, Berrien-Elliott, Melissa M., Foltz, Jennifer A., Becker-Hapak, Michelle, Neal, Carly C., Foster, Mark, Schappe, Timothy, McClain, Ethan, Pence, Patrick P., Desai, Sweta, Kersting-Schadek, Samantha, Wong, Pamela, Russler-Germain, David A., Fisk, Bryan, Lie, Wen-Rong, Eisele, Jeremy, Hyde, Stephanie, Bhatt, Sima T., Griffith, Obi L., Griffith, Malachi, Petti, Allegra A., Cashen, Amanda F., Fehniger, Todd A. ^*

Source: In Blood 17 March 2022 139(11):1670-1683

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Authors: Rehm, Heidi L., Page, Angela J.H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J.S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., Brudno, Michael, Brush, Matthew H., Bujold, David, Burdett, Tony, Buske, Orion J., Cabili, Moran N., Cameron, Daniel L., Carroll, Robert J., Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P., Chen, Shu Hui, Cherry, J. Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L., Cook-Deegan, Robert M., Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M., Denisko, Danielle, Doerr, Megan J., Dolman, Lena I., Dove, Edward S., Dursi, L. Jonathan, Dyke, Stephanie O.M., Eddy, James A., Eilbeck, Karen, Ellrott, Kyle P., Fairley, Susan, Fakhro, Khalid A., Firth, Helen V., Fitzsimons, Michael S., Fiume, Marc, Flicek, Paul, Fore, Ian M., Freeberg, Mallory A., Freimuth, Robert R., Fromont, Lauren A., Fuerth, Jonathan, Gaff, Clara L., Gan, Weiniu, Ghanaim, Elena M., Glazer, David, Green, Robert C., Griffith, Malachi, Griffith, Obi L., Grossman, Robert L., Groza, Tudor, Guidry Auvil, Jaime M., Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A., Hamosh, Ada, Hansen, David P., Hart, Reece K., Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M., Ho, Calvin W.L., Hobb, Ashley E., Hoffman, Michael M., Hofmann, Oliver M., Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E., Husami, Ammar, Jacobsen, Julius O., Jamuar, Saumya S., Janes, Elizabeth L., Jeanson, Francis, Jené, Aina, Johns, Amber L., Joly, Yann, Jones, Steven J.M., Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M., Kekesi-Lafrance, Kristina, Kelleher, Jerome, Kerry, Giselle, Khor, Seik-Soon, Knoppers, Bartha M., Konopko, Melissa A., Kosaki, Kenjiro, Kuba, Martin, Lawson, Jonathan, Leinonen, Rasko, Li, Stephanie, Lin, Michael F., Linden, Mikael, Liu, Xianglin, Liyanage, Isuru Udara, Lopez, Javier, Lucassen, Anneke M., Lukowski, Michael, Mann, Alice L., Marshall, John, Mattioni, Michele, Metke-Jimenez, Alejandro, Middleton, Anna, Milne, Richard J., Molnár-Gábor, Fruzsina, Mulder, Nicola, Munoz-Torres, Monica C., Nag, Rishi, Nakagawa, Hidewaki, Nasir, Jamal, Navarro, Arcadi, Nelson, Tristan H., Niewielska, Ania, Nisselle, Amy, Niu, Jeffrey, Nyrönen, Tommi H., O’Connor, Brian D., Oesterle, Sabine, Ogishima, Soichi, Ota Wang, Vivian, Paglione, Laura A.D., Palumbo, Emilio, Parkinson, Helen E., Philippakis, Anthony A., Pizarro, Angel D., Prlic, Andreas, Rambla, Jordi, Rendon, Augusto, Rider, Renee A., Robinson, Peter N., Rodarmer, Kurt W., Rodriguez, Laura Lyman, Rubin, Alan F., Rueda, Manuel, Rushton, Gregory A., Ryan, Rosalyn S., Saunders, Gary I., Schuilenburg, Helen, Schwede, Torsten, Scollen, Serena, Senf, Alexander, Sheffield, Nathan C., Skantharajah, Neerjah, Smith, Albert V., Sofia, Heidi J., Spalding, Dylan, Spurdle, Amanda B., Stark, Zornitza, Stein, Lincoln D., Suematsu, Makoto, Tan, Patrick, Tedds, Jonathan A., Thomson, Alastair A., Thorogood, Adrian, Tickle, Timothy L., Tokunaga, Katsushi, Törnroos, Juha, Torrents, David, Upchurch, Sean, Valencia, Alfonso, Guimera, Roman Valls, Vamathevan, Jessica, Varma, Susheel, Vears, Danya F., Viner, Coby, Voisin, Craig, Wagner, Alex H., Wallace, Susan E., Walsh, Brian P., Williams, Marc S., Winkler, Eva C., Wold, Barbara J., Wood, Grant M., Woolley, J. Patrick, Yamasaki, Chisato, Yates, Andrew D., Yung, Christina K., Zass, Lyndon J., Zaytseva, Ksenia, Zhang, Junjun, Goodhand, Peter, North, Kathryn, Birney, Ewan

Source: In Cell Genomics 10 November 2021 1(2)

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

Authors: Wagner, Alex H., Babb, Lawrence, Alterovitz, Gil, Baudis, Michael, Brush, Matthew, Cameron, Daniel L., Cline, Melissa, Griffith, Malachi, Griffith, Obi L., Hunt, Sarah E., Kreda, David, Lee, Jennifer M., Li, Stephanie, Lopez, Javier, Moyer, Eric, Nelson, Tristan, Patel, Ronak Y., Riehle, Kevin, Robinson, Peter N., Rynearson, Shawn, Schuilenburg, Helen, Tsukanov, Kirill, Walsh, Brian, Konopko, Melissa, Rehm, Heidi L., Yates, Andrew D., Freimuth, Robert R., Hart, Reece K.

Source: In Cell Genomics 10 November 2021 1(2)

Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens

Authors: Linette, Gerald P., Becker-Hapak, Michelle, Skidmore, Zachary L., Baroja, Miren Lorea, Xu, Chong, Hundal, Jasreet, Spencer, David H., Fu, Weixuan, Cummins, Casey, Robnett, Maya, Kaabinejadian, Saghar, Hildebrand, William H., Magrini, Vincent, Demeter, Ryan, Krupnick, Alexander S., Griffith, Obi L., Griffith, Malachi, Mardis, Elaine R., Carreno, Beatriz M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Nov . 116(47), 23662-23670.

Access URL: https://www.jstor.org/stable/26861953

Rapid progression of adult T-cell leukemia/lymphoma as tumor-infiltrating Tregs after PD-1 blockade

Authors: Rauch, Daniel A., Conlon, Kevin C., Janakiram, Murali, Brammer, Jonathan E., Harding, John C., Ye, B.Hilda, Zang, Xingxing, Ren, Xiaoxin, Olson, Sydney, Cheng, Xiaogang, Miljkovic, Milos D., Sundaramoorthi, Hemalatha, Joseph, Ancy, Skidmore, Zachary L., Griffith, Obi, Griffith, Malachi, Waldmann, Thomas A., Ratner, Lee

Source: In Blood 24 October 2019 134(17):1406-1414

Noninvasive Detection of High-Risk Adenomas Using Stool-Derived Eukaryotic RNA Sequences as Biomarkers

Authors: Barnell, Andrew R., Campbell, Katie M., Kruse, Kimberly R., Messina, Dave, Kodner, Ira, Manary, Mark, Needleman, Phil, Barnell, Erica K., Kang, Yiming, Wurtzler, Elizabeth M., Griffith, Malachi, Chaudhuri, Aadel A., Griffith, Obi L.

Source: In Gastroenterology September 2019 157(3):884-887