Preprints, Publications & Abstracts

"If you write a problem down clearly, you have solved half of it."

- James Clavell (Kidlin's Law)

Bold indicates authors from the Iqbal Lab. * indicates the corresponding author. For Abstracts/Poster, the primary presenter is underlined.

Preprints

Rissom PF, Sarmiento PY, Safer JF, Coley CW, Renard BY, Heyne HO*, Iqbal S*. Decoding protein language models: insights from embedding space analysis. bioRxiv. Feb 2025; doi: https://doi.org/10.1101/2024.06.21.600139.
Rissom PF, Sarmiento PY, Safer JF, Coley CW, Renard BY, Heyne HO*, Iqbal S*. ema-tool: a Python Library for the Comparative Analysis of Embeddings from Biomedical Foundation Models. bioRxiv. Jun 2024; doi: https://doi.org/10.1101/2024.06.21.600139.
Arbesfeld JA, Da EY, Stevenson JS, Kuzma K, Paul A, Farris T, Capodanno BJ, Grindstaff SB, Riehle K, Saraiva-Agostinho N, Safer JF, Milosavljevic A, Foreman J, Firth HV, Hunt SE, Iqbal S, Cline MS, Rubin AF, Wagner AH. Mapping MAVE data for use in human genomics applications. bioRxiv. Jun 2024. doi: 10.1101/2023.06.20.545702. PMID: 38979347; PMCID: PMC11230167.
Arnaudi M, Beltrame L, Degn K, Utichi M, Scrima S, Besora PS, Krzesińska K, Estad AH, Maselli F, Dorčaková T, Safer JF, Meldgård K, Becker P, Sora V, Pettenella A, Brockhoff JB, Nielsen AD, Vinhas J, Sackett PW, Cava A, Rohlin A, Nilbert M, Iqbal S, Lambrughi M, Tiberti M, Papaleo E. MAVISp: A Modular Structure-Based Framework for Genomic Variant Interpretation. bioRxiv. Nov 2023; doi: https://doi.org/10.1101/2022.10.22.513328.

Publications

Iqbal S*, Jiang W, Hansen E, Aristotelous T, Liu S, Reidenbach A, et al. DEL+ML paradigm for actionable hit discovery – a cross DEL and cross ML model assessment. npj Drug Discovery. Mar 2025; doi: 10.1038/s44386-025-00007-4.

Kwon S, Safer J, Nguyen DT, Hoksza D, May P, Arbesfeld JA, Rubin AF, Campbell AJ, Burgin A, Iqbal S*. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures. Nature Methods. Aug, 2024. doi: https://doi.org/10.1038/s41592-024-02409-0. PMID: 39294369; PMCID: PMC10802383.
Pecci F, Nakazawa S, Ricciuti B, Harada G, Lee JK, Alessi JV, Barrichello A, Vaz VR, Lamberti G, Di Federico A, Gandhi MM, Gazgalis D, Feng WW, Jiang J, Baldacci S, Locquet MA, Gottlieb FH, Chen MF, Lee E, Haradon D, Smokovich A, Voligny E, Nguyen T, Goel VK, Zimmerman Z, Atwal S, Wang X, Bahcall M, Heist RS, Iqbal S, Gandhi N, Elliott A, Vanderwalde AM, Ma PC, Halmos B, Liu SV, Che J, Schrock AB, Drilon A, Jänne PA, Awad MM. Activating Point Mutations in the MET Kinase Domain Represent a Unique Molecular Subset of Lung Cancer and Other Malignancies Targetable with MET Inhibitors. Cancer Discov. 2024 Aug 2;14(8):1440-1456. doi: 10.1158/2159-8290.CD-23-1217. PMID: 38564707; PMCID: PMC11294820.
Shepard N, Baez-Nieto D, Iqbal S, Kurganov E, Budnik N, Campbell AJ, Pan JQ, Sheng M, Farsi Z. Differential functional consequences of GRIN2A mutations associated with schizophrenia and neurodevelopmental disorders. Sci Rep. 2024 Feb 2;14(1):2798. doi: 10.1038/s41598-024-53102-3. PMID: 38307912; PMCID: PMC10837427.
Dilliott AA, Kwon S, Rouleau GA, Iqbal S*, Farhan SMK*. Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes. Brain. 2023 Nov 2;146(11):4608-4621. doi: 10.1093/brain/awad224. PMID: 37394881; PMCID: PMC10629772.

Abstracts/poster

Safer J, Francesca PR, Sarmiento PY, Brunklaus A, Balaz D, Castelli R, Coley CW, Depienne C, George AL, Kurganov E, Marini C, Møller RS, Moroni A, Pan JQ, Santoro B, Renard BY, Heyne HO*, Iqbal S*. Predicting Loss- and Gain-of-Function Variants on Voltage-Gated Ion Channels. Abstract/Poster, American Society of Human Genetics (ASHG) Annual Meeting, 2024.
Francesca PR, Safer J, Sarmiento PY, Brunklaus A, Balaz D, Castelli R, Coley CW, Depienne C, George AL, Kurganov E, Marini C, Møller RS, Moroni A, Pan JQ, Santoro B, Renard BY, Iqbal S*, Heyne HO*. Leveraging protein language models to predict loss- and gain-of-function effects in ion channel variants. Abstract/Poster, International Society of Molecular Biology Annual Meeting, ISMB 2024.
Francesca PR, Safer J, Sarmiento PY, Brunklaus A, Coley CW, Depienne C, George AL, Kurganov E, Lemke J, Møller RS, Pan JQ, Santoro B, Syrbe S, Renard BY, Iqbal S*, Heyne HO*. Towards leveraging machine learning to predict the functional effects of genetic variants in ion channels. Abstract/Poster, Mutational Scanning Symposium, MSS 2024.
Kwon S, Safer J, Lin J, Pablo JL, Greka A, Iqbal S*. Unraveling the conformational dynamics of UMOD protein variants in autosomal dominant tubulointerstitial kidney disease: Insights from molecular dynamics simulations. Biophysical Society Annual Meeting, Abstract (Selected for platform talk), Biophysical Society Annual Meeting, BPS 2024, Volume 123, Issue 3, 15a, Biophysical Journal.
Safer J, Kwon S, Arnaudi M, Tiberti M, Papaleo E, Iqbal S*. Characterizing 127 understudied kinases through in silico saturation mutagenesis of predicted protein structures. Abstract/Poster, Biophysical Society Annual Meeting, BPS 2024, Volume 123, Issue 3, 282a, Biophysical Journal.
Safer J, Nguyen D, Kwon S, Burgin A, Iqbal S*. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures. Abstract/Poster, American Society of Human Genetics Annual Meeting, ASHG 2023.
S. Kwon, J. Safer, S. Iqbal*. Comprehensive statistical analysis on the impact of missense mutations toward improving variant interpretation. Abstract/Poster, American Society of Human Genetics Annual Meeting, ASHG 2023.
Hansen E, Jiang W, Sigel E, Soutter H, Iqbal S*. DEL+ML–An ultra-high-throughput technology for novel scaffold discovery using the power of small molecule binding data and ML. Poster (Best Poster Award), American Chemical Society, ACS Fall 2023 .

Publications prior to 2023 / iqbal lab

Iqbal S*, Brünger T, Pérez-Palma E, Macnee M, Brunklaus A, Daly MJ, Campbell AJ, Hoksza D, May P, Lal D. Delineation of functionally essential protein regions for 242 neurodevelopmental genes. Brain. 2023 Feb 13;146(2):519-533. doi: 10.1093/brain/awac381. PMID: 36256779; PMCID: PMC9924913.
Miller PG, Sathappa M, Moroco JA, Jiang W, Qian Y, Iqbal S, Guo Q, Giacomelli AO, Shaw S, Vernier C, Bajrami B, Yang X, Raffier C, Sperling AS, Gibson CJ, Kahn J, Jin C, Ranaghan M, Caliman A, Brousseau M, Fischer ES, Lintner R, Piccioni F, Campbell AJ, Root DE, Garvie CW, Ebert BL. Allosteric inhibition of PPM1D serine/threonine phosphatase via an altered conformational state. Nat Commun. 2022 Jun 30;13(1):3778. doi: 10.1038/s41467-022-30463-9. PMID: 35773251; PMCID: PMC9246869.
Woodard J, Iqbal S, Mashaghi A. Circuit topology predicts pathogenicity of missense mutations. Proteins. 2022 Sep;90(9):1634-1644. doi: 10.1002/prot.26342. Epub 2022 Apr 23. PMID: 35394672; PMCID: PMC9543832.
Ahmed SS, Rifat ZT, Lohia R, Campbell AJ, Dunker AK, Rahman MS, Iqbal S*. Characterization of intrinsically disordered regions in proteins informed by human genetic diversity. PLoS Comput Biol. 2022 Mar 11;18(3):e1009911. doi: 10.1371/journal.pcbi.1009911. PMID: 35275927; PMCID: PMC8942211.
Johannesen KM, Iqbal S, Guazzi M, Mohammadi NA, Pérez-Palma E, Schaefer E, De Saint Martin A, Abiwarde MT, McTague A, Pons R, Piton A, Kurian MA, Ambegaonkar G, Firth H, Sanchis-Juan A, Deprez M, Jansen K, De Waele L, Briltra EH, Verbeek NE, van Kempen M, Fazeli W, Striano P, Zara F, Visser G, Braakman HMH, Haeusler M, Elbracht M, Vaher U, Smol T, Lemke JR, Platzer K, Kennedy J, Klein KM, Au PYB, Smyth K, Kaplan J, Thomas M, Dewenter MK, Dinopoulos A, Campbell AJ, Lal D, Lederer D, Liao VWY, Ahring PK, Møller RS, Gardella E. Structural mapping of GABRB3 variants reveals genotype-phenotype correlations. Genet Med. 2022 Mar;24(3):681-693. doi: 10.1016/j.gim.2021.11.004. Epub 2021 Dec 7. PMID: 34906499.
Bayat A, Iqbal S, Borredy K, Amiel J, Zweier C, Barcia G, Kraus C, Weyhreter H, Bassuk AG, Chopra M, Rubboli G, Møller RS. PRICKLE2 revisited-further evidence implicating PRICKLE2 in neurodevelopmental disorders. Eur J Hum Genet. 2021 Aug;29(8):1235-1244. doi: 10.1038/s41431-021-00912-y. Epub 2021 Jun 7. PMID: 34092786; PMCID: PMC8385026.
Necci M, Piovesan D; CAID Predictors; DisProt Curators; Tosatto SCE. Critical assessment of protein intrinsic disorder prediction. Nat Methods. 2021 May;18(5):472-481. doi: 10.1038/s41592-021-01117-3. Epub 2021 Apr 19. PMID: 33875885; PMCID: PMC8105172.
Mendez R, Iqbal S, Vishnopolska S, Martinez C, Dibner G, Aliano R, Zaiat J, Biagioli G, Fernandez C, Turjanski A, Campbell AJ, Mercado G, Marti MA. Oculocutaneous albinism type 1B associated with a functionally significant tyrosinase gene polymorphism detected with Whole Exome Sequencing. Ophthalmic Genet. 2021 Jun;42(3):291-295. doi: 10.1080/13816810.2021.1888129. Epub 2021 Feb 18. PMID: 33599182.
Madison JM, Duong K, Vieux EF, Udeshi ND, Iqbal S, Requadt E, Fereshetian S, Lewis MC, Gomes AS, Pierce KA, Platt RJ, Zhang F, Campbell AJ, Lal D, Wagner FF, Clish CB, Carr SA, Sheng M, Scolnick EM, Cottrell JR. Regulation of purine metabolism connects KCTD13 to a metabolic disorder with autistic features. iScience. 2020 Dec 11;24(1):101935. doi: 10.1016/j.isci.2020.101935. PMID: 33409479; PMCID: PMC7773955.
El Achkar CM, Harrer M, Smith L, Kelly M, Iqbal S, Maljevic S, Niturad CE, Vissers LELM, Poduri A, Yang E, Lal D, Lerche H, Møller RS, Olson HE; GABRB2 Working Group. Characterization of the GABRB2-Associated Neurodevelopmental Disorders. Ann Neurol. 2021 Mar;89(3):573-586. doi: 10.1002/ana.25985. Epub 2020 Dec 24. Erratum in: Ann Neurol. 2021 Nov;90(5):859. doi: 10.1002/ana.26215. PMID: 33325057; PMCID: PMC9161810.
Goodspeed K, Pérez-Palma E, Iqbal S, Cooper D, Scimemi A, Johannesen KM, Stefanski A, Demarest S, Helbig KL, Kang J, Shaffo FC, Prentice B, Brownstein CA, Lim B, Helbig I, De Los Reyes E, McKnight D, Crunelli V, Campbell AJ, Møller RS, Freed A, Lal D. Current knowledge of SLC6A1-related neurodevelopmental disorders. Brain Commun. 2020 Oct 13;2(2):fcaa170. doi: 10.1093/braincomms/fcaa170. PMID: 33241211; PMCID: PMC7677605.
Iqbal S*, Pérez-Palma E, Jespersen JB, May P, Hoksza D, Heyne HO, Ahmed SS, Rifat ZT, Rahman MS, Lage K, Palotie A, Cottrell JR, Wagner FF, Daly MJ, Campbell AJ, Lal D. Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants. Proc Natl Acad Sci U S A. 2020 Nov 10;117(45):28201-28211. doi: 10.1073/pnas.2002660117. Epub 2020 Oct 26. PMID: 33106425; PMCID: PMC7668189.
Heyne HO, Baez-Nieto D, Iqbal S, Palmer DS, Brunklaus A, May P; Epi25 Collaborative; Johannesen KM, Lauxmann S, Lemke JR, Møller RS, Pérez-Palma E, Scholl UI, Syrbe S, Lerche H, Lal D, Campbell AJ, Wang HR, Pan J, Daly MJ. Predicting functional effects of missense variants in voltage-gated sodium and calcium channels. Sci Transl Med. 2020 Aug 12;12(556):eaay6848. doi: 10.1126/scitranslmed.aay6848. PMID: 32801145.
Iqbal S*, Hoksza D, Pérez-Palma E, May P, Jespersen JB, Ahmed SS, Rifat ZT, Heyne HO, Rahman MS, Cottrell JR, Wagner FF, Daly MJ, Campbell AJ, Lal D. MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. Nucleic Acids Res. 2020 Jul 2;48(W1):W132-W139. doi: 10.1093/nar/gkaa361. PMID: 32402084; PMCID: PMC7319582.
Brunklaus A, Leu C, Gramm M, Pérez-Palma E, Iqbal S, Lal D. Time to move beyond genetics towards biomedical data-driven translational genomic research in severe paediatric epilepsies. Eur J Paediatr Neurol. 2020 Jan;24:35-39. doi: 10.1016/j.ejpn.2019.12.001. Epub 2019 Dec 17. PMID: 31924506.
Pérez-Palma E, May P, Iqbal S, Niestroj LM, Du J, Heyne HO, Castrillon JA, O'Donnell-Luria A, Nürnberg P, Palotie A, Daly M, Lal D. Identification of pathogenic variant enriched regions across genes and gene families. Genome Res. 2020 Jan;30(1):62-71. doi: 10.1101/gr.252601.119. Epub 2019 Dec 23. PMID: 31871067; PMCID: PMC6961572.
Balak C, Benard M, Schaefer E, Iqbal S, Ramsey K, Ernoult-Lange M, Mattioli F, Llaci L, Geoffroy V, Courel M, Naymik M, Bachman KK, Pfundt R, Rump P, Ter Beest J, Wentzensen IM, Monaghan KG, McWalter K, Richholt R, Le Béchec A, Jepsen W, De Both M, Belnap N, Boland A, Piras IS, Deleuze JF, Szelinger S, Dollfus H, Chelly J, Muller J, Campbell A, Lal D, Rangasamy S, Mandel JL, Narayanan V, Huentelman M, Weil D, Piton A. Rare De Novo Missense Variants in RNA Helicase DDX6 Cause Intellectual Disability and Dysmorphic Features and Lead to P-Body Defects and RNA Dysregulation. Am J Hum Genet. 2019 Sep 5;105(3):509-525. doi: 10.1016/j.ajhg.2019.07.010. Epub 2019 Aug 15. PMID: 31422817; PMCID: PMC6731366.
Du J, Sudarsanam M, Pérez-Palma E, Ganna A, Francioli L, Iqbal S, Niestroj LM, Leu C, Weisburd B, Poterba T, Nürnberg P, Daly MJ, Palotie A, May P, Lal D. Variant Score Ranker-a web application for intuitive missense variant prioritization. Bioinformatics. 2019 Nov 1;35(21):4478-4479. doi: 10.1093/bioinformatics/btz252. PMID: 31086968.
Olson HE, Demarest ST, Pestana-Knight EM, Swanson LC, Iqbal S, Lal D, Leonard H, Cross JH, Devinsky O, Benke TA. Cyclin-Dependent Kinase-Like 5 Deficiency Disorder: Clinical Review. Pediatr Neurol. 2019 Aug;97:18-25. doi: 10.1016/j.pediatrneurol.2019.02.015. Epub 2019 Feb 23. PMID: 30928302; PMCID: PMC7120929.
Iqbal S, Hoque MT. PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence. Bioinformatics. 2018 Oct 1;34(19):3289-3299. doi: 10.1093/bioinformatics/bty352. PMID: 29726965.

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