Publications are linked via the title - please contact Alex directly if paywalls get in your way!



Holehouse, AS† & Sukenik, S†
Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning
biorxiv pre-print (2019) (†-co-corresponding authors)

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.), In Press

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.

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)


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


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, In Press (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)


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.
Uncovering the interplay between sequence- and context-dependent determinants of con- formations of disordered tails and linkers 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)


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-