Iman Hajirasouliha
@hajirasouliha
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Associate Professor at @WeillCornell Alum @SFU @BrownUniversity @Stanford (CS) @UCBerkeley Computational genomics, Pathology, AI in Medicine, IVF
New York City, NY
Joined June 2009
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Last Friday I received a call officially confirming my promotion to Associate Professor. I cannot stop thinking about all the folks who helped me to make this possible! Photo taken moments after - a celebratory sushi lunch with a wonderful friend and collaborator in Cambridge.
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My first PhD student,
@CamirRicketts
, joined NVIDIA as a Bioinformatics/AI Scientist right after graduation 3 years ago. I always think someday he will come back, hands me a cup of coffee, a dozen H100 GPUs and says here is also a $5 million gift to the lab :)
NVIDIA is officially worth more than Amazon and Google:
1. 🇺🇸 Microsoft: $3.1 trillion
2. 🇺🇸 Apple: $2.9 trillion
3. 🇸🇦 Saudi Aramco: $2 trillion
4. 🇺🇸 NVIDIA: $1.83 trillion
5. 🇺🇸 Alphabet: $1.82 trillion
6. 🇺🇸 Amazon: $1.8 trillion
7. 🇺🇸 Meta: $1.2 trillion
v/
@stats_feed
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Tomorrow is September and this came in today! Very happy and honored to receive a 5 year
@NIGMS
award to do algorithms for metagenomics. Thankful to my amazing lab (especially
@dcdanko
,
@meleshko_da
,
@CamirRicketts
and Lauren Mak who helped with this and the related projects)
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Our first SV detection method using deep learning (Cue), led by the incomparable Victoria Popic, is now online
@naturemethods
... introducing a novel framework that can shift SV calling and genotyping from ad-hoc rule-based methods to a generalizable learning-based model.
Cue, from Victoria Popic and colleagues, achieves versatile and performant structural variant (SV) calling and genotyping using a deep learning approach.
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My first paper on linked-read metagenomics is out open access on
@genomeresearch
Congratulations to incomparable Ph.D. students David
@dcdanko
and Dmitri
@meleshko_da
! grateful for collaborations w
@10xgenomics
@mason_lab
@Daniela_Bezdan
@illumina
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I am grateful to have received the Irma T. Hirschl and Monique Weill-Caulier Research Award. This will enable more AI in Medicine research in my lab
@WeillCornell
, especially related to AI in IVF and Embryology!
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Finally got to meet my academic grandpa and he got to see his great great academic son!
#RECOMB2019
#fourgenerations
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Our paper on using AI for robust assessment of human embryos after in vitro fertilization is out: Congrats to my postdoc, Pegah! Thanks to
@EhsanKazzemi
@ElementoLab
@EngIPM
and amazing embryology collaborators at
@WeillCornell
, Spain and the UK
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8 years ago, today! I was at
@WeillCornell
for my job interview! Took this photo when I had a moment before my first meeting with
@ElementoLab
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In
@10xgenomics
Linked-Read sequencing, each barcode typically matches reads from 2-20 long fragments of DNA. In this work, we presented
#Minerva
, a novel method to deconvolve
#metagenomics
linked-reads with a single barcode into clusters that represent single long fragments.
NEW online:
@genomeresearch
publishes
#Minerva
: an alignment- and reference-free approach to deconvolve linked-reads for
#metagenomics
. FREE open access article -->
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Congratulations to my incomparable Ph.D. student, Josue Barnes, who diligently led this work! Also, grateful to have 5 other amazing
@WeillCornell
@WeillCornellGS
Ph.D. students (Matthew Brendel, Vianne Gao, Suraj Rajendran, Junbum Kim, and Qianzi Li)
NEW Research on the development of
#ArtificialIntelligence
models to predict blastocyst ploidy in
#IVF
.
Read it here:
@hajirasouliha
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Delighted to be a Finalist for the 2019 Agilent Early Career Professor Award
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The tech for the next decade: promises and challenges in genome biology … Our
#AGBT19
meeting report (with the incomparable
@hagentilgner
) is now published in
@GenomeBiology
. Already cannot wait for next year's (
#AGBT20
20TH ANNIVERSARY)
@agbt
meeting!
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I am excited to chair next year's RECOMB Computational Cancer meeting together with
@ewa_szczurek
.
Full paper/ abstract submission deadlines will be Feb 17, 2020. The meeting will be held on May 8-9, 2020 immediately before the
@recomb2020
meeting in Padova, Italy.
#recombccb2020
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Our new manuscript led by the incomparable friend and colleague Victoria Popic is now on bioRxiv. A novel deep learning formulation for structural variant discovery that is highly generalizable, sequencing technology independent and can handle complex and clustered SVs.
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Congratulations Dr. Ricketts! Very proud of my very first Ph.D. student for a successful thesis defense today
@cbm_student
@WeillCornellGS
@WeillCornell
... keep going!
Today I became Dr. Ricketts
#LifeIsGood
. I’ll always be grateful for the mentorship I’ve received in the
@hajirasouliha
Lab and from the
@WeillCornellGS
community!
#Jamaica
got another doctor 🇯🇲
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Grateful for the support from Starr Cancer Consortium. Super excited for our new deep learning studies with applications to the genomics of cancer and pathology.
Two multi-institutional teams led by Drs.
@LisaRoth_MD
and Iman Hajirasouliha (
@hajirasouliha
) of
#WCM
win grant support from Starr Cancer Consortium to study tumor biology.
Learn more:
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@NYCMayor
Close the schools and shutdown the subway. Ask people to stay home. Having the largest city makes us less safe. You’re already too late. Just look at Italy.
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Our new methods paper, Ariadne, is just out
@GenomeBiology
! Led by my incredible Ph.D. student
@cbm_student
@WeillCornell
Lauren Mak - with contributions from several other current or former students including
@meleshko_da
@dcdanko
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Very proud of my PhD student and a rising star, Camir Ricketts
@RickettsCamir
(from
@WeillCornell
@cbm_student
program) who just received the highly prestigious prime minister youth award at 🇯🇲 House!!!
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[Please R/T] Two major projects on deep learning imaging with original applications to human genetics, cancer genomics, and pathology are funded.
Postdoc positions available in my lab in 2022 -- in collaboration with Dr. Popic
@broadinstitute
or
@ElementoLab
@WCMEnglanderIPM
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This upcoming semester, I'm teaching a NEW class, Data Structures & Algorithms for Computational Biology (CMPB 5002 01) at
@WeillCornell
Please see for a tentative outline. Feedbacks are indeed welcome!
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Our newest journal article is now out! Shout out to incredible Ph.D.
@cbm_student
from the lab, Dr.
@meleshko_da
, and wonderful
@WeillCornell
collaborator
@hagentilgner
:
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I just gave my first
@WeillCornellGS
full lecture via
@zoom_us
The experience was way better than expected. My one hour planned lecture lasted 1 h 35 mins because students were surprisingly very engaged! Thank you
@WeillCornell
for facilitating online classes.
#WorkFromHome
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Our paper is out! Hats off to amazing and hardworking
@cbm_student
@RickettsCamir
#DanielSeidman
(and grateful for awesome collaborators
#VictoriaPopic
@DavisCompGen
@SerafimBatz
) Meltos: Multi-Sample Tumor Phylogeny Reconstruction for Structural Variants
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Congratulations Lauren Mak
@cbm_student
for winning a 3-year
@NSERC_CRSNG
Canada Graduate Scholarships for her doctoral research in the lab! Well done!
@WeillCornell
@WeillCornellGS
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Our most recent paper led by star students
@BrendelMatt
and
@VGetseva
is out! Weakly-supervised tumor purity prediction from frozen H&E slides
@Pegahkhosravi1
@ElementoLab
@WCMEnglanderIPM
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A short interview with me about our newest paper: A New Computational Model to Understand Tumor Evolution
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Great keynote talk
@recomb2020
by Pavel Pevzner. Describing SPAdes and Flye assembly tools for short and long reads. Also featuring our BiosyntheticSPAdes tool led by the incomparable
@cbm_student
Dmitrii Meleshko
@meleshko_da
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We're very glad to be involved and have a small contribution in this important
@GenomeInABottle
resource for robust benchmarking of germline structural variants (just published in
@NatureBiotech
) with
@CamirRicketts
@WeillCornell
@WeillCornellGS
@EngIPM
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Our work on how AI can improve the success for IVF processes is featured in the Time magazine. The main paper will be out soon! Stay tuned :)
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Our new manuscript describing two new algorithms for classification of
@10xGenomics
metagenomic reads. Led by the incomparable
@dcdanko
. With the gang (
@meleshko_da
@Daniela_Bezdan
@mason_lab
) comments are welcome!
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Very excited to announce our recent
@genomeresearch
paper on
@10xGenomics
linked-read deconvolution has been selected for a
#highlight
talk at the main
@recomb2019
conference! see you there. And yeah
@dcdanko
is an excellent speaker!
In
@10xgenomics
Linked-Read sequencing, each barcode typically matches reads from 2-20 long fragments of DNA. In this work, we presented
#Minerva
, a novel method to deconvolve
#metagenomics
linked-reads with a single barcode into clusters that represent single long fragments.
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RECOMB Computational Cancer Biology 2020 meeting
@recomb2020
will be happening virtually and the registration will be open and free of charge. Dates are June 18-19 (approximately from 9 AM to 3 PM EST).
@ewa_szczurek
and I will post the registration link and the program soon.
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Our most recent human genome structural variant detection paper is out in
@GenomeBiology
. An amazing and fruitful collaboration with my academic brother
@calkan_cs
. Congrats to incomparable and soon-to-graduate
@cbm_student
@CamirRicketts
@WeillCornell
and
@fkaraoglan_cs
and co
VALOR2: from
@fkaraoglan_cs
,
@CamirRicketts
,
@hajirasouliha
,
@calkan_cs
and co, a method for using linked reads to identify structural variants. It works particularly well for large variants and segmental duplications. Applied to Yoruban and European data
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Hiring a Computational Genomics / Computer Science postdoc (
@WCMICB
,
@EngIPM
, and
@MeyerCancer
of
@WeillCornell
in
#NewYorkCity
) Please help spread the word! For more info go to
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Our paper "Inferring Cancer Progression from Single-Cell Sequencing while Allowing Mutation Losses" is now online
Congratulations Simone Ciccolella and
@CamirRicketts
! A wonderful collaboration with
@giandellavedova
and his team and
@DSilverbush
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I am excited to be an invited speaker at the
#amp2023
meeting. If you're at the conference and want to catch up drop me a line!
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First lab dinner after so many months! Was pretty surreal seeing some faces after 16 months or for the first-time!
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Our latest work led by the incomparable
@cbm_student
@WeillCornellGS
Lauren Mak. Ariadne: Barcoded Linked-Read Deconvolution Using de Bruijn Graphs
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Our new paper is out (open access): A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology–Radiology Fusion
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Happy Norooz! Added some mini DJ vibe to the haft-sin table (for no reason!)
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Our method, Meltos: multi-sample tumor phylogeny reconstruction for structural variants, is published in the latest issue of Bioinformatics: Congrats
@CamirRicketts
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TWO oral presentations accepted in
#ISMB2019
from us (total 12 accepted from 99 submissions in the
@HiTSeq
track). Both new SV detection methods using
@10xGenomics
linked-reads! congrats to students
@meleshko_da
@RickettsCamir
and academic brother
@calkan_cs
and his group!
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10 years ago (!!!) today I defended my Ph.D. This is one of the back rows in the room where it happens
@SFU
@cenksahinalp
@InancBirol
@halperineran
(on Skype from Spain)
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Our latest work on tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data is now available online at
@genomeresearch
(joint with
@cenksahinalp
of
@NCIResearchCtr
)
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Very grateful to work with amazing students at
@WeillCornellGS
. Happy thanksgiving holidays all!
p.s: note the medals :) the photo is a bit old.
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So glad and excited to have PANGAIA (Pan-genome Graph Algorithms and Data Integration), our Horizon 2020 project, funded by the European Commission!
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Super excited to host Dr. Paul Medvedev
@pashadag
next week for an ICB seminar! Don't miss it!
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Our manuscript describing a novel method for detection and assembly of novel insertions using
@10xGenomics
linked reads. With no need of a whole genome de novo assembly. Led by star student
@meleshko_da
. Great help from
@SvenAT
and
@patrickjmarks
of 10xGenomics.
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7
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Taking the
@weillcornell
@cornell
campus to campus bus today up to Ithaca for the first time after the pandemic! Excited to reconnect with several Computational Biology colleagues
@CornellCALS
and give a seminar!
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I’m super excited to be joining the
@nvidia
Genomics Team. Ready to make an impact in healthcare through genomics and artificial intelligence
#NVIDIAlife
@NVIDIAHealth
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We are live!!! Harnessing Artificial Intelligence Technology for IVF Embryo Selection
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One year ago, today. We had our last in-person group meeting.
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Our new collaborative work with
@calkan_cs
on characterization of segmental duplications and large inversions using
@10xgenomics
Linked-Reads
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Our new method for the recovery of RNA viruses (e.g. Coronaviruses) [led by incomparable
@meleshko_da
and
@akorobeynikov
] coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
1
12
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Our Latest work led by star
@WeillCornellGS
PhD student Matthew Brendel and undergrad intern Vanesa Getseva: Weakly-Supervised Tumor Purity Prediction From Frozen H&E Stained Slides
2
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Simone Zaccaria
@ZaccaSimo
from
@benjraphael
group discusses his recent tool CHISEL (Preprint available on biorxiv, to be appear in
@NatureBiotech
)
#recombccb2020
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The RECOMB Satellite Workshop on Computational Cancer Biology (RECOMB-CCB2020), will be held in Padova (Italy) on 8-9 May 2020. Call for paper and registration open:
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Check out our updated manuscript and tool (Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics) ...
@dcdanko
added some new math, biology, and utility!
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I serve as Industry Chair of
@RECOMBconf
2024 in Boston. I'll send out emails to contacts for sponsorship opportunities. If you're in tech, biotech, genomics, AI, sequencing, computational biology, medicine, or relevant domains feel free to get in touch:
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Looking forward to
#RECOMB2023
-- in Istanbul already, checking in with the boss :)
@RECOMBconf
@calkan_cs
@crashius
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Last lab outing of 2022 ... missing the remote folks! Happy holidays!
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NVIDIA Collaborates With Genentech to Accelerate Drug Discovery Using Generative AI
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4
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Congratulations Josue Barnes
@WCM_PhysBio
for winning a training award from the WCM Clinical and Translational Science Center! This enables a collaborative research on AI, reproductive medicine, and developmental biology
@WeillCornell
@WeillCornellGS
@WCMEnglanderIPM
1
4
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My student, Josue Barnes, is defending his Ph.D. thesis today at 12 pm EST
@WeillCornell
@WeillCornellGS
@WCMEnglanderIPM
@WCM_PhysBio
... here is a link to the event:
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2
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Stirring biopic of the first woman to win top maths prize
1
3
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I know it's not possible to get as many views as Jian's
@jmuiuc
@UCLA_CGSI
talk would get. But here is the video of my talk about deep learning applications in digital pathology and In Verto Fertilization (IVF):
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6
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The manuscript describing our COVID-19 daily reporting tool is now published in
@NatureMedicine
Glad to be a part of this initiative led by incomparable
@segal_eran
and with other colleagues at
@EngIPM
@ElementoLab
@asbonerw
@AlexSigaras
@WeillCornell
In our new
@NatureMedicine
paper we join forces with 11 countries to standardize efforts to use daily self-reported surveys of COVID-19 symptoms to track viral spread
We call on more countries to join:
@zhangf
@ophirshalem
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5
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Optimal compressed representation of high throughput sequence data via light assembly
0
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We have three wonderful invited speakers for our
@recomb2020
computational cancer biology: Martin Miller
@MillerLab4
, Teresa Przytycka
@przytycka
, and Maria Rodriguez Martinez
@MariaRoCompBio
. Also, we received several high quality papers. Looking forward to this meeting!
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5
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Our Genome Informatics 2022 meeting report
#GI2022
is now online
@GenomeBiology
... sooo many great and interesting talks and we were only able to highlight a few. Hopefully you will be convinced to attend
#GI2023
(this time
@CSHL
):
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Another great paper showing the power of using multiple
@GenomeInABottle
short-reads and long-reads: "The addition of PacBio HiFi data resulted in slightly more total sequence in the assembly (2.99 Gb vs. 2.88 Gb) and a substantially larger contig N50 size (18.2 Mb vs. 4.9 Mb)."
Our paper on the first human reference genome, fully annotated and created from a single individual is out in
@GenomeBiology
. Kudos to
@alaina_shumate
@AlekseyZimin5
@rshermanjhu
@elapertea
@bioetalons
@GenomeInABottle
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Excited to be an invited speaker at the First Workshop On Pangenomics Algorithms for Omics Data in Milan later this month. More info here for those interested in participating:
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6
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Lab meeting today (over bowling) -- for those who wonder Reviewer 2 won the games.
1
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Our coronaSPAdes paper is out! presents a robust tool for the assembly of viral genomes (including coronaviruses). Led by Dima, my star Ph.D. student
@cbm_student
@WeillCornell
@meleshko_da
and incomparable
@spadesassembler
collaborator
@akorobeynikov
0
3
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We already have a record number of participants for our upcoming RECOMB Computational Cancer Biology (CCB)
@recomb2020
meeting. By far! But there is still time to register for the meeting. See our website here for more details:
1
11
21
Paper submission is now open for
@recomb2020
Computational Cancer Biology (RECOMB-CCB) (submission deadline: Feb 17). Selected papers will be published in
@PLOSCompBiol
. See the CFP and program here: (Please R/T)
1
12
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Looking forward to speaking at the 5th Digital Pathology & AI Congress In NYC on June 13th-14th!
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1
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Good to see the genome sequencing cost slide for the 87th time at a talk (yes I do keep track)
#recomb2019
0
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Our latest "accepted" manuscript led by recently-graduated
@cbm_student
@WeillCornellGS
Dr. Meleshko of the lab. Fruitful collaboration with my dear friend
@hagentilgner
! cloudrnaSPAdes: Isoform assembly using bulk barcoded RNA sequencing data
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3
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Our manuscript on "Using LICHeE and BAMSE for Reconstructing Cancer Phylogenetic Trees" - - Current Protocols in Bioinformatics (with
@RickettsCamir
#VictoriaPopic
@Hosein2C
)
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Many congratulations 🍾🎊
@SerafimBatz
and
@benjraphael
my postdoc mentors who both made it to the ISCB 2020 class of fellows this year!
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And she won a prize for that :)
Pegah Khosravi, postdoc in the
@hajirasouliha
lab presenting her work on ‘Classification of Digital Pathology Images using Deep Neural Networks’ at
#MLIM
#MLIM18
@WeillCornell
@WCMICB
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Excited to attend
#ISMBECCB19
after a couple-year-break! We'll have 3 talks: 1)
@calkan_cs
will present VALOR2, our newest linked-read SV caller 2) I will present Novel-X, a new linked-read method for novel insertions assembly led by
@meleshko_da
3)
@dcdanko
will present MetaSUB
1
2
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Our new collaborative work with the Royan Institute,
@EngIPM
and
@ElementoLab
: Breast Cancer Histopathological Image Classification: A Deep Learning Approach
0
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