Lab Updates, Talks & News!
"If you don't have to make a decision about something, then don't decide."
- William Falkland
Embedded Files
2024-25 Winter (dec'24-mar'25)
2024-25 Winter (dec'24-mar'25)
Mar 12, 2025
20250312_BroadE_Workshop_SI_G2P_Public.pdf
Mar 5, 2025
A flash overview of EmmaEmb: A Python library designed to facilitate the initial comparison of diverse embedding spaces in embeddings for molecular biology. By incorporating user-defined feature data on the natural grouping of data points, EmmaEmb enables users to compare global statistics and understand the differences in clustering of natural groupings across different embedding spaces.
Dec 2, 2024
New postdoctoral associate YooChan started in the lab. YooChan will lead new collaborations between Iqbal and Brian Liau's lab- looking forward to seeing what YooChan does in the next few years!
2024 Fall (SEP-Nov)
2024 Fall (SEP-Nov)
Jordan presents at the American Society of Human Genetics (ASHG) meeting!
Jordan presents at the American Society of Human Genetics (ASHG) meeting!
Nov 8, 2024
Jordan presents a poster on his project: Predicting Loss- and Gain-of-Function Variants on Voltage-Gated Ion Channels, at the ASHG 2024 meeting.
Oct 7, 2024
Mikias joined the G2P portal team as a web/UIX developer and SWE consultant! Excitedly looking forward to Mikias's experienced contribution to the project!
sumaiya presents at The L2C Accelerator and Eric and Wendy Schmidt Center Joint Symposium Connecting the Dots: Biology at Scale in the Age of AI
sumaiya presents at The L2C Accelerator and Eric and Wendy Schmidt Center Joint Symposium Connecting the Dots: Biology at Scale in the Age of AI
Sep 27, 2024
Title: Gene Variations to Protein Functional Impact at Scale - Using Biologically Interpretable Features and AI.
PS. Thanks to our science illustrator partner Behnoush Hajian for the cover!
Sumaiya gives a course on Machine Learning and Artificial Intelligence for Drug Discovery at the Master of Medical Sciences in Clinical Investigation program at HMS
Sumaiya gives a course on Machine Learning and Artificial Intelligence for Drug Discovery at the Master of Medical Sciences in Clinical Investigation program at HMS
Sep 16, 2024
Title: AI/ML in Drug Discovery. Details ➡️ Slides!
Agenda:
A primer on AI/ML
AI/ML for Drug Discovery
Case-study
AI/ML in Health and Medicine – challenges, opportunities, guidelines
MMSCI_HMS_course_slides_toShare.pdfSep 18, 2024
2024 Summer (Jul-Aug)
2024 Summer (Jul-Aug)
Sumaiya gives a "Genomics 2 Proteins Portal Workshop" at the Cancer Genomics Consortium (CGC) Annual Meeting, Bioinformatics Workshop Session
Sumaiya gives a "Genomics 2 Proteins Portal Workshop" at the Cancer Genomics Consortium (CGC) Annual Meeting, Bioinformatics Workshop Session
Aug 04, 2024
The Genomics 2 Proteins portal is developed to help biologists, clinicians, and researchers understand the effect of mutations on protein structure and function. In the bioinformatics workshop at the Cancer Genomics Consortium annual meeting, Sumaiya showcases two case studies: Investigating resistant mutations in BTK and Investigating LOF mutations and functional data on TP53 using the Genomics to Proteins portal. Check out the full workshop below!
CGC_SI_20240804.pdf2024 Spring (Apr-Jun)
2024 Spring (Apr-Jun)
Great time and lab participation at the Mutational Scanning Symposium (MSS'24): Jordan gives a talk and Francesca presents a poster! Sumaiya and Doug Fowler share their reflections in a post-symposium News Letter!
Great time and lab participation at the Mutational Scanning Symposium (MSS'24): Jordan gives a talk and Francesca presents a poster! Sumaiya and Doug Fowler share their reflections in a post-symposium News Letter!
May 22-23, 2024
Jordan presents how the resource developed in the lab, the Genomics 2 Proteins or G2P portal, can be used to map and analyze functional readouts of mutational scans on protein sequence and structure. Francesca presents her work on "Towards leveraging machine learning to predict the functional effects of genetic variants in ion channels" during the poster session. Finally, read the post-symposium reflections shared by Sumaiya and Doug Fowler!
Title: Genomics 2 Proteins portal (G2P): A discovery portal to link genetic screening outputs to protein sequence and structure.
mss_2024_francesca_ion_channel_project.pdfTitle: Towards leveraging machine learning to predict the functional effects of genetic variants in ion channels.
Apr 24, 2024
Sumaiya speaks at the SLAS Technology Idea Exchange event – about the big and complex biological data integration challenges around developing and maintaining the Genomics 2 Proteins / G2P portal, and it's potential applications in translating genomic discoveries!
G2P_Technology_Idea_Exchange_SLS_04242024.pdfGMT20240408-202700_Recording_1920x1080.mp4Apr 08, 2024
Title: A Birds-eye Overview of Bioinformatics in 2024.
PS. Do you know who is the mother and father of "Bioinformatics"? It's Margaret Dayhoff! Learn more about how the field of bioinformatics started and where it is now - in the slidedeck!
New Members in the lab - Welcome, Francesca and Paulo!
New Members in the lab - Welcome, Francesca and Paulo!
Apr-May, 2024
Two graduate students, Pia Francesca Rissom and Paulo Yanez Sarmiento, joined the lab as visiting researchers! Francesca and Paulo are obtaining their PhDs at the Hasso Plattner Institute, Germany, and will spend the Spring/Summer with us! We are thrilled to have you on board!
2023-24 Winter (dec'23-mar'24)
2023-24 Winter (dec'23-mar'24)
Mar 22, 2024
It's been an incredible six months into this inter-continental (😃) and inter-disciplinary collaboration between Hasso Plattner Institute, Potsdam, Germany (Henrike Heyne's group) and Broad Institute/MIT, Cambridge, MA (Iqbal lab and Coley research group)! Jointly, we are exploring the functional effect of genetic variants in ion-channels. So proud of Francesca, Jordan and Paulo for spearheading this project!
Iqbal Lab presents at the Biophysical Society (BPS) Annual Meeting! Seulki is invited to give a platform talk and Jordan presents a poster - congrats team!
Iqbal Lab presents at the Biophysical Society (BPS) Annual Meeting! Seulki is invited to give a platform talk and Jordan presents a poster - congrats team!
Feb 11-13, 2024
Computational biophysics and Structural bioinformatics are the two primary toolboxes we use to investigate the effect of genetic mutations on protein structure-function relationship and druggability assessment of targets. Congratulations to Seulki and Jordan for showcasing use cases on UMOD mutations causing rare genetic kidney disease (ADTKD) and 127 understudied (but potentially draggable!) protein kinases associated with many rare diseases.
Title: Unraveling the conformational dynamics of UMOD protein variants in autosomal dominant tubulointerstitial kidney disease: Insights from molecular dynamics simulations (Read the abstract!).
BPS_2024_JS_poster_understudiedkinase.pdfTitle: Characterizing 127 understudied kinases through in silico saturation mutagenesis of predicted protein structures
(Read the abstract!)
SLAS_DEL_ML_02052024_Final.pdfsumaiya shares the stage with Holly Soutter at the SLAS 2024 International Conference and Exhibition to present our DEL+ML Paradigm!
sumaiya shares the stage with Holly Soutter at the SLAS 2024 International Conference and Exhibition to present our DEL+ML Paradigm!
Feb 05, 2024
Title: DEL+ML Paradigm for Discovering Actionable Hits – a comparative analysis of three diverse DNA-encoded libraries (DEL) and multiple machine learning (ML) algorithms.
It's Retreat Time! Sumaiya showcases the G2P portal to the Institute COmmunity at the Broad Institute Retreat 2023!
It's Retreat Time! Sumaiya showcases the G2P portal to the Institute COmmunity at the Broad Institute Retreat 2023!
Dec 12, 2023
2023 FALL (Sep-Nov)
2023 FALL (Sep-Nov)
Nov 2-3, 2023
It's the annual (signature) human genetics meeting time! As a team, we strive to unveil the effect of genetic variants on protein function and mechanism. Congrats to the lab members for moving one step toward our goal, by developing resources (Jordan's poster) and statistical methods (Seulki's poster)
ASHG_2023_JordanSafer_poster_g2p.pptx.pdfTitle: Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures
Presenter: Jordan Safer
ASHG_2023_Seulki_poster_missense.pdfTitle: Comprehensive Statistical Analysis on the Impact of Missense Mutations Toward Improving Variant Interpretation
Presenter: Seulki Kwon
New grant! our project, "PREDICTING FUNCTIONAL EFFECTS OF ION-Channel VARIANTS," is among the ten funded projects under “Designing for Sustainability” Program
New grant! our project, "PREDICTING FUNCTIONAL EFFECTS OF ION-Channel VARIANTS," is among the ten funded projects under “Designing for Sustainability” Program
Oct 6, 2023
Henrike Heyne and Sumaiya gave their collaborative project pitch on "Ion-channel variant effect prediction" at the HPI-MIT Fall 2023 workshop at the Hasso-Palttner Institute, Potsdam, Germany! Excited about this collaboration involving Connor W. Coley, Bernhard Renard, and many others. Read our LinkedIn post about this collaboration!
2023 Summer (Jul-aug)
2023 Summer (Jul-aug)
Yearly lab outing @ Spectacle island!
Yearly lab outing @ Spectacle island!
Aug 27, 2023
Once a year, Saina gets to bury a lab member while Sumaiya takes her yearly nap on the beach 😪😃
That amazing moment when A lab member gets recognition for their brilliant work! BEST poster Award for eric at the acs fall 2023!
That amazing moment when A lab member gets recognition for their brilliant work! BEST poster Award for eric at the acs fall 2023!
Aug 16, 2023
Eric received the ACS COMP Undergraduate Poster Award for presenting: "DEL+ML–An ultra-high-throughput technology for novel scaffold discovery using the power of small molecule binding data and ML" in ACS Fall 2023: Harnessing the power of data! Congrats, Eric!
sumaiya presents at the Inaugural Ladders to Cures Symposium: Achieving escape velocity in rare genetic diseases!
sumaiya presents at the Inaugural Ladders to Cures Symposium: Achieving escape velocity in rare genetic diseases!
July 18, 2023
Title: In silico druggability assessment of target-rare disease pair-- by scalable linking of genetic mutations to protein structure & function
Watch the full video 👉 https://www.youtube.com/watch?v=5MmNdu8MWUE
2023 Spring (Apr-Jun)
2023 Spring (Apr-Jun)
Jun 11, 2023
A fantastic collaborative study with Sali Farhan (a colleague and friend from when we were both postdocs!) and Allison Dilliott is published in Brain! And did I mention that this is Seulki's first publication as a lab member? Congrats Seulki! Collaboration is vital to a successful, multidisciplinary investigation of complex biological problems - which, this study exemplifies!
May 23, 2023
Sumaiya and four other BroadIgnite awardees are featured at the Broad Institute Discovery Series! In the 5-min(!) pitch, Sumaiya shares how she aims to integrate genomics, proteomics, and structural biology data to inform rare disease-target druggability assessment.
May 23, 2023
Eric Hansen gave his final lab presentation on his DNA-encoded library + Machine Learning work! After finishing his Bachelors in Computer Sciences and Economics from Harvard University and working with us for over a year as a Research Intern, Eric is ready for his next adventure as a Trader. Good luck, Eric!
April, 2023
A month of new members!
Seulki Kwon joined the team as a Postdoctoral Fellow, and Jordan Safer as a Computational associate on April 3rd. And on April 10, Chengkuan Chen joined the team as a Machine Learning Engineer.
prior to iqbal lab
prior to iqbal lab
Did you know how it all started? A new journey begins with awards from the merkin institute of Data and technology development for transformative healthcare and broadignite
Did you know how it all started? A new journey begins with awards from the merkin institute of Data and technology development for transformative healthcare and broadignite
Sep 30, 2022
In 2021, Sumaiya started building the Genomics 2 Proteins (G2P) portal with the Broad Institute SPARC award and three fantastic undergrads via the MIT UROP program. On Mar 18, 2022, the beta version of the G2P portal (@G2Pportal) was publicly released for the first time (see the tweet 👉). Today, Sumaiya was awarded a Merkin Institute Prize for Transformative Technologies in Health Care to support further development of the portal and expand its impact on the scientific community. The portal aims to help understand the relationship between genetic mutations and protein structure and generate hypotheses as to how those mutations impact protein function and drug binding.
Nov 15, 2022
Rare genetic mutations profoundly impact protein structure. Today, Sumaiya received the BroadIgnite award for applying the G2P portal, a multi-omics bioinformatics resource and an integrative method to link genetic screening output to protein sequence and structure, to inform target selection and druggability assessment, especially in the field of rare diseases.
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