PUBLICATIONS

Publications are linked via the title - please contact Alex directly if paywalls get in your way! See also Google Scholar.

bold = Holehouse lab members / † - corresponding/co-corresponding / *- first/co-first

PREPRINTS (7)

Sequence-ensemble-function relationships for disordered proteins in live cells
Emenecker, R. J.*, Guadalupe, K.*, Shamoon, N. M., Sukenik, S.† & Holehouse, A. S.†
bioRxiv 2023.10.29.564547 (2023). doi:10.1101/2023.10.29.564547
In revisions

Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation.
Alston, J., Soranno, A. & Holehouse, A. S.
bioRxiv 2023.08.06.552128 (2023). doi:10.1101/2023.08.06.552128
In revisions

Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease.
Boeynaems, S.†, Rosa Ma, X.*, Yeong, V.*, Ginell, G. M.*, Chen, J.-H., Blum, J. A., Nakayama, L., Sanyal, A., Briner, A., Van Haver, D., Pauwels, J., Ekman, A., Broder Schmidt, H., Sundararajan, K., Porta, L., Lasker, K., Larabell, C., Hayashi, M. A. F., Kundaje, A., Impens, F., Obermeyer, A., Holehouse, A. S. & Gitler, A. D†.
bioRxiv 2023.03.09.531820 (2023). doi:10.1101/2023.03.09.531820
In revisions

  • Supporting data: Link

Composition can buffer protein dynamics within liquid-like condensates.
Jelenic, S., Bindics, J., Czermak, P., Pillai, B. R., Ruer, M., Holehouse, A. S., & Saha, S. (2022).
bioRxiv (p. 2022.05.16.492059). https://doi.org/10.1101/2022.05.16.492059
In revisions

The kinetic landscape of human transcription factors.
Mamrak, N. E., Alerasool, N., Griffith, D., Holehouse, A. S., Taipale, M. & Lionnet, T.
bioRxiv 2022.06.01.494187 (2022). doi:10.1101/2022.06.01.494187
In revisions

Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions.
Langstein-Skora, I., Schmid, A., Emenecker, R. J., Richardson, M. O. G., Götz, M. J., Payer, S. K., Korber, P.†, & Holehouse, A. S.†
bioRxiv (p. 2022.02.10.480018).
In revisions

Emenecker, R. J., Griffith, D., & Holehouse, A. S. (2022).
Metapredict V2: An update to metapredict, a fast, accurate, and easy-to-use predictor of consensus disorder and structure.
bioRxiv (p. 2022.06.06.494887). https://doi.org/10.1101/2022.06.06.494887
Permanent preprint

2024 (8)

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.
Nat. Commun. 15, 3523 (2024).

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.†
Nat. Microbiol. 9, 1021–1035 (2024).
News Coverage

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., Woutersen, S., Sukenik, S., Woolfson, D. N., Holehouse, A. S. & Boothby, T. C.
Protein Sci. 33, e4941 (2024).

Direct prediction of intrinsically disordered protein conformational properties from sequence.
Lotthammer, J. M.*, Ginell, G. M.*, Griffith, D.*, Emenecker, R. J. & Holehouse, A. S.
Nat. Methods 21, 465–476 (2024).

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.
Nat. Struct. Mol. Biol. 1–10 (2024).

Helicity of a tardigrade disordered protein promotes desiccation tolerance
Biswas, S., Gollub, E., Yu, F., Ginell, G., Holehouse, A.S, Sukenik, S. & Boothby, T. C.
Protein Sci. 33, e4872 (2024).

Dissecting the biophysics and biology of intrinsically disordered proteins
Banerjee, P. R., Holehouse, A. S., Kriwacki, R., Robustelli, P., Jiang, H., Sobolevsky, A. I., Hurley, J. M. & Mendell, J. T. Trends Biochem. Sci. 49, 101–104 (2024).

The disordered N-terminal tail of SARS CoV-2 Nucleocapsid protein forms a dynamic complex with RNA.
Cubuk, J., Alston, J. J., Jeremías Incicco, J., Holehouse, A. S., Hall, K. B., Stuchell-Brereton, M. D. & Soranno, A.
Nucleic Acids Research 52, 2609–2624 (2024).

2023 (13)

Stress granules offer first aid for leaky organelles
Plassmeyer, S. P. & Holehouse, A. S.
Nature (2023). doi:10.1038/d41586-023-03417-4
Invited News & Views

The molecular basis for cellular function of intrinsically disordered protein regions
Holehouse, A.S.† & Kragelund, B.K.†
Nature Reviews Molecular Cell Biology 1-25 (2023)
Access link

Using graphs and charts in scientific figures (invited opinion)
Buda, K., Cermakova, K., Hodges, H. C., Fornasiero, E. F., Sukenik, S. & Holehouse, A. S.
Trends Biochem. Sci. 48, 913–916 (2023).
Invited perspective

Intrinsically disordered regions are poised to act as sensors of cellular chemistry
Moses, D.*, Ginell, G.M.*, Holehouse, A.S.†, and Sukenik, S†.
Trends in Biochemical Sciences 48, 1019–1034 (2023).
Editors Choice for Trends in Biochemical Sciences (2023)

Virus induced membraneless organelles and biomolecular condensates.
Mouland, A. J., Parent, L., Weber, S. C. & Holehouse, A. S.
J. Mol. Biol. 435, 168213 (2023).
Editorial overview

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.
Biophys. J. 122, 2396–2403 (2023).

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. de, Chaisupa, P., Wright, R. C., Holehouse, A. S., Strader, L. C. & Zuo, J.
J. Genet. Genomics 50, 473–485 (2023).

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.
Mol. Cell 83, 2020–2034.e6 (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., Fairbrother, W. G.* & Mosammaparast, N*.
Mol. Cell 83, 2258–2275.e11 (2023).

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.
J. Phys. Chem. B 127, 4746–4760 (2023).

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.
J. Chem. Theory Comput. 19, 5609–5620 (2023). doi:10.1021/acs.jctc.3c00190

SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets.
Ginell, G. M., Flynn, A. J. & Holehouse, A. S.
Bioinformatics (2023). doi:10.1093/bioinformatics/btad488

An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates.
Ginell, G. M. & Holehouse, A. S.
Methods Mol. Biol. 2563, 95–116 (2023).

2022 (8)

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.†
Nat. Struct. Mol. Biol. 29, 781–790 (2022).

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.†
Nat. Commun. 13, 5643 (2022).

Intrinsically disordered CO2 sensors
Emenecker, R. J., & Holehouse, A. S. (2022).
Nature Cell Biology, 24(7), 1013–1014.
Invited News & Views

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. (2022).
Journal of Molecular Biology, 434(16), 167685.

Liquid Phase Partitioning in Virus Replication: Observations and Opportunities
Wu, C., Holehouse, A. S., Leung, D. W., Amarasinghe, G. K., & Dutch, R. E. (2022).
Annual Review of Virology 9, 285–306 (2022).

Hyperphosphorylation tunes TDP-43 solubility
Ginell, G. M., & Holehouse, A. S. (2022).
The EMBO Journal, 41(8), e111062.
Invited News & Views

SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence.
Gutierrez, J. I., Brittingham, G. P., Karadeniz, Y. B., Tran, K. D., Dutta, A., Holehouse, A. S., Peterson, C. L., & Holt, L. J. (2022).
eLife, 11. https://doi.org/10.7554/eLife.70344

Staller, M. V.†, Ramirez, E., Kotha, S. R., Holehouse, A. S., Pappu, R. V., & Cohen, B. A.†
Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains.
Cell Systems (2022). https://doi.org/10.1016/j.cels.2022.01.002

2021 (15)

Holehouse, A. S.†, Ginell, G. M., Griffith, D., & Böke, E†.
Clustering of aromatic residues in prion-like domains can tune the formation, state, and organization of biomolecular condensates.
Biochemistry, 60(47), 3566–3581. (2021)

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.† (2021).
Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development. Developmental Cell, 56(20), 2886–2901.e6. (2021)

Griffith, D., & Holehouse, A. S.
PARROT is a flexible recurrent neural network framework for analysis of large protein datasets.
eLife, 10. (2021)

Resources:

Taneja, I., & Holehouse, A. S.
Folded domain charge properties influence the conformational behavior of disordered tails.
Current Research in Structural Biology, 3, 216–228. (2021)

Resources:

Emenecker, R. J., Griffith, D., & Holehouse, A. S.
Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure
Biophysical Journal 120(20), 4312–4319. (2021)
https://doi.org/10.1016/j.bpj.2021.08.039
Resources:

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†.
A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation.
Cell, 184(16), 4284–4298.e27.
Commentaries: Developmental Cell, Nature Chemical Biology, Science, PNAS

Minhas, S., & Holehouse, A. S.
Step on the cGAS! Viral inhibition of cGAS phase separation with cytosolic DNA.
Molecular Cell, (2021) 81(13), 2688–2689.

Burgie, E.S., Gannam, Z.T.K., McLoughlin, K.E., Holehouse, A.S., Sherman, C.S., Stankey, R.C., Vierstra, R.D.
Differing Biophysical Properties Underpin the Unique Signaling Potentials Within the Plant Phytochrome Photoreceptor Families
Proc. Natl. Acad. Sci. U. S. A. (2021) 118 (22)

Emenecker J.R., Holehouse, A.S.†, Strader, L.C.†
Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis
Cell Communication and Signaling (2021), 19(1), 65.

Sanders, D.W., Jumper, C.C., Ackerman, P.J., Bracha, D., Donlic, A., Kim, H., Kenney, D., Castello-Serrano, I., Suzuki, S., Tamura, T., Tavares, A.H., Saeed, M., Holehouse, A.S., Ploss, A., Levental, I., Douam, F., Padera, R.F., Levy, B.D., and Brangwynne, C.P.
SARS-CoV-2 Requires Cholesterol for Viral Entry and Pathological Syncytia Formation
eLife (2021) 10, https://doi.org/10.7554/eLife.65962

Alston, J. J., Soranno, A.† & Holehouse, A. S.†
Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins
Methods (2021) (online only doi:10.1016/j.ymeth.2021.03.018)
Free-to-distribute unformatted preprint provided under CC BY-NC-ND 4.0

Cubuk, J., Alston, J. J., Jeremías Incicco, J., Singh, S., Stuchell-Brereton, M. D., Ward, M. D., Zimmerman, M. I., Vithani, N., Griffith, D., Wagoner, J. A., Bowman, G. R., Hall, K. B., Soranno, A.† & Holehouse, A. S.†
The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA.
Nature Communications (2021) 12, 1–17.

Holehouse, A. S.
Mapping from sequence to droplets. (Invited Perspective - “Journal Club”)
Nat. Rev. Mol. Cell Biol. (2021). doi:10.1038/s41580-021-00333-1

Davis, Z. H., Mediani, L., Antoniani, F., Vinet, J., Li, S., Alberti, S., Lu, B., Holehouse, A. S., Carra, S. & Brandman, O. Protein products of nonstop mRNA disrupt nucleolar homeostasis.
Cell Stress Chaperones (2021). doi:10.1007/s12192-021-01200-w

Emenecker J.R., Holehouse, A.S.†, Strader, L.C.†
Biological phase separation and biomolecular condensates in plants
Annual Reviews in Plant Biology 72, 17–46. (2021)

2020 (8)

Martin, E.W., Holehouse, A.S.
Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof
Emerging Topics in Life Sciences 4, 307–329. (2020)

Emenecker, R.J., Holehouse, A.S.†, and Strader, L.C.†
Emerging Roles for Phase Separation in Plants.
Developmental Cell 55, 69–83. (2020)

Moses, D.*, Yu, F.*, Ginell, G.M., Shamoon, N.M., Koenig, P.S., Holehouse, A.S.†, and Sukenik, S†.
Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment
Journal of Physical Chemistry Letters 11, 10131-10136 (2020)

Stenzoski, N. E., Zou, J., Piserchio, A., Ghose, R., Holehouse, A. S.† & Raleigh†, D. P.
The Cold-Unfolded State is Expanded but Contains Long- and Medium-range Contacts and Is Poorly Described by Homopolymer Models
Biochemistry 59, 3290–3299 (2020)

Ginell, GM. & Holehouse, AS.
Analyzing the Sequences of Intrinsically Disordered Regions with CIDER and localCIDER
Intrinsically Disordered Proteins: Methods and Protocols (Methods in Molecular Biology), Springer Nature Invited book chapter (B. Kragelund & K. Skriver, ed.), 103–126 (Springer US, 2020).

Fernandes, J. D.*, Sarabipour, S.*, Smith, C. T., Niemi, N. M., Jadavji, N. M., Kozik, A. J., Holehouse, A. S., Pejaver, V., Symmons, O., Bisson Filho, A. W. & Haage, A.
A survey-based analysis of the academic job market.
Elife 9, (2020).

Rawlings, A. E., Liravi, P., Corbett, S., Holehouse, A. S. & Staniland, S. S.
Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6
PLoS One 15, e0228708 (2020).

Holehouse, A. S.† & Sukenik, S.†
Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning.
J. Chem. Theory Comput. (2020). doi:10.1021/acs.jctc.9b00604 (†-co-corresponding authors)

2019 (2)


Holehouse, AS.
IDPs and IDRs in biomolecular condensates
Intrinsically Disordered Proteins: Dynamics, Binding, and Function, Elsevier (Academic Press) (2019)
Invited book chapter (N. Salvi, ed.), pp. 209–255. (2019)

Harding, RJ.†, Loppnau, P., Ackloo, S., Lemak, S., Hutchinson, A., Hunt, B., Holehouse, AS., Ho, J., Fan, L., Toledo-Sherman, L., Seitova, A., Arrowsmith, C.†
Design and characterization of mutant and wild-type huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems
Journal of Chemical Biology, RA118. 007204 (2019) (†-co-corresponding authors) (2019)

2018 (2)

Stenzoski, N., Luan, B., Holehouse, AS., D. Raleigh
The unfolded state of the C-terminal domain of L9 expands at low temperature but not at elevated temperatures
Biophysical Journal, 115: 655-663 (2018)

Ortega, E., Rengachari, S., Ibrahim, Z., Hoghoughi, N., Gaucher, J., Holehouse, AS., Khochbin, S., Panne, D.
Transcription factor dimerization activates the p300 acetyltransferase
Nature, 562: 538-544 (2018)

Select Previous work (Alex’ postdoc & graduate work)

2020

Zeng, X., Holehouse, A. S., Mittag, T., Chilkoti, A. & Pappu, R. V.
Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins.
Biophys. J. 119, 402–418 (2020).

Guillén-Boixet, J.*, Kopach, A.*, Holehouse, A. S., Wittmann, S., Jahnel, M., Schlüßler, R., Kim, K., Trussina, I. R. E. A., Wang, J., Mateju, D., Poser, I., Maharana, S., Ruer-Gruß, M., Richter, D., Zhang, X., Chang, Y.-T., Guck, J., Honigmann, A., Mahamid, J., Hyman, A. A., Pappu, R. V., Alberti, S. & Franzmann, T. M.
RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation.
Cell 181, 346–361.e17 (2020).

Choi, J.-M., Holehouse, A. S. & Pappu, R. V.
Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions.
Annual Reviews in Biophysics 49, 107–133 (2020).

Martin, E. W.*, Holehouse, A. S.*, Peran, I.,* Farag, M., Incicco, J. J., Bremer, A., Grace, C. R., Soranno, A., Pappu, R. V.† & Mittag, T.†
Valence and patterning of aromatic residues determine the phase behavior of prion-like domains.
Science 367, 694–699 (2020) (*-co-first authors, †-co-corresponding authors)

Greig, J. A., Nguyen, T. A., Lee, M., Holehouse, A. S., Posey, A. E., Pappu, R. V. & Jedd, G.
Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation
Molecular Cell, doi:10.1016/j.molcel.2020.01.025 (2020).


2019

Powers, SK., Holehouse, AS., Korasick, DA., Schreiber, KH., Clark, NM., Jing, H., Emenecker, R., Han, S., Tycksen, E., Hwang, I., Sozzani, R., Jez, JM., Pappu, RV. & Strader, LC.
Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana.
Molecular Cell, 76, 177–190.e5 (2019)

Peran, I.*, Holehouse, AS.*, Carrico, IS., Pappu, RV., Bilsel, O., and Raleigh, DP.
Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions.
Proc. Natl. Acad. Sci. U. S. A. 116, 12301–12310. (2019) (*-co-first authors)

Boeynaems, S.†, Holehouse, AS., Weinhardt, V., Kovacs, D., Van Lindt, J., Larabell, C., Van Den Bosch, L., Das, R., Tompa, PS., Pappu, RV.†, and Gitler, AD.†
Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties
Proc. Natl. Acad. Sci. U. S. A. 116, 7889–7898. (2019)

Ruff, KM.†, Pappu, RV.†, Holehouse, AS.†
Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: Insights from multiscale simulations
Current Opinions in Structural Biology, 56: 1-10 (2019) (†-co-corresponding authors)

2018

Posey, AE.*, Holehouse, AS.*, Pappu, RV.
Phase separation of intrinsically disordered proteins
Methods in Enzymology, 611: 1-30 (2018) (*-co-first authors)

Wang, J., Choi, JM., Holehouse, AS., HO. Lee, X. Zhang, M. Jahnel, S. Maharana, R. Lemaitre, A. Pozniakovsky, D. Drechsel, I. Poser, R.V. Pappu, Alberti, S.†, Hyman, A.A.†.
A molecular grammar underlying the driving forces for phase separation of prion-like RNA binding proteins
Cell, 174: 688-699 (2018) (†-co-corresponding authors)

Mittal, A., Holehouse, AS., Pappu, RV.
Sequence-to-conformation relationships of disordered regions tethered to folded domains of proteins
Journal of Molecular Biology, 430: 2403-2421 (2018)

Harmon, TS., Holehouse, AS., Pappu, RV.
Sequence-specific preferential solvation of intrinsically disordered linkers in multivalent proteins enables the formation of spatially organized droplets
New Journal of Physics, 20: 045002 (2018)

Holehouse, AS.†, Pappu, RV†.
Functional implications of intracellular phase transitions
Biochemistry, 57:(17), 2415-2423 (2018) (†-co-corresponding authors)

Staller, MV., Holehouse, AS., Swain-Lenz, D., Das, RK., Pappu, RV., Cohen, BC.
A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain
Cell Systems, 6: 444-455 (2018)

Franzmann, TM., Jahnel, M., Mahamid, J., Holehouse, AS., Poznakowski, P., Richter, D., Nuske, E., Baumeister, W., Grill, S., RK. Pappu, RV., Hyman, AT., Alberti, S.
Protein phase separation by a yeast prion protein promotes cellular fitness
Science, 359: 6371 (2018)

Holehouse, AS.†, Pappu, RV†.
Collapse transitions of proteins and the interplay amongst backbone, sidechain, and solvent interactions
Annual Reviews in Biophysics, 47:19-39 (2018) (†-co-corresponding authors)

2017

Fei, J., Jadaliha, M., Harmon, TS., Li, ITS., Hua, B., Freier, SM., Holehouse, AS., Pappu, RV. Prasanth, KV., Ha, T.
Protein and RNA molecules drive multi-layer organization of nuclear speckles
Journal of Cell Science, 130: 4180-4192 (2017)

Harmon, TS., Holehouse, AS., Rosen, MK., Pappu, RV.
Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins
eLife, 6: 30294 (2017)

Holehouse, AS., Pappu, RV.
FUS zigzags its way to cross beta
Cell, 171: 499-500 (2017)

Ruff, KM.†, Holehouse, AS.
SAXS vs. FRET: A matter of heterogeneity?
Biophysical Journal, 113: 971-973 ( †corresponding author) (2017)

Wei, SMT*., Elbaum-Garfinkle, S.*, Holehouse, AS.*, Chen, C., Feric, M., Arnold CB., Priestley RD., Pappu RV†., Brangwynne CP†.
Phase separation of intrinsically disordered proteins yield low-density semi-dilute liquids
Nature Chemistry, 9:, 971-973 (*-co-first authors, †-co-corresponding authors) (2017)

Harmon, TS., Holehouse, AS., Pappu RV.
To mix, or to demix, that is the question
Biophysical Journal, 112: 565-567 (2017)

Holehouse, AS.†, Das, RK., Ahad, J., Richardson, MOG., Pappu RV†
CIDER: Resources to analyze sequence-ensemble relationships of intrinsically disordered proteins
Biophysical Journal, 112: 16-21 (†-co-corresponding authors) (2017)

2016 or earlier

Pak, CW., Kosno, M., Holehouse, AS., Padrick, SB., Mittal, A., Ali, M., Yunus, A., Pappu†, RV., Rosen, MK†.
Sequence determinants of intracellular phase separation by complex coacervation of a disordered protein
Molecular Cell, 63: 72-85 (2016) (†-co-corresponding authors)

Martin, EW.*, Holehouse, AS.*, Grace, CR., Hughes, A., Pappu RV†., Mittag, T†.
Sequence determinants of the conformational properties of an intrinsically disordered protein prior to and upon multisite phosphorylation
Journal of the American Chemical Society, 138: 15323-15335 (*-co-first authors, †-co-corresponding authors) (2016)

Holehouse, AS., Pappu, RV.
Protein polymers: encoding phase transitions
Nature Materials, 14: 1083-1084 (2015)

Holehouse, AS., Naegle, KM.
Reproducible analysis of proteomes: The relationship between disease-related mutations and post-translational modifications
PLoS One, 10: e0144692 (2015)

Holehouse, AS., Lyle, N., Garai, K. Vitalis, A., and Pappu, RV.
Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation
Journal of the American Chemical Society, 137: 2984-2995 (2015)

Matlock, M, Holehouse, AS., Naegle, K.
ProteomeScout: an integrated repository and analysis resource for post-translational modifications and proteins
Nucleic Acids Research, Vol. 43 D521-D530, (2015)

Holehouse, A., Yang, X., Adcock, I., Guo, Y.
Developing a novel integrated model of p38 MAPK and glucocorticoid signalling pathways
IEEE Computational Intelligence in Bioinformatics and Computational Biology 2012, p69-