Inclusion, Diversity, Equity, Allyship and Social Justice (IDEAS)

2024

Chemotherapy activates inflammasomes to cause inflammation-associated bone loss

Wang, C., Kaur, K., Xu, C., Abu-Amer, Y. & Mbalaviele, G., Apr 11 2024, In: eLife. 13

Research output: Contribution to journal › Article › peer-review

Open Access

Direct prediction of intrinsically disordered protein conformational properties from sequence

Lotthammer, J. M., Ginell, G. M., Griffith, D., Emenecker, R. J. & Holehouse, A. S., Mar 2024, In: Nature Methods. 21, 3, p. 465-476 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator

Jankowski, M. S., Griffith, D., Shastry, D. G., Pelham, J. F., Ginell, G. M., Thomas, J., Karande, P., Holehouse, A. S. & Hurley, J. M., Dec 2024, In: Nature communications. 15, 1, 3523.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

DNA hypomethylation ameliorates erosive inflammatory arthritis by modulating interferon regulatory factor-8

Swarnkar, G., Semenkovich, N. P., Arra, M., Mims, D. K., Naqvi, S. K., Peterson, T., Mbalaviele, G., Wu, C. L. & Abu-Amer, Y., Feb 13 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 7, e2310264121.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Helicity of a tardigrade disordered protein contributes to its protective function during desiccation

Biswas, S., Gollub, E., Yu, F., Ginell, G., Holehouse, A., Sukenik, S. & Boothby, T. C., Feb 2024, In: Protein Science. 33, 2, e4872.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Identification of plant transcriptional activation domains

Morffy, N., Van den Broeck, L., Miller, C., Emenecker, R. J., Bryant, J. A., Lee, T. M., Sageman-Furnas, K., Wilkinson, E. G., Pathak, S., Kotha, S. R., Lam, A., Mahatma, S., Pande, V., Waoo, A., Wright, R. C., Holehouse, A. S., Staller, M. V., Sozzani, R. & Strader, L. C., Aug 1 2024, In: Nature. 632, 8023, p. 166-173 8 p.

Research output: Contribution to journal › Article › peer-review

Labile assembly of a tardigrade protein induces biostasis

Sanchez-Martinez, S., Nguyen, K., Biswas, S., Nicholson, V., Romanyuk, A. V., Ramirez, J., Kc, S., Akter, A., Childs, C., Meese, E. K., Usher, E. T., Ginell, G. M., Yu, F., Gollub, E., Malferrari, M., Francia, F., Venturoli, G., Martin, E. W., Caporaletti, F. & Giubertoni, G. & 5 others, Woutersen, S., Sukenik, S., Woolfson, D. N., Holehouse, A. S. & Boothby, T. C., Apr 2024, In: Protein Science. 33, 4, e4941.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

NLRP1 inflammasome promotes senescence and senescence-associated secretory phenotype

Muela-Zarzuela, I., Suarez-Rivero, J. M., Gallardo-Orihuela, A., Wang, C., Izawa, K., de Gregorio-Procopio, M., Couillin, I., Ryffel, B., Kitaura, J., Sanz, A., von Zglinicki, T., Mbalaviele, G. & Cordero, M. D., Aug 2024, In: Inflammation Research. 73, 8, p. 1253-1266 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Phase transition of GvpU regulates gas vesicle clustering in bacteria

Li, Z., Shen, Q., Usher, E. T., Anderson, A. P., Iburg, M., Lin, R., Zimmer, B., Meyer, M. D., Holehouse, A. S., You, L., Chilkoti, A., Dai, Y. & Lu, G. J., Apr 2024, In: Nature microbiology. 9, 4, p. 1021-1035 15 p.

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells

Katerndahl, C. D. S., Rogers, O. R. S., Day, R. B., Xu, Z., Helton, N. M., Ramakrishnan, S. M., Miller, C. A. & Ley, T. J., Apr 30 2024, In: Proceedings of the National Academy of Sciences of the United States of America. 121, 18, e2317690121.

Research output: Contribution to journal › Article › peer-review

Open Access

Proteogenomic analysis reveals cytoplasmic sequestration of RUNX1 by the acute myeloid leukemia–initiating CBFB::MYH11 oncofusion protein

Day, R. B., Hickman, J. A., Xu, Z., Katerndahl, C. D. S., Ferraro, F., Ramakrishnan, S. M., Erdmann-Gilmore, P., Sprung, R. W., Mi, Y., Townsend, R. R., Miller, C. A. & Ley, T. J., Feb 15 2024, In: Journal of Clinical Investigation. 134, 4, 1e176311.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

SARS-CoV-2 Omicron BA.1 Variant Infection of Human Colon Epithelial Cells

Antia, A., Alvarado, D. M., Zeng, Q., Casorla-Perez, L. A., Davis, D. L., Sonnek, N. M., Ciorba, M. A. & Ding, S., Apr 2024, In: Viruses. 16, 4, 634.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Structural biases in disordered proteins are prevalent in the cell

Moses, D., Guadalupe, K., Yu, F., Flores, E., Perez, A. R., McAnelly, R., Shamoon, N. M., Kaur, G., Cuevas-Zepeda, E., Merg, A. D., Martin, E. W., Holehouse, A. S. & Sukenik, S., Feb 2024, In: Nature Structural and Molecular Biology. 31, 2, p. 283-292 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA

Cubuk, J., Alston, J. J., Incicco, J. J., Holehouse, A. S., Hall, K., Stuchell-Brereton, M. D. & Soranno, A., Mar 21 2024, In: Nucleic acids research. 52, 5, p. 2609-2624 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

Tmem178 Negatively Regulates IL-1β Production Through Inhibition of the NLRP3 Inflammasome

Khanna, K., Yan, H., Mehra, M., Rohatgi, N., Mbalaviele, G., Mellins, E. D. & Faccio, R., Jan 2024, In: Arthritis and Rheumatology. 76, 1, p. 107-118 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

2023

A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy

Townley, B. A., Buerer, L., Tsao, N., Bacolla, A., Mansoori, F., Rusanov, T., Clark, N., Goodarzi, N., Schmidt, N., Srivatsan, S. N., Sun, H., Sample, R. A., Brickner, J. R., McDonald, D., Tsai, M. S., Walter, M. J., Wozniak, D. F., Holehouse, A. S., Pena, V. & Tainer, J. A. & 2 others, Fairbrother, W. G. & Mosammaparast, N., Jul 6 2023, In: Molecular cell. 83, 13, p. 2258-2275.e11

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

CAID prediction portal: A comprehensive service for predicting intrinsic disorder and binding regions in proteins

CAID predictors, Del Conte, A., Bouhraoua, A., Mehdiabadi, M., Clementel, D., Monzon, A. M., Tosatto, S. C. E., Piovesan, D., Holehouse, A. S., Griffith, D., Emenecker, R. J., Patil, A., Sharma, R., Tsunoda, T., Sharma, A., Tang, Y. J., Liu, B., Mirabello, C., Wallner, B. & Rost, B. & 44 others, Ilzhöfer, D., Littmann, M., Heinzinger, M., Krautheimer, L. I. M., Bernhofer, M., McGuffin, L. J., Callebaut, I., Feildel, T. B., Liu, J., Cheng, J., Guo, Z., Xu, J., Wang, S., Malhis, N., Gsponer, J., Kim, C. S., Han, K. S., Ma, M. C., Kurgan, L., Ghadermarzi, S., Katuwawala, A., Zhao, B., Peng, Z., Wu, Z., Hu, G., Wang, K., Hoque, M. T., Ul Kabir, M. W., Vendruscolo, M., Sormanni, P., Li, M., Zhang, F., Jia, P., Wang, Y., Lobanov, M. Y., Galzitskaya, O. V., Vranken, W., Díaz, A., Litfin, T., Zhou, Y., Hanson, J., Paliwal, K., Dosztányi, Z. & Erdős, G., Jul 5 2023, In: Nucleic acids research. 51, W1, p. W62-W69

Research output: Contribution to journal › Article › peer-review

Open Access

17 Scopus citations

Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma

Puram, S. V., Mints, M., Pal, A., Qi, Z., Reeb, A., Gelev, K., Barrett, T. F., Gerndt, S., Liu, P., Parikh, A. S., Ramadan, S., Law, T., Mroz, E. A., Rocco, J. W., Adkins, D., Thorstad, W. L., Gay, H. A., Ding, L., Paniello, R. C. & Pipkorn, P. & 7 others, Jackson, R. S., Wang, X., Mazul, A., Chernock, R., Zevallos, J. P., Silva-Fisher, J. & Tirosh, I., Apr 2023, In: Nature Genetics. 55, 4, p. 640-650 11 p.

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

FIREBALL: A tool to fit protein phase diagrams based on mean-field theories for polymer solutions

Farag, M., Holehouse, A. S., Zeng, X. & Pappu, R. V., Jun 20 2023, In: Biophysical Journal. 122, 12, p. 2396-2403 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

Inflammatory Bowel Disease Is Associated With an Increased Risk of Incident Acute Arterial Events: Analysis of the United Kingdom Biobank

Alayo, Q. A., Loftus, E. V., Yarur, A., Alvarado, D., Ciorba, M. A., de las Fuentes, L. & Deepak, P., Mar 2023, In: Clinical Gastroenterology and Hepatology. 21, 3, p. 761-770.e13

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

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

Russler-Germain, D. A., Krysiak, K., Ramirez, C., Mosior, M., Watkins, M. P., Gomez, F., Skidmore, Z. L., Trani, L., Gao, F., Geyer, S., Cashen, A. F., Mehta-Shah, N., Kahl, B. S., Bartlett, N. L., Alderuccio, J. P., Lossos, I. S., Ondrejka, S. L., Hsi, E. D., Martin, P. & Leonard, J. P. & 3 others, Griffith, M., Griffith, O. L. & Fehniger, T. A., Sep 26 2023, In: Blood Advances. 7, 18, p. 5524-5539 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Nitric oxide-mediated S-nitrosylation of IAA17 protein in intrinsically disordered region represses auxin signaling

Jing, H., Yang, X., Emenecker, R. J., Feng, J., Zhang, J., Figueiredo, M. R. A. D., Chaisupa, P., Wright, R. C., Holehouse, A. S., Strader, L. C. & Zuo, J., Jul 2023, In: Journal of Genetics and Genomics. 50, 7, p. 473-485 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates

Boeynaems, S., Dorone, Y., Zhuang, Y., Shabardina, V., Huang, G., Marian, A., Kim, G., Sanyal, A., Şen, N. E., Griffith, D., Docampo, R., Lasker, K., Ruiz-Trillo, I., Auburger, G., Holehouse, A. S., Kabashi, E., Lin, Y. & Gitler, A. D., Jun 15 2023, In: Molecular cell. 83, 12, p. 2020-2034.e6

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

RBM47 regulates intestinal injury and tumorigenesis by modifying proliferation, oxidative response, and inflammatory pathways

Soleymanjahi, S., Blanc, V., Molitor, E. A., Alvarado, D. M., Xie, Y., Gazit, V., Brown, J. W., Byrnes, K., Liu, T. C., Mills, J. C., Ciorba, M. A., Rubin, D. C. & Davidson, N. O., 2023, In: JCI Insight. 8, 9, e161118.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets

Ginell, G. M., Flynn, A. J. & Holehouse, A. S., Aug 1 2023, In: Bioinformatics. 39, 8, btad488.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins

Lalmansingh, J. M., Keeley, A. T., Ruff, K. M., Pappu, R. V. & Holehouse, A. S., Aug 22 2023, In: Journal of Chemical Theory and Computation. 19, 16, p. 5609-5620 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins

Alston, J. J., Ginell, G. M., Soranno, A. & Holehouse, A. S., Jun 1 2023, In: Journal of Physical Chemistry B. 127, 21, p. 4746-4760 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma

Gomez, F., Fisk, B., McMichael, J. F., Mosior, M., Foltz, J. A., Skidmore, Z. L., Duncavage, E. J., Miller, C. A., Abel, H., Li, Y. S., Russler-Germain, D. A., Krysiak, K., Watkins, M. P., Ramirez, C. A., Schmidt, A., Rodrigues, F. M., Trani, L., Khanna, A., Wagner, J. A. & Fulton, R. S. & 11 others, Fronick, C. C., O'Laughlin, M. D., Schappe, T., Cashen, A. F., Mehta-Shah, N., Kahl, B. S., Walker, J., Bartlett, N. L., Griffith, M., Fehniger, T. A. & Griffith, O. L., Nov 2023, In: Cancer research communications. 3, 11, p. 2312-2330 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

2022

Compound loss of GSDMD and GSDME function is necessary to achieve maximal therapeutic effect in colitis

Xiao, J., Sun, K., Wang, C., Abu-Amer, Y. & Mbalaviele, G., Jan 2022, In: Journal of Translational Autoimmunity. 5, 100162.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Conformational buffering underlies functional selection in intrinsically disordered protein regions

González-Foutel, N. S., Glavina, J., Borcherds, W. M., Safranchik, M., Barrera-Vilarmau, S., Sagar, A., Estaña, A., Barozet, A., Garrone, N. A., Fernandez-Ballester, G., Blanes-Mira, C., Sánchez, I. E., de Prat-Gay, G., Cortés, J., Bernadó, P., Pappu, R. V., Holehouse, A. S., Daughdrill, G. W. & Chemes, L. B., Aug 2022, In: Nature Structural and Molecular Biology. 29, 8, p. 781-790 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

44 Scopus citations

Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains

Staller, M., Ramirez, E., Kotha, S. R., Holehouse, A. S., Pappu, R. V. & Cohen, B. A., Apr 20 2022, In: Cell Systems. 13, 4, p. 334-345.e5

Research output: Contribution to journal › Article › peer-review

Open Access

46 Scopus citations

Fracture healing is delayed in the absence of gasdermin-interleukin-1 signaling

Sun, K., Wang, C., Xiao, J., Brodt, M. D., Yuan, L., Yang, T., Alippe, Y., Hu, H., Hao, D., Abu-Amer, Y., Silva, M. J., Shen, J. & Mbalaviele, G., Mar 2022, In: eLife. 11, e75753.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

Glutamine metabolism modulates chondrocyte inflammatory response

Arra, M., Swarnkar, G., Adapala, N. S., Naqvi, S. K., Cai, L., Rai, M. F., Singamaneni, S., Mbalaviele, G., Brophy, R. & Abu-Amer, Y., 2022, In: eLife. 11, e80725.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Scopus citations

IL-1β expression in bone marrow dendritic cells is induced by TLR2 agonists and regulates HSC function

Li, S., Yao, J. C., Oetjen, K. A., Krambs, J. R., Xia, J., Zhang, J., Schmidt, A. P., Helton, N. M., Fulton, R. S., Heath, S. E., Turnbull, I. R., Mbalaviele, G., Ley, T. J., Walter, M. J. & Link, D. C., Oct 6 2022, In: Blood. 140, 14, p. 1607-1620 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

IκB-ζ signaling promotes chondrocyte inflammatory phenotype, senescence, and erosive joint pathology

Arra, M., Swarnkar, G., Alippe, Y., Mbalaviele, G. & Abu-Amer, Y., Dec 2022, In: Bone Research. 10, 1, 12.

Research output: Contribution to journal › Article › peer-review

Open Access

28 Scopus citations

LINC00355 regulates p27^KIP expression by binding to MENIN to induce proliferation in late-stage relapse breast cancer

Eteleeb, A. M., Thunuguntla, P. K., Gelev, K. Z., Tang, C. Y., Rozycki, E. B., Miller, A., Lei, J. T., Jayasinghe, R. G., Dang, H. X., White, N. M., Reis-Filho, J. S., Mardis, E. R., Ellis, M. J., Ding, L., Silva-Fisher, J. M. & Maher, C. A., Dec 2022, In: npj Breast Cancer. 8, 1, 49.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

Mesalamine Reduces Intestinal ACE2 Expression Without Modifying SARS-CoV-2 Infection or Disease Severity in Mice

Alvarado, D. M., Son, J., Thackray, L. B., Gomez Castro, M. F., Prasad, S., Cui, X., Sonnek, N. M., Diamond, M., Ding, S. & Ciorba, M. A., Feb 1 2022, In: Inflammatory bowel diseases. 28, 2, p. 318-321 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

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

Ward, J. P., Berrien-Elliott, M. M., Gomez, F., Luo, J., Becker-Hapak, M., Cashen, A. F., Wagner-Johnston, N. D., Maddocks, K., Mosior, M., Foster, M., Krysiak, K., Schmidt, A., Skidmore, Z. L., Desai, S., Watkins, M. P., Fischer, A., Griffith, M., Griffith, O. L., Fehniger, T. A. & Bartlett, N. L., Mar 31 2022, In: Blood. 139, 13, p. 1999-2010 12 p.

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Shelterin Components Modulate Nucleic Acids Condensation and Phase Separation in the Context of Telomeric DNA

Soranno, A., Incicco, J. J., De Bona, P., Tomko, E. J., Galburt, E. A., Holehouse, A. S. & Galletto, R., Aug 30 2022, In: Journal of Molecular Biology. 434, 16, 167685.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence

Gutierrez, J. I., Brittingham, G. P., Karadeniz, Y., Tran, K. D., Dutta, A., Holehouse, A. S., Peterson, C. L. & Holt, L. J., Feb 2022, In: eLife. 11, e70344.

Research output: Contribution to journal › Article › peer-review

Open Access

17 Scopus citations

The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems

Lasker, K., Boeynaems, S., Lam, V., Scholl, D., Stainton, E., Briner, A., Jacquemyn, M., Daelemans, D., Deniz, A., Villa, E., Holehouse, A. S., Gitler, A. D. & Shapiro, L., Dec 2022, In: Nature communications. 13, 1, 5643.

Research output: Contribution to journal › Article › peer-review

Open Access

36 Scopus citations

2021

Actions of the NLRP3 and NLRC4 inflammasomes overlap in bone resorption

Alippe, Y., Kress, D., Ricci, B., Sun, K., Yang, T., Wang, C., Xiao, J., Abu-Amer, Y. & Mbalaviele, G., Sep 2021, In: FASEB Journal. 35, 9, e21837.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development

Sankaranarayanan, M., Emenecker, R. J., Wilby, E. L., Jahnel, M., Trussina, I. R. E. A., Wayland, M., Alberti, S., Holehouse, A. S. & Weil, T. T., Oct 25 2021, In: Developmental cell. 56, 20, p. 2886-2901 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus citations

A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation

Dorone, Y., Boeynaems, S., Flores, E., Jin, B., Hateley, S., Bossi, F., Lazarus, E., Pennington, J. G., Michiels, E., De Decker, M., Vints, K., Baatsen, P., Bassel, G. W., Otegui, M. S., Holehouse, A. S., Exposito-Alonso, M., Sukenik, S., Gitler, A. D. & Rhee, S. Y., Aug 5 2021, In: Cell. 184, 16, p. 4284-4298.e27

Research output: Contribution to journal › Article › peer-review

Open Access

103 Scopus citations

Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates

Holehouse, A. S., Ginell, G. M., Griffith, D. & Böke, E., Nov 30 2021, In: Biochemistry. 60, 47, p. 3566-3581 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

45 Scopus citations

Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families

Sethe Burgie, E., Gannam, Z. T. K., McLoughlin, K. E., Sherman, C. D., Holehouse, A. S., Stankey, R. J. & Vierstra, R. D., Jun 1 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 22, e2105649118.

Research output: Contribution to journal › Article › peer-review

Open Access

28 Scopus citations

Effects of the TNFRSF11B Mutation Associated With Calcium Pyrophosphate Deposition Disease in Osteoclastogenesis in a Murine Model

Mitton-Fitzgerald, E., Gohr, C. M., Williams, C. J., Ortiz, A., Mbalaviele, G. & Rosenthal, A. K., Aug 2021, In: Arthritis and Rheumatology. 73, 8, p. 1543-1549 7 p.

Research output: Contribution to journal › Article › peer-review