Strain-Level Identification and Analysis of Avian Coronavirus Using Raman Spectroscopy and Interpretable Machine Learning

Authors: Jin, Peng, Yeh, Yin-Ting, Ye, Jiarong, Wang, Ziyang, Xue, Yuan, Zhang, Na, Huang, Shengxi, Ghedin, Elodie, Lu, Huaguang, Schmitt, Anthony, Huang, Sharon X., Terrones, Mauricio

Source: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) Biomedical Imaging (ISBI), 2023 IEEE 20th International Symposium on. :1-5 Apr, 2023

Relation: 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)

Integrative cytogenetic and molecular studies unmask “chromosomal mimicry” in hematologic malignancies

Authors: Zhao, Melissa ¹, Ryall, Scott ¹, Brody, Samuel J. ¹, Harris, Amyah C. ², Cabral, Kristin ³, Brownstein, Catherine ^{3, 4}, Kim, Jaeseung C. ¹, Smith, Adam C. ⁵, Dal Cin, Paola ¹, Narayan, Rupa ², Sikkink, Kristin ⁶, Schmitt, Anthony ⁶, Hobbs, Gabriela S. ², Fathi, Amir T. ², Griffin, Gabriel K. ^{1, 7, 8}, Sait, Sheila N. J. ⁹, Iafrate, Anthony J. ¹⁰, Aster, Jon C. ¹, Graubert, Timothy A. ², Nardi, Valentina ^{1, 10}, Dubuc, Adrian M. ^{1, 9, ∗}

Source: In Blood Advances 11 March 2025 9(5):1003-1012

Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture

Authors: Galbraith, Kristyn ^{∗, ∗}, Wu, Jamin ^∗, Sikkink, Kristin ^†, Mohamed, Hussein ^∗, Reid, Derek ^†, Perez-Arreola, Michelle ^†, Belton, Jon-Matthew ^†, Nomikou, Sofia ^†, Melnyk, Shadi ^†, Yang, Yiying ^∗, Liechty, Benjamin L. ^‡, Jour, George ^∗, Tsirigos, Aristotelis ^{∗, §, ¶}, Hermel, David J. ^‖, Beck, Alyssa ^∗∗, Sigal, Darren ^‖, Dahl, Nathan A. ^††, Vibhakar, Rajeev ^††, Schmitt, Anthony ^†, Snuderl, Matija ^{∗, ‡‡, ∗}

Source: In The Journal of Molecular Diagnostics January 2025

Evaluation of Hi-C Sequencing for Detection of Gene Fusions in Hematologic and Solid Tumor Pediatric Cancer Samples.

Authors: Schmitt, Anthony D.¹ (AUTHOR) anthony@arimagenomics.com, Sikkink, Kristin¹ (AUTHOR) shadi@arimagenomics.com, Ahmed, Atif A.² (AUTHOR), Melnyk, Shadi¹ (AUTHOR) bretreid10@gmail.com, Reid, Derek¹ (AUTHOR) vanmeter.logan@gmail.com, Van Meter, Logan¹ (AUTHOR), Guest, Erin M.^3,4 (AUTHOR), Lansdon, Lisa A.^5,6 (AUTHOR) ipushel@cmh.edu, Pastinen, Tomi^4,5 (AUTHOR), Pushel, Irina⁵ (AUTHOR), Yoo, Byunggil^5,6 (AUTHOR), Farooqi, Midhat S.^4,5,6 (AUTHOR) anthony@arimagenomics.com

Source: Cancers. Sep2024, Vol. 16 Issue 17, p2936. 14p.

Subject Terms: *LEUKEMIA diagnosis, *TUMORS in children, *HEMATOLOGIC malignancies, *GENOMICS, *SARCOMA, *CHROMOSOME abnormalities, *GENETIC polymorphisms, *GENES, *MYELOID leukemia, *RHABDOMYOSARCOMA, *SEQUENCE analysis, *MOLECULAR diagnosis, DIAGNOSIS of tumors in children

The Science of COVID-19 An online course for teachers and their students

Authors: Johnson, Matthew, Lewis, Tiffany, Martin, Kit, Cesare, Amber, Schmitt, Anthony, Lengerich, Eugene, Bittner, Kristin, Divyak, Chris

Source: Science teacher. 90(3):12-19

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631053899&indx=1&recIds=ETOCRN631053899

RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis

Authors: Rheinemann, Lara, Downhour, Diane Miller, Bredbenner, Kate, Mercenne, Gaelle, Davenport, Kristen A., Schmitt, Phuong Tieu, Necessary, Christina R., McCullough, John, Schmitt, Anthony P., Simon, Sanford M., Sundquist, Wesley I., Elde, Nels C.

Source: In Cell 14 October 2021 184(21):5419-5431

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

Authors: Yu, Miao, Zemke, Nathan R., Chen, Ziyin, Juric, Ivan, Hu, Rong, Raviram, Ramya, Abnousi, Armen, Fang, Rongxin, Zhang, Yanxiao, Gorkin, David U., Li, Yang E., Zhao, Yuan, Lee, Lindsay, Mishra, Shreya, Schmitt, Anthony D., Qiu, Yunjiang, Dickel, Diane E., Visel, Axel, Pennacchio, Len A., Hu, Ming, Ren, Bing

Source: Nature Structural and Molecular Biology; March 2025, Vol. 32 Issue: 3 p479-490, 12p

Nectar antimicrobial compounds and their potential effects on pollinators

Authors: Schmitt, Anthony, Roy, Rahul, Carter, Clay J

Source: In Current Opinion in Insect Science April 2021 44:55-63

Temporally distinct 3D multi-omic dynamics in the developing human brain.

Authors: Heffel, Matthew G., Zhou, Jingtian, Zhang, Yi, Lee, Dong-Sung, Hou, Kangcheng, Pastor-Alonso, Oier, Abuhanna, Kevin D., Galasso, Joseph, Kern, Colin, Tai, Chu-Yi, Garcia-Padilla, Carlos, Nafisi, Mahsa, Zhou, Yi, Schmitt, Anthony D., Li, Terence, Haeussler, Maximilian, Wick, Brittney, Zhang, Martin Jinye, Xie, Fangming, Ziffra, Ryan S.

Source: Nature; Nov2024, Vol. 635 Issue 8038, p481-489, 9p

957 3D Genomic and Epigenetic Landscape of Uterine Mesenchymal Tumors

Authors: Chiang, Sarah ¹, Yang, Yiying ², Schroff, Chanel ², Oliva, Esther ³, Stewart, Colin ⁴, Stolnicu, Simona ⁵, Post, Miriam ⁶, McCluggage, Glenn ⁷, Murali, Rajmohan ¹, Boroujeni, Amir Momeni ¹, Chui, M. Herman ¹, Park, Kay ¹, Ellenson, Lora ¹, Antonescu, Cristina ¹, Schmitt, Anthony ⁸, Snuderl, Matija ²

Source: In Laboratory Investigation March 2025 105(3) Supplement

Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

Authors: Dall’Agnese, Alessandra, Caputo, Luca, Nicoletti, Chiara, di Iulio, Julia, Schmitt, Anthony, Gatto, Sole, Diao, Yarui, Ye, Zhen, Forcato, Mattia, Perera, Ranjan, Bicciato, Silvio, Telenti, Amalio, Ren, Bing, Puri, Pier Lorenzo

Source: In Molecular Cell 7 November 2019 76(3):453-472

Large B‐cell lymphoma with mystery rearrangement: Applying Hi‐C to the detection of clinically relevant structural abnormalities.

Authors: Prior, Daniel¹ (AUTHOR), Schmitt, Anthony D.² (AUTHOR), Louissaint, Abner³ (AUTHOR), Mata, Douglas A.⁴ (AUTHOR), Massaro, Stephanie¹ (AUTHOR), Nardi, Valentina³ (AUTHOR), Xu, Mina L.⁵ (AUTHOR) mina.xu@yale.edu

Source: British Journal of Haematology. Sep2024, Vol. 205 Issue 3, p1225-1229. 5p.

Subject Terms: *LOCUS (Genetics), *GENE rearrangement, *CYTOLOGY, *LIFE sciences, *CELL populations

The major nectar protein of Brassica rapa is a non-specific lipid transfer protein, BrLTP2.1, with strong antifungal activity

Authors: Schmitt, Anthony J., Sathoff, Andrew E., Holl, Catherine, Bauer, Brittany, Samac, Deborah A., Carter, Clay J.

Source: Journal of Experimental Botany, 2018 Nov 01. 69(22), 5587-5597.

Access URL: https://www.jstor.org/stable/26961374

A compendium of promoter-centered long-range chromatin interactions in the human genome

Authors: Jung, Inkyung, Schmitt, Anthony, Diao, Yarui, Lee, Andrew, Liu, Tristin, Yang, Dongchan, Tan, Catherine, Eom, Junghyun, Chan, Marilynn, Chee, Sora, Chiang, Zachary, Kim, Changyoun, Masliah, Eliezer, Barr, Cathy, Li, Bin, Kuan, Samantha, Kim, Dongsup, Ren, Bing

Source: Nature genetics. 51(10):1442-1449

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190824893.0x000001&indx=1&recIds=ETOCvdc_100190824893.0x000001

Common DNA sequence variation influences 3-dimensional conformation of the human genome

Authors: Gorkin, David, Qiu, Yunjiang, Hu, Ming, Fletez-Brant, Kipper, Liu, Tristin, Schmitt, Anthony, Noor, Amina, Chiou, Joshua, Gaulton, Kyle, Sebat, Jonathan, Li, Yun, Hansen, Kasper, Ren, Bing

Source: Genome biology. 20(1):1-25

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190650750.0x000001&indx=1&recIds=ETOCvdc_100190650750.0x000001

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

Authors: Greenwald, William, Li, He, Benaglio, Paola, Jakubosky, David, Matsui, Hiroko, Schmitt, Anthony, Selvaraj, Siddarth, D'Antonio, Matteo, D'Antonio-Chronowska, Agnieszka, Smith, Erin, Frazer, Kelly

Source: Nature communications. 10(1):1-17

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125952077.0x000001&indx=1&recIds=ETOCvdc_100125952077.0x000001

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Authors: Dahn, Hollis A, Mountcastle, Jacquelyn, Balacco, Jennifer, Winkler, Sylke, Bista, Iliana, Schmitt, Anthony D, Pettersson, Olga Vinnere, Formenti, Giulio, Oliver, Karen, Smith, Michelle, Tan, Wenhua, Kraus, Anne, Mac, Stephen, Komoroske, Lisa M, Lama, Tanya, Crawford, Andrew J, Murphy, Robert W, Brown, Samara, Scott, Alan F, Morin, Phillip A, Jarvis, Erich D, Fedrigo, Olivier

Source: GigaScience. 11

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100165608762.0x000001&indx=1&recIds=ETOCvdc_100165608762.0x000001

Review: Nectar biology: From molecules to ecosystems

Authors: Roy, Rahul, Schmitt, Anthony J., Thomas, Jason B., Carter, Clay J.

Source: In Plant Science September 2017 262:148-164

Msn2p, a Zinc Finger DNA-Binding Protein, is the Transcriptional Activator of the Multistress Response in Saccharomyces cerevisiae

Authors: Schmitt, Anthony P., McEntee, Kevin

Source: Proceedings of the National Academy of Sciences of the United States of America, 1996 Jun 01. 93(12), 5777-5782.

Access URL: https://www.jstor.org/stable/39623

High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

Authors: Rosa-Garrido, Manuel, Chapski, Douglas J., Schmitt, Anthony D., Kimball, Todd H., Karbassi, Elaheh, Monte, Emma, Balderas, Enrique, Pellegrini, Matteo, Shih, Tsai-Ting, Soehalim, Elizabeth, Liem, David, Ping, Peipei, Galjart, Niels J., Ren, Shuxun, Wang, Yibin, Ren, Bing, Vondriska, Thomas M.

Source: Circulation. 136(17):1613-1625

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100049850348.0x000001&indx=1&recIds=ETOCvdc_100049850348.0x000001