Advancing deep variant phenotyping of mitochondrial enzyme complexes for precision medicine in allogeneic hematopoietic stem-cell transplantation

Authors: Dong, Jing ^{a, b, c, ⁎}, Zimmermann, Michael T. ^{c, d, e}, Haque, Neshatul ^c, Arsang-Jang, Shahram ^a, Saber, Wael ^{a, f}, Gai, Xiaowu ^c, Urrutia, Raul ^{c, d, g}

Source: In Transplantation Reports February 2025 10(1)

MARK2 variants cause autism spectrum disorder via the downregulation of WNT/β-catenin signaling pathway

Authors: Gong, Maolei, Li, Jiayi, Qin, Zailong, Machado Bressan Wilke, Matheus Vernet, Liu, Yijun, Li, Qian, Liu, Haoran, Liang, Chen, Morales-Rosado, Joel A., Cohen, Ana S.A., Hughes, Susan S., Sullivan, Bonnie R., Waddell, Valerie, van den Boogaard, Marie-José H., van Jaarsveld, Richard H., van Binsbergen, Ellen, van Gassen, Koen L., Wang, Tianyun, Hiatt, Susan M., Amaral, Michelle D., Kelley, Whitley V., Zhao, Jianbo, Feng, Weixing, Ren, Changhong, Yu, Yazhen, Boczek, Nicole J., Ferber, Matthew J., Lahner, Carrie, Elliott, Sherr, Ruan, Yiyan, Mignot, Cyril, Keren, Boris, Xie, Hua, Wang, Xiaoyan, Popp, Bernt, Zweier, Christiane, Piard, Juliette, Coubes, Christine, Mau-Them, Frederic Tran, Safraou, Hana, Innes, A. Micheil, Gauthier, Julie, Michaud, Jacques L., Koboldt, Daniel C., Sylvie, Odent, Willems, Marjolaine, Tan, Wen-Hann, Cogne, Benjamin, Rieubland, Claudine, Braun, Dominique, McLean, Scott Douglas, Platzer, Konrad, Zacher, Pia, Oppermann, Henry, Evenepoel, Lucie, Blanc, Pierre, El Khattabi, Laïla, Haque, Neshatul, Dsouza, Nikita R., Zimmermann, Michael T., Urrutia, Raul, Klee, Eric W., Shen, Yiping, Du, Hongzhen, Rappaport, Leonard, Liu, Chang-Mei, Chen, Xiaoli

Source: In The American Journal of Human Genetics 7 November 2024 111(11):2392-2410

Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression

Authors: Bursch, Karina L., Goetz, Christopher J., Jiao, Guanming, Nuñez, Raymundo, Olp, Michael D., Dhiman, Alisha, Khurana, Mallika, Zimmermann, Michael T., Urrutia, Raul A., Dykhuizen, Emily C., Smith, Brian C.

Source: In Journal of Biological Chemistry April 2024 300(4)

Bi-allelic variants in HMGCR cause an autosomal-recessive progressive limb-girdle muscular dystrophy

Authors: Morales-Rosado, Joel A., Schwab, Tanya L., Macklin-Mantia, Sarah K., Foley, A. Reghan, Pinto e Vairo, Filippo, Pehlivan, Davut, Donkervoort, Sandra, Rosenfeld, Jill A., Boyum, Grace E., Hu, Ying, Cong, Anh T.Q., Lotze, Timothy E., Mohila, Carrie A., Saade, Dimah, Bharucha-Goebel, Diana, Chao, Katherine R., Grunseich, Christopher, Bruels, Christine C., Littel, Hannah R., Estrella, Elicia A., Pais, Lynn, Kang, Peter B., Zimmermann, Michael T., Lupski, James R., Lee, Brendan, Schellenberg, Matthew J., Clark, Karl J., Wierenga, Klaas J., Bönnemann, Carsten G., Klee, Eric W.

Source: American journal of human genetics. 110(6):989-997

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191548866.0x000001&indx=1&recIds=ETOCvdc_100191548866.0x000001

RAG genomic variation causes autoimmune diseases through specific structure-based mechanisms of enzyme dysregulation

Authors: Haque, Neshatul, Kawai, Tomoki, Ratnasinghe, Brian D., Wagenknecht, Jessica B., Urrutia, Raul, Notarangelo, Luigi D., Zimmermann, Michael T.

Source: In iScience 20 October 2023 26(10)

Advanced computational analysis of CD40LG variants in atypical X-linked hyper-IgM syndrome

Authors: Pazhanisamy, Amudha, Jorge, Salomao Doria, Zimmermann, Michael T., Kitcharoensakkul, Maleewan, Abdalgani, Manar, Khojah, Amer, Victor, Christian, Rueda, Cesar, Urrutia, Raul, Abraham, Roshini S.

Source: In Clinical Immunology August 2023 253

Priming therapy by targeting enhancer-initiated pathways in patient-derived pancreatic cancer cells

Authors: Fraunhoffer, Nicolas A., Moreno Vega, Aura I., Abuelafia, Analía Meilerman, Morvan, Marie, Lebarbier, Emilie, Mary-Huard, Tristan, Zimmermann, Michael T., Lomberk, Gwen, Urrutia, Raul, Dusetti, Nelson, Blum, Yuna, Nicolle, Remy, Iovanna, Juan

Source: In eBioMedicine June 2023 92

Laboratory perspectives in the development of polygenic risk scores for disease: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG)

Authors: Reddi, Honey V., Wand, Hannah, Funke, Birgit, Zimmermann, Michael T., Lebo, Matthew S., Qian, Emily, Shirts, Brian H., Zou, Ying S., Zhang, Bing M., Rose, Nancy C., Abu-El-Haija, Aya

Source: In Genetics in Medicine May 2023 25(5)

A multi-layered computational structural genomics approach enhances domain-specific interpretation of Kleefstra syndrome variants in EHMT1

Authors: Chi, Young-In, Jorge, Salomão D., Jensen, Davin R., Smith, Brian C., Volkman, Brian F., Mathison, Angela J., Lomberk, Gwen, Zimmermann, Michael T., Urrutia, Raul

Source: In Computational and Structural Biotechnology Journal 2023 21:5249-5258

Beyond structural bioinformatics for genomics with dynamics characterization of an expanded KRAS mutational landscape

Authors: Ratnasinghe, Brian D., Haque, Neshatul, Wagenknecht, Jessica B., Jensen, Davin R., Valdivia Esparza, Guadalupe K., Leverence, Elise N., Milech De Assuncao, Thiago, Mathison, Angela J., Lomberk, Gwen, Smith, Brian C., Volkman, Brian F., Urrutia, Raul, Zimmermann, Michael T.

Source: In Computational and Structural Biotechnology Journal 2023 21:4790-4803

A domain ontology for the Non-Coding RNA field

Authors: Huang, Jingshan, Eilbeck, Karen, Blake, Judith A., Dou, Dejing, Natale, Darren A., Ruttenberg, Alan, Smith, Barry, Zimmermann, Michael T., Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zhang, He, Zixing Liu, Tan, Ming

Source: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. :621-624 Nov, 2015

Relation: 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Enhanced interpretation of 935 hotspot and non-hotspot RAS variants using evidence-based structural bioinformatics

Authors: Tripathi, Swarnendu, Dsouza, Nikita R., Mathison, Angela J., Leverence, Elise, Urrutia, Raul, Zimmermann, Michael T.

Source: Computational and Structural Biotechnology Journal. 20:117-127

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190063613.0x000001&indx=1&recIds=ETOCvdc_100190063613.0x000001

Structural bioinformatics enhances the interpretation of somatic mutations in KDM6A found in human cancers

Authors: Chi, Young-In, Stodola, Timothy J., De Assuncao, Thiago M., Leverence, Elise N., Smith, Brian C., Volkman, Brian F., Mathison, Angela J., Lomberk, Gwen, Zimmermann, Michael T., Urrutia, Raul

Source: Computational and Structural Biotechnology Journal. 20:2200-2211

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190063286.0x000001&indx=1&recIds=ETOCvdc_100190063286.0x000001

Computational modeling reveals key molecular properties and dynamic behavior of disruptor of telomeric silencing 1‐like (DOT1L) and partnering complexes involved in leukemogenesis

Authors: Stodola, Timothy J., Chi, Young‐In, De Assuncao, Thiago M., Leverence, Elise N., Tripathi, Swarnendu, Dsouza, Nikita R., Mathison, Angela J., Volkman, Brian F., Smith, Brian C., Lomberk, Gwen, Zimmermann, Michael T., Urrutia, Raul

Source: Proteins. 90(1):282-298

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100147555567.0x000001&indx=1&recIds=ETOCvdc_100147555567.0x000001

Hypomorphic RAG2 Deficiency Promotes Selection of Self-Reactive B Cells.

Authors: Thouvenel, Christopher D., Tipton, Christopher M., Yamazaki, Yasuhiro, Zhang, Ting-ting, Rylaarsdam, Stacey, Hom, Jennifer R., Snead, Catherine, Zhu, Chengsong, Li, Quan-Zhen, Lee, Yu Nee, Kawai, Tomoki, Haque, Neshatul, Zimmermann, Michael T., Ponnan, Sivasankaran Munusamy, Jackson, Shaun W., James, Rich G., Sanz, Ignacio, Notarangelo, Luigi D., Torgerson, Troy R., Ochs, Hans D.

Source: Journal of Clinical Immunology; 1/15/2025, Vol. 45 Issue 1, p1-14, 14p

Subject Terms: REGULATORY T cells, IMMUNOLOGIC memory, B cells, COMMON variable immunodeficiency, WHOLE genome sequencing

An Analytical Approach that Combines Knowledge from Germline and Somatic Mutations Enhances Tumor Genomic Reanalyses in Precision Oncology.

Authors: DeVoe, Elias, Reddi, Honey V., Taylor, Bradley W., Stachowiak, Samantha, Geurts, Jennifer L., George, Ben, Shaker, Reza, Urrutia, Raul, Zimmermann, Michael T.

Source: Journal of Computational Biology; Jan2025, Vol. 32 Issue 1, p89-103, 15p

Emergent properties of the lysine methylome reveal regulatory roles via protein interactions and histone mimicry.

Authors: Pollin, Gareth, Chi, Young-In, Mathison, Angela J., Zimmermann, Michael T., Lomberk, Gwen, Urrutia, Raul

Source: Epigenomics; Jan2025, Vol. 17 Issue 1, p5-20, 16p

Somatic PIK3R1 variation as a cause of vascular malformations and overgrowth

Authors: Cottrell, Catherine E., Bender, Nicole R., Zimmermann, Michael T., Heusel, Jonathan W., Corliss, Meagan, Evenson, Michael J., Magrini, Vincent, Corsmeier, Donald J., Avenarius, Matthew, Dudley, Jeffrey N., Johnston, Jennifer J., Lindhurst, Marjorie J., Vigh-Conrad, Katinka, Davies, Olivia M.T., Coughlin, Carrie C., Frieden, Ilona J., Tollefson, Megha, Zaenglein, Andrea L., Ciliberto, Heather, Tosi, Laura L., Semple, Robert K., Biesecker, Leslie G., Drolet, Beth A.

Source: In Genetics in Medicine October 2021 23(10):1882-1888

SASH3 variants cause a novel form of X-linked combined immunodeficiency with immune dysregulation

Authors: Delmonte, Ottavia M., Bergerson, Jenna R.E., Kawai, Tomoki, Kuehn, Hye Sun, McDermott, David H., Cortese, Irene, Zimmermann, Michael T., Dobbs, A. Kerry, Bosticardo, Marita, Fink, Danielle, Majumdar, Shamik, Palterer, Boaz, Pala, Francesca, Dsouza, Nikita R., Pouzolles, Marie, Taylor, Naomi, Calvo, Katherine R., Daley, Stephen R., Velez, Daniel, Agharahimi, Anahita, Myint-Hpu, Katherine, Dropulic, Lesia K., Lyons, Jonathan J., Holland, Steven M., Freeman, Alexandra F., Ghosh, Rajarshi, Similuk, Morgan B., Niemela, Julie E., Stoddard, Jennifer, Kuhns, Douglas B., Urrutia, Raul, Rosenzweig, Sergio D., Walkiewicz, Magdalena A., Murphy, Philip M., Notarangelo, Luigi D. ^*

Source: In Blood 23 September 2021 138(12):1019-1033

Impact of integrated translational research on clinical exome sequencing

Authors: Klee, Eric W. ^*, Cousin, Margot A., Pinto e Vairo, Filippo, Morales-Rosado, Joel A., Macke, Erica L., Jenkinson, W. Garrett, Ferrer, Alejandro, Schultz-Rogers, Laura E., Olson, Rory J., Oliver, Gavin R., Sigafoos, Ashley N., Schwab, Tanya L., Zimmermann, Michael T., Urrutia, Raul A., Kaiwar, Charu, Gupta, Aditi, Blackburn, Patrick R., Boczek, Nicole J., Prochnow, Carri A., Lowy, Rebecca J., Mulvihill, Lindsay A., McAllister, Tammy M., Aoudia, Stacy L., Kruisselbrink, Teresa M., Gunderson, Lauren B., Kemppainen, Jennifer L., Fisher, Laura J., Tarnowski, Jessica M., Hager, Megan M., Kroc, Sarah A., Bertsch, Nicole L., Agre, Katherine E., Jackson, Jessica L., Macklin-Mantia, Sarah K., Murphree, Marine I., Rust, Laura M., Summer Bolster, Jolene M., Beck, Scott A., Atwal, Paldeep S., Ellingson, Marissa S., Barnett, Sarah S., Rasmussen, Kristen J., Lahner, Carrie A., Niu, Zhiyv, Hasadsri, Linda, Ferber, Matthew J., Marcou, Cherisse A., Clark, Karl J., Pichurin, Pavel N., Deyle, David R., Morava-Kozicz, Eva, Gavrilova, Ralitza H., Dhamija, Radhika, Wierenga, Klaas J., Lanpher, Brendan C., Babovic-Vuksanovic, Dusica, Farrugia, Gianrico, Schimmenti, Lisa A., Stewart, A. Keith, Lazaridis, Konstantinos N. ^*

Source: In Genetics in Medicine March 2021 23(3):498-507