Researcher Profile

Smith, D, Bastug, K, Burgoine, K, Broach, JR, Hammershaimb, EA, Hehnly, C, Morton, SU, Osman, M, Schiff, SJ & Ericson, JE 2024, 'A Systematic Review of Human Paenibacillus Infections and Comparison of Adult and Pediatric Cases', Pediatric Infectious Disease Journal. https://doi.org/10.1097/INF.0000000000004668

NYGC ALS Consortium 2024, 'A framework for sharing of clinical and genetic data for precision medicine applications', Nature Medicine, vol. 30, no. 12, 134, pp. 3578-3589. https://doi.org/10.1038/s41591-024-03239-5

Costa, ACT, Schneper, L, Russo, M, Fernandes, AAR, Broach, JR & Fernandes, PMB 2024, 'Comparative Transcriptome Analysis of Industrial and Laboratory Saccharomyces cerevisiae Strains after Sequential Stresses', Fermentation, vol. 10, no. 8, 395. https://doi.org/10.3390/fermentation10080395

Ferreira, RC, Rodrigues, CR, Broach, JR & Briones, MRS 2024, 'Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals', International journal of molecular sciences, vol. 25, no. 7, 3785. https://doi.org/10.3390/ijms25073785

NYGC ALS Consortium 2024, 'Correction to: TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A (Nature, (2022), 603, 7899, (131-137), 10.1038/s41586-022-04436-3)', Nature, vol. 631, no. 8020, pp. E7. https://doi.org/10.1038/s41586-024-07577-9

Budurlean, L, Tukaramrao, DB, Zhang, L, Dovat, S & Broach, J 2024, 'Integrating Optical Genome Mapping and Whole Genome Sequencing in Somatic Structural Variant Detection', Journal of Personalized Medicine, vol. 14, no. 3, 291. https://doi.org/10.3390/jpm14030291

The International ALS Genomics Consortium, ITALSGEN Consortium, SLAGEN Consortium, Project MinE ALS Sequencing Consortium & The American Genome Center 2024, 'Mechanism-free repurposing of drugs for C9orf72-related ALS/FTD using large-scale genomic data', Cell Genomics, vol. 4, no. 11, 100679. https://doi.org/10.1016/j.xgen.2024.100679

NYGC ALS Consortium 2024, 'Mitochondrial genome variants associated with amyotrophic lateral sclerosis and their haplogroup distribution', Muscle and Nerve, vol. 70, no. 4, pp. 862-872. https://doi.org/10.1002/mus.28230

The New York Genome Center ALS Sequencing Consortium, Scottish Genomes Partnership, ALS COSMOS Study Group, PLS COSMOS Study Group & GTAC Investigators 2024, 'Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS', BMC genomics, vol. 25, no. 1, 651. https://doi.org/10.1186/s12864-024-10538-1

PROSPECT Consortium, The American Genome Center, International LBD Genomics Consortium & International ALS/FTD Consortium 2023, 'Genome-wide structural variant analysis identifies risk loci for non-Alzheimer's dementias', Cell Genomics, vol. 3, no. 6, 100316. https://doi.org/10.1016/j.xgen.2023.100316

Salameh, TJ, Roth, K, Schultz, L, Ma, Z, Bonavia, AS, Broach, JR, Hu, B & Howrylak, JA 2023, 'Gut microbiome dynamics and associations with mortality in critically ill patients', Gut Pathogens, vol. 15, no. 1, 66. https://doi.org/10.1186/s13099-023-00567-8

Yu, M, Peterson, MR, Cherukuri, V, Hehnly, C, Mbabazi-Kabachelor, E, Mulondo, R, Nsubuga Kaaya, B, Broach, JR, Schiff, SJ & Monga, V 2023, 'Infection diagnosis in hydrocephalus CT images: a domain enriched attention learning approach', Journal of neural engineering, vol. 20, no. 3, 036033. https://doi.org/10.1088/1741-2552/acd9ee

Ericson, JE, Burgoine, K, Kumbakumba, E, Ochora, M, Hehnly, C, Bajunirwe, F, Bazira, J, Fronterre, C, Hagmann, C, Kulkarni, AV, Kumar, MS, Magombe, J, Mbabazi-Kabachelor, E, Morton, SU, Movassagh, M, Mugamba, J, Mulondo, R, Natukwatsa, D, Kaaya, BN, Olupot-Olupot, P, Onen, J, Sheldon, K, Smith, J, Ssentongo, P, Ssenyonga, P, Warf, B, Wegoye, E, Zhang, L, Kiwanuka, J, Paulson, JN, Broach, JR & Schiff, SJ 2023, 'Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda', Clinical Infectious Diseases, vol. 77, no. 5, pp. 768-775. https://doi.org/10.1093/cid/ciad337

Levy, B, Baughn, LB, Akkari, Y, Chartrand, S, LaBarge, B, Claxton, D, Lennon, PA, Cujar, C, Kolhe, R, Kroeger, K, Pitel, B, Sahajpal, N, Sathanoori, M, Vlad, G, Zhang, L, Fang, M, Kanagal-Shamanna, R & Broach, JR 2023, 'Optical genome mapping in acute myeloid leukemia: a multicenter evaluation', Blood Advances, vol. 7, no. 7, pp. 1297-1307. https://doi.org/10.1182/bloodadvances.2022007583

Morton, SU, Hehnly, C, Burgoine, K, Ssentongo, P, Ericson, JE, Kumar, MS, Hagmann, C, Fronterre, C, Smith, J, Movassagh, M, Streck, N, Bebell, LM, Bazira, J, Kumbakumba, E, Bajunirwe, F, Mulondo, R, Mbabazi-Kabachelor, E, Nsubuga, BK, Natukwatsa, D, Nalule, E, Magombe, J, Erickson, T, Ngonzi, J, Ochora, M, Olupot-Olupot, P, Onen, J, Ssenyonga, P, Mugamba, J, Warf, BC, Kulkarni, AV, Lane, J, Whalen, AJ, Zhang, L, Sheldon, K, Meier, FA, Kiwanuka, J, Broach, JR, Paulson, JN & Schiff, SJ 2023, 'Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study', The Lancet Microbe, vol. 4, no. 8, pp. e601-e611. https://doi.org/10.1016/S2666-5247(23)00106-4

Costa, ACT, Russo, M, Fernandes, AAR, Broach, JR & Fernandes, PMB 2023, 'Transcriptional Response of Multi-Stress-Tolerant Saccharomyces cerevisiae to Sequential Stresses', Fermentation, vol. 9, no. 2, 195. https://doi.org/10.3390/fermentation9020195

NYGC ALS Consortium 2022, 'Cell environment shapes TDP-43 function with implications in neuronal and muscle disease', Communications Biology, vol. 5, no. 1, 314. https://doi.org/10.1038/s42003-022-03253-8

Hehnly, C, Ssentongo, P, Bebell, LM, Burgoine, K, Bazira, J, Fronterre, C, Kumbakumba, E, Mulondo, R, Mbabazi-Kabachelor, E, Morton, SU, Ngonzi, J, Ochora, M, Olupot-Olupot, P, Mugamba, J, Onen, J, Roberts, DJ, Sheldon, K, Sinnar, SA, Smith, J, Ssenyonga, P, Kiwanuka, J, Paulson, JN, Meier, FA, Ericson, JE, Broach, JR & Schiff, SJ 2022, 'Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus', International Journal of Infectious Diseases, vol. 118, pp. 24-33. https://doi.org/10.1016/j.ijid.2022.02.005

Kumar, MS, Slud, EV, Hehnly, C, Zhang, L, Broach, J, Irizarry, RA, Schiff, SJ & Paulson, JN 2022, 'Differential richness inference for 16S rRNA marker gene surveys', Genome biology, vol. 23, no. 1, 166. https://doi.org/10.1186/s13059-022-02722-x

Labarge, B, Hennessy, M, Zhang, L, Goldrich, D, Chartrand, S, Purnell, C, Wright, S, Goldenberg, D & Broach, JR 2022, 'Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer', Molecular Cancer Research, vol. 20, no. 9, pp. 1420-1428. https://doi.org/10.1158/1541-7786.MCR-21-0831

Shi, A, Fan, F & Broach, JR 2022, 'Microbial adaptive evolution', Journal of Industrial Microbiology and Biotechnology, vol. 49, no. 2, kuab076. https://doi.org/10.1093/jimb/kuab076

Stine, JG, Schreibman, IR, Faust, AJ, Dahmus, J, Stern, B, Soriano, C, Rivas, G, Hummer, B, Kimball, SR, Geyer, NR, Chinchilli, VM, Loomba, R, Schmitz, K, Sciamanna, C, Strine, C, Wentzel, R, Marlin, S, Sica, C, Vesek, J, Eyster, E, Sinoway, L, Bentz, K, Handley, N, Hershey Fell, B, Mottilla, S, Christ, C, George, S, Novchich, T, Beyer, M, Clarke, K, Myers, T, Glading-Steinruck, M, Krok, K, Ma, T, Riley, T, Thompson, E, Tressler, H, Broach, J, Doan, T, Patrick, S, Reed, S, Hamilton, C, Slavoski, K & Tregea, D 2022, 'NASHFit: A randomized controlled trial of an exercise training program to reduce clotting risk in patients with NASH', Hepatology, vol. 76, no. 1, pp. 172-185. https://doi.org/10.1002/hep.32274

NYGC ALS Consortium 2022, 'NOS1AP is a novel molecular target and critical factor in TDP-43 pathology', Brain Communications, vol. 4, no. 5. https://doi.org/10.1093/braincomms/fcac242

Budurlean, L, Baker, M & Broach, J 2022, 'Rare MYC-N11S germline mutation indicative of inherited breast cancer in a multigeneration family', BMJ case reports, vol. 15, no. 11, e251336. https://doi.org/10.1136/bcr-2022-251336

Wasserfall, C, Dyer, AM, Speake, C, Andersen, DK, Baab, KT, Bellin, MD, Broach, JR, Campbell-Thompson, M, Chinchilli, VM, Lee, PJ, Park, WG, Pratley, RE, Saloman, JL, Sims, EK, Tang, G, Yadav, D, Yazici, C & Conwell, DL 2022, 'Standard Operating Procedures for Biospecimen Collection, Processing, and Storage: From the Type 1 Diabetes in Acute Pancreatitis Consortium', Pancreas, vol. 51, no. 6, pp. 593-597. https://doi.org/10.1097/MPA.0000000000002077

Xu, J, Song, F, Lyu, H, Kobayashi, M, Zhang, B, Zhao, Z, Hou, Y, Wang, X, Luan, Y, Jia, B, Stasiak, L, Wong, JHY, Wang, Q, Jin, Q, Jin, Q, Fu, Y, Yang, H, Hardison, RC, Dovat, S, Platanias, LC, Diao, Y, Yang, Y, Yamada, T, Viny, AD, Levine, RL, Claxton, D, Broach, JR, Zheng, H & Yue, F 2022, 'Subtype-specific 3D genome alteration in acute myeloid leukaemia', Nature, vol. 611, no. 7935, pp. 387-398. https://doi.org/10.1038/s41586-022-05365-x

NYGC ALS Consortium 2022, 'TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A', Nature, vol. 603, no. 7899, pp. 131-137. https://doi.org/10.1038/s41586-022-04436-3

Type 1 Diabetes in Acute Pancreatitis Consortium (T1DAPC) 2022, 'Type 1 Diabetes in Acute Pancreatitis Consortium: From Concept to Reality', Pancreas, vol. 51, no. 6, pp. 563-567. https://doi.org/10.1097/MPA.0000000000002073

Hehnly, C, Shi, A, Ssentongo, P, Zhang, L, Isaacs, A, Morton, SU, Streck, N, Erdmann-Gilmore, P, Tolstoy, I, Reid Townsend, R, Limbrick, DD, Paulson, JN, Ericson, JE, Galperin, MY, Schiff, SJ & Broach, JR 2022, 'Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus', mBio, vol. 13, no. 6. https://doi.org/10.1128/mbio.02688-22

Movassagh, M, Morton, SU, Hehnly, C, Smith, J, Doan, TT, Irizarry, R, Broach, JR, Schiff, SJ, Bailey, JA & Paulson, JN 2022, 'mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis', BMC genomics, vol. 23, no. 1, 439. https://doi.org/10.1186/s12864-022-08558-w

Mishra, D, Bepler, T, Teague, B, Berger, B, Broach, J & Weiss, R 2021, 'An engineered protein-phosphorylation toggle network with implications for endogenous network discovery', Science, vol. 373, no. 6550, eaav0780. https://doi.org/10.1126/science.aav0780

The NeuroLINCS Consortium & NYGC ALS Consortium 2021, 'An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients', iScience, vol. 24, no. 11, 103221. https://doi.org/10.1016/j.isci.2021.103221

Johnson, JO, Chia, R, Miller, DE, Li, R, Kumaran, R, Abramzon, Y, Alahmady, N, Renton, AE, Topp, SD, Gibbs, JR, Cookson, MR, Sabir, MS, Dalgard, CL, Troakes, C, Jones, AR, Shatunov, A, Iacoangeli, A, Al Khleifat, A, Ticozzi, N, Silani, V, Gellera, C, Blair, IP, Dobson-Stone, C, Kwok, JB, Bonkowski, ES, Palvadeau, R, Tienari, PJ, Morrison, KE, Shaw, PJ, Al-Chalabi, A, Brown, RH, Calvo, A, Mora, G, Al-Saif, H, Gotkine, M, Leigh, F, Chang, IJ, Perlman, SJ, Glass, I, Scott, AI, Shaw, CE, Basak, AN, Landers, JE, Chiò, A, Crawford, TO, Smith, BN, Traynor, BJ, Smith, BN, Fallini, C, Gkazi, AS, Topp, SD, Scotter, EL, Kenna, KP, Keagle, P, Tiloca, C, Vance, C, Troakes, C, Colombrita, C, King, A, Pensato, V, Castellotti, B, Baas, F, Ten Asbroek, ALMA, McKenna-Yasek, D, McLaughlin, RL, Polak, M, Asress, S, Esteban-Pérez, J, Stevic, Z, D'Alfonso, S, Mazzini, L, Comi, GP, Del Bo, R, Ceroni, M, Gagliardi, S, Querin, G, Bertolin, C, Van Rheenen, W, Rademakers, R, Van Blitterswijk, M, Lauria, G, Duga, S, Corti, S, Cereda, C, Corrado, L, Sorarù, G, Williams, KL, Nicholson, GA, Blair, IP, Leblond-Manry, C, Rouleau, GA, Hardiman, O, Morrison, KE, Veldink, JH, Van Den Berg, LH, Pall, H, Turner, MR, Talbot, K, Taroni, F, García-Redondo, A, Wu, Z, Glass, JD, Gellera, C, Ratti, A, Brown, RH, Landers, JE, Dalgard, CL, Adeleye, A, Soltis, AR, Alba, C, Viollet, C, Bacikova, D, Hupalo, DN, Sukumar, G, Pollard, HB, Wilkerson, MD, Martinez, EMG, Abramzon, Y, Ahmed, S, Arepalli, S, Baloh, RH, Bowser, R, Brady, CB, Brice, A, Broach, J, Campbell, RH, Camu, W, Cooper-Knock, J, Ding, J, Drepper, C, Drory, VE, Dunckley, TL, Eicher, JD, England, BK, Faghri, F, Feldman, E, Floeter, MK, Fratta, P, Geiger, JT, Gerhard, G, Gibbs, JR, Gibson, SB, Glass, JD, Hardy, J, Harms, MB, Heiman-Patterson, TD, Hernandez, DG, Jansson, L, Kirby, J, Kowall, NW, Laaksovirta, H, Landeck, N, Landi, F, Le Ber, I, Lumbroso, S, Macgowan, DJL, Maragakis, NJ, Mouzat, K, Murphy, NA, Myllykangas, L, Nalls, MA, Orrell, RW, Ostrow, LW, Pamphlett, R, Pickering-Brown, S, Pioro, EP, Pletnikova, O, Pliner, HA, Pulst, SM, Ravits, JM, Renton, AE, Rivera, A, Robberecht, W, Rogaeva, E, Rollinson, S, Rothstein, JD, Scholz, SW, Sendtner, M, Sidle, KC, Simmons, Z, Singleton, AB, Smith, N, Stone, DJ, Tienari, PJ, Troncoso, JC, Valori, M, Van Damme, P, Van Deerlin, VM, Van Den Bosch, L, Zinman, L, Landers, JE, Chiò, A, Traynor, BJ, Angelocola, SM, Ausiello, FP, Barberis, M, Bartolomei, I, Battistini, S, Bersano, E, Bisogni, G, Borghero, G, Brunetti, M, Cabona, C, Calvo, A, Canale, F, Canosa, A, Cantisani, TA, Capasso, M, Caponnetto, C, Cardinali, P, Carrera, P, Casale, F, Chiò, A, Colletti, T, Conforti, FL, Conte, A, Conti, E, Corbo, M, Cuccu, S, Dalla Bella, E, D'Errico, E, Demarco, G, Dubbioso, R, Ferrarese, C, Ferraro, PM, Filippi, M, Fini, N, Floris, G, Fuda, G, Gallone, S, Gianferrari, G, Giannini, F, Grassano, M, Greco, L, Iazzolino, B, Introna, A, La Bella, V, Lattante, S, Liguori, R, Logroscino, G, Logullo, FO, Lunetta, C, Mandich, P, Mandrioli, J, Manera, U, Manganelli, F, Marangi, G, Marinou, K, Marrosu, MG, Martinelli, I, Messina, S, Moglia, C, Mosca, L, Murru, MR, Origone, P, Passaniti, C, Petrelli, C, Petrucci, A, Pozzi, S, Pugliatti, M, Quattrini, A, Ricci, C, Riolo, G, Riva, N, Russo, M, Sabatelli, M, Salamone, P, Salivetto, M, Salvi, F, Santarelli, M, Sbaiz, L, Sideri, R, Simone, I, Simonini, C, Spataro, R, Tanel, R, Tedeschi, G, Ticca, A, Torriello, A, Tranquilli, S, Tremolizzo, L, Trojsi, F, Vasta, R, Vacchiano, V, Vita, G, Volanti, P, Zollino, M & Zucchi, E 2021, 'Association of Variants in the SPTLC1 Gene with Juvenile Amyotrophic Lateral Sclerosis', JAMA neurology, vol. 78, no. 10, pp. 1236-1248. https://doi.org/10.1001/jamaneurol.2021.2598

Costa, ACT, Hornick, J, Antunes, TFS, Santos, AMC, Fernandes, AAR, Broach, JR & Fernandes, PMB 2021, 'Complete genome sequence and analysis of a Saccharomyces cerevisiae strain used for sugarcane spirit production', Brazilian Journal of Microbiology, vol. 52, no. 3, pp. 1087-1095. https://doi.org/10.1007/s42770-021-00444-z

Ssentongo, P, Hehnly, C, Birungi, P, Roach, MA, Spady, J, Fronterre, C, Wang, M, Murray-Kolb, LE, Al-Shaar, L, Chinchilli, VM, Broach, JR, Ericson, JE & Schiff, SJ 2021, 'Congenital Cytomegalovirus Infection Burden and Epidemiologic Risk Factors in Countries with Universal Screening: A Systematic Review and Meta-analysis', JAMA network open, vol. 4, no. 8, e2120736, pp. E2120736. https://doi.org/10.1001/jamanetworkopen.2021.20736

Goldrich, DY, Labarge, B, Chartrand, S, Zhang, L, Sadowski, HB, Zhang, Y, Pham, K, Way, H, Lai, CYJ, Pang, AWC, Clifford, B, Hastie, AR, Oldakowski, M, Goldenberg, D & Broach, JR 2021, 'Identification of somatic structural variants in solid tumors by optical genome mapping', Journal of Personalized Medicine, vol. 11, no. 2, 142, pp. 1-21. https://doi.org/10.3390/jpm11020142

Isaacs, AM, Morton, SU, Movassagh, M, Zhang, Q, Hehnly, C, Zhang, L, Morales, DM, Sinnar, SA, Ericson, JE, Mbabazi-Kabachelor, E, Ssenyonga, P, Onen, J, Mulondo, R, Hornig, M, Warf, BC, Broach, JR, Townsend, RR, Limbrick, DD, Paulson, JN & Schiff, SJ 2021, 'Immune activation during Paenibacillus brain infection in African infants with frequent cytomegalovirus co-infection', iScience, vol. 24, no. 4, 102351. https://doi.org/10.1016/j.isci.2021.102351

Raca, G, Abdel-Azim, H, Yue, F, Broach, J, Payne, JL, Reeves, ME, Gowda, C, Schramm, J, Desai, D, Dovat, E, Hu, T, Berg, AS, Bhojwani, D, Payne, KJ & Dovat, S 2021, 'Increased Incidence of IKZF1 deletions and IGH-CRLF2 translocations in B-ALL of Hispanic/Latino children—a novel health disparity', Leukemia, vol. 35, no. 8, pp. 2399-2402. https://doi.org/10.1038/s41375-021-01133-4

The American Genome Center (TAGC), The FALS Sequencing Consortium, The Genomics England Research Consortium, The International ALS/FTD Genomics Consortium (iAFGC), The International FTD Genetics Consortium (IFGC), The International LBD Genomics Consortium (iLBDGC), The NYGC ALS Consortium, the University of Maryland Brain and Tissue Bank and NIH NeuroBioBank & The PROSPECT Consortium 2021, 'Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis', Neuron, vol. 109, no. 3, pp. 448-460.e4. https://doi.org/10.1016/j.neuron.2020.11.005

Movassagh, M, Bebell, LM, Burgoine, K, Hehnly, C, Zhang, L, Moran, K, Sheldon, K, Sinnar, SA, Mbabazi-Kabachelor, E, Kumbakumba, E, Bazira, J, Ochora, M, Mulondo, R, Nsubuga, BK, Weeks, AD, Gladstone, M, Olupot-Olupot, P, Ngonzi, J, Roberts, DJ, Meier, FA, Irizarry, RA, Broach, JR, Schiff, SJ & Paulson, JN 2021, 'Vaginal microbiome topic modeling of laboring Ugandan women with and without fever', npj Biofilms and Microbiomes, vol. 7, no. 1, 75. https://doi.org/10.1038/s41522-021-00244-1