Photo of Sumaiya Iqbal,  PhD

Sumaiya Iqbal, PhD

Broad Institute of MIT and Harvard

Broad Institute of MIT and Harvard


sumaiya@broadinstitute.org

Sumaiya Iqbal, PhD

Broad Institute of MIT and Harvard

EDUCATIONAL TITLES

  • Group Lead, The Center for Development of Therapeutics, Broad Institute of MIT and Harvard

DF/HCC PROGRAM AFFILIATION

Research Abstract

I lead the Bioinformatics and Computational Biology (BCB) group at the Center for Development of Therapeutics, Broad Institute. The overarching objective of my group is to develop mechanistic and predictive models that are data and machine learning (ML) driven, yet actionable and interpretable, to generate novel hypotheses for complex drug actions, discover new biomedical knowledge, and support decision-making in drug discovery and clinical practice. One large focus of my group is developing methods for drug target analysis by rationalizing functional consequences of genetic variants and variants generated by base-editing technology on protein structure and function, including the identification and analysis of 3D protein functional hotspots. Additionally, my group develops ML-driven innovative tools for small-molecule hit identification using data from DNA-encoded library (DEL) screening, HTS, Imaging, etc.

Publications from Harvard Catalyst Profiles

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  • 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; 146:519-533. PubMed
  • Woodard J, Iqbal S, Mashaghi A. Circuit topology predicts pathogenicity of missense mutations. Proteins 2022; 90:1634-1644. PubMed
  • 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; 13:3778. PubMed
  • 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; 18:e1009911. PubMed
  • 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; 24:681-693. PubMed
  • 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; 29:1235-1244. PubMed
  • 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; 42:291-295. PubMed
  • 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, . Characterization of the GABRB2-Associated Neurodevelopmental Disorders. Ann Neurol 2021; 89:573-586. PubMed
  • 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 2021; 24:101935. PubMed
  • 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; 117:28201-28211. PubMed
  • Heyne HO, Baez-Nieto D, Iqbal S, Palmer DS, Brunklaus A, May P, , 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. PubMed
  • 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; 48:W132-W139. PubMed
  • Friedmann T, Bai JDK, Ahmad S, Barbieri RM, Iqbal S, Richman PS. Outcomes of Introducing a Mobile Interactive Learning Resource in a Large Medical School Course. Med Sci Educ 2020; 30:25-29. PubMed
  • 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; 24:35-39. PubMed
  • 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; 30:62-71. PubMed
  • 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; 2:fcaa170. PubMed
  • 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; 35:4478-4479. PubMed
  • 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; 105:509-525. PubMed
  • 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; 97:18-25. PubMed
  • Iqbal S, Hoque MT. PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence. Bioinformatics 2018; 34:3289-3299. PubMed
  • Tarafder S, Toukir Ahmed M, Iqbal S, Tamjidul Hoque M, Sohel Rahman M. RBSURFpred: Modeling protein accessible surface area in real and binary space using regularized and optimized regression. J Theor Biol 2018; 441:44-57. PubMed
  • Mishra A, Iqbal S, Hoque MT. Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom. J Theor Biol 2016; 398:112-21. PubMed
  • Rashid MA, Iqbal S, Khatib F, Hoque MT, Sattar A. Guided macro-mutation in a graded energy based genetic algorithm for protein structure prediction. Comput Biol Chem 2016; 61:162-77. PubMed
  • Nasrul Islam M, Iqbal S, Katebi AR, Tamjidul Hoque M. A balanced secondary structure predictor. J Theor Biol 2016; 389:60-71. PubMed
  • Iqbal S, Hoque MT. Estimation of Position Specific Energy as a Feature of Protein Residues from Sequence Alone for Structural Classification. PLoS ONE 2016; 11:e0161452. PubMed
  • Iqbal S, Mishra A, Hoque MT. Improved prediction of accessible surface area results in efficient energy function application. J Theor Biol 2015; 380:380-91. PubMed
  • Iqbal S, Hoque MT. DisPredict: A Predictor of Disordered Protein Using Optimized RBF Kernel. PLoS ONE 2015; 10:e0141551. PubMed
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