aamir mir
Associate Director at Tessera Therapeutics
associate director tessera therapeutic
extensive experience crispr-based genome editing , molecular biology , biochemistry , rna structural biology .
Tessera Therapeutics
https://www.linkedin.com/company/tessera-therapeutics
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Associate Director
Tessera Therapeutics
https://www.linkedin.com/company/tessera-therapeutics
Cambridge, Massachusetts, United States
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Senior Scientist
Inscripta, Inc.
https://www.linkedin.com/company/inscriptainc
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Consultant
Inscripta, Inc.
https://www.linkedin.com/company/inscriptainc
United States
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Senior Scientist II
Inscripta, Inc.
https://www.linkedin.com/company/inscriptainc
Pleasanton, California
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Senior Scientist l
Inscripta, Inc.
https://www.linkedin.com/company/inscriptainc
Pleasanton, California
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Scientist
University of Massachusetts Medical School
https://www.linkedin.com/company/umasschan
My research efforts are focused on the following:
•	Development of new CRISPR-based genome editing tools for therapeutic applications
•	Discovery and characterization of new CRISPR nucleases and their off-switches 
•	Effects of nucleic acids modifications on CRISPR-based genome engineering
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Postdoctoral Research Fellow
Purdue University
https://www.linkedin.com/company/purdue-university
My projects have been focused on discovery, structure, and function of catalytic RNAs. I am using advanced genomic techniques, structural and biochemical approaches to understand these catalytic RNAs.
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Graduate Research Assistant
Lawrence University
https://www.linkedin.com/company/lawrence-university
At Lawrence, I worked on RNA targets of angiogenein. Specifically, I wanted to understand whether angiogenin modulates the levels of microRNAs in order to promote blood vessel growth.
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Student Research Assistant
Lawrence University
https://www.linkedin.com/company/lawrence-university
I assisted a professor to conduct lab sessions for a biology class.
Appleton, Wisconsin
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Lab Assistant
Lawrence University
https://www.linkedin.com/company/lawrence-university
I helped the Lawrence faculty and students with computer related issues such as installing softwares, fixing software issues, installing harwares etc.
Appleton, Wisconsin
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Microcomputer Assistant
Core: Credential of Readiness
HBX CORe (Credential of Readiness) is a 120-150 hour certificate program on the fundamentals of business from Harvard Business School. CORe is comprised of three courses - Business Analytics, Economics for Managers, and Financial Accounting – developed by leading Harvard Business School faculty and delivered in an active learning environment based on the HBS signature case-based learning model.
Pass with Honors
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HBX / Harvard Business School
https://www.linkedin.com/school/onlinehbs/
Doctor of Philosophy (Ph.D.)
Senator, Purdue Graduate Student Government 

Chair, Student hosted seminar committee

Coordinator, Grad/Postdoc seminar series

Member, Purdue Graduate Student Government Career Fair Committee

Member, Purdue University Consulting Club

Member, Purdue Graduate Student Government Grant Review and Allocation Committee
Biochemistry
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Purdue University
https://www.linkedin.com/school/purdue-university/
Bachelor of Arts
Biology-Chemistry
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Lawrence University
https://www.linkedin.com/school/lawrence-university/
Froebel's International School
Lawrence College, Murree, Pakistan
American Chemical Society
Member
RNA Society
Member
American Society for Biochemistry and Molecular Biology
Member
Purdue Graduate Student Government
Senator
Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) has been extensively used for genome editing. Currently, three Cas9 orthologs have been adapted for in vivo genome engineering applications: Streptococcus pyogenes Cas9 (SpyCas9), Staphylococcus aureus Cas9 (SauCas9), and Campylobacter jejuni (CjeCas9). However, additional in vivo editing platforms are needed, in part to enable a greater range of sequences to be accessed via viral vectors, especially those in which Cas9 and sgRNA are combined into a single vector genome.
All-in-One Adeno-associated Virus Delivery and Genome Editing by Neisseria meningitidis Cas9 in vivo
Genome Biology
https://doi.org/10.1186/s13059-018-1515-0
RNA-based drugs depend on chemical modifications to increase potency and to decrease immunogenicity in vivo. Chemical modification will likely improve the guide RNAs involved in CRISPR-Cas9-based therapeutics as well. Cas9 orthologs are RNA-guided microbial effectors that cleave DNA. Here, we explore chemical modifications at all positions of the crRNA guide and tracrRNA cofactor. We identify several heavily modified versions of crRNA and tracrRNA that are more potent than their unmodified counterparts. In addition, we describe fully chemically modified crRNAs and tracrRNAs (containing no 2′-OH groups) that are functional in human cells. These designs will contribute to Cas9-based therapeutics since heavily modified RNAs tend to be more stable in vivo (thus increasing potency). We anticipate that our designs will improve the use of Cas9 via RNP and mRNA delivery for in vivo and ex vivo purposes.
Heavily and Fully Modified RNAs Guide Efficient SpyCas9-Mediated Genome Editing
Nature Communicationsvolume
https://doi.org/10.1038/s41467-018-05073-z
Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach that directly addresses the underlying genetic basis of disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied DNA repair template (donor) directly into a targeted genomic location. Unfortunately, particularly for long insertions, toxicity and delivery considerations associated with repair template DNA can limit the number of donor molecules available to the HDR machinery, thus limiting HDR efficacy. Here, we explore modifications to both double-stranded and single-stranded repair template DNAs and describe simple 5′ end modifications that consistently and dramatically increase donor potency and HDR efficacy across cell types and species.
5′ Modifications Improve Potency and Efficacy of DNA Donors for Precision Genome Editing
bioRxiv
https://doi.org/10.1101/354480
CRISPR-Cas systems are widely used for genome engineering technologies, and in their natural setting, they play crucial roles in bacterial and archaeal adaptive immunity, protecting against phages and other mobile genetic elements. Previously we discovered bacteriophage-encoded Cas9-specific anti-CRISPR (Acr) proteins that serve as countermeasures against host bacterial immunity by inactivating their CRISPR-Cas systems. We hypothesized that the evolutionary advantages conferred by anti-CRISPRs would drive the widespread occurrence of these proteins in nature. We have identified new anti-CRISPRs using the bioinformatic approach that successfully identified previous Acr proteins against Neisseria meningitidis Cas9 (NmeCas9). In this work we report two novel anti-CRISPR families in strains of Haemophilus parainfluenzae and Simonsiella muelleri, both of which harbor type II-C CRISPR-Cas systems. We characterize the type II-C Cas9 orthologs from H. parainfluenzae and S. muelleri, show that the newly identified Acrs are able to inhibit these systems, and define important features of their inhibitory mechanisms. The S. muelleri Acr is the most potent NmeCas9 inhibitor identified to date. Although inhibition of NmeCas9 by anti-CRISPRs from H. parainfluenzae and S. muelleri reveals cross-species inhibitory activity, more distantly related type II-C Cas9s are not inhibited by these proteins. The specificities of anti-CRISPRs and divergent Cas9s appear to reflect co-evolution of their strategies to combat or evade each other. Finally, we validate these new anti-CRISPR proteins as potent off-switches for Cas9 genome engineering applications.
Potent Cas9 inhibition in bacterial and human cells by new anti-CRISPR protein families
bioRxiv
https://doi.org/10.1101/350504
The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild-type SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large (e.g. mammalian) genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively large (~4.2 kb) open reading frame, limiting its utility in applications that require size-restricted delivery strategies such as adeno-associated virus vectors. In contrast, some genome-editing-validated Cas9 orthologs (e.g. from Staphylococcus aureus, Campylobacter jejuni, Geobacillus stearothermophilus and Neisseria meningitidis) are considerably smaller and therefore better suited for viral delivery. Results: Here we show that wild-type NmeCas9, when programmed with guide sequences of natural length (24 nucleotides), exhibits a nearly complete absence of unintended editing in human cells, even when targeting sites that are prone to off-target activity with wildtype SpyCas9. We also validate at least six variant protospacer adjacent motifs (PAMs), in addition to the preferred consensus PAM (5′-N4GATT-3′), for NmeCas9 genome editing in human cells. Conclusions: Our results show that NmeCas9 is a naturally high-fidelity genome editing enzyme and suggest that additional Cas9 orthologs may prove to exhibit similarly high accuracy, even without extensive engineering.
NmeCas9 is an intrinsically high-fidelity genome editing platform
bioRxiv
https://doi.org/10.1101/172650
Mapping proteomic composition at distinct genomic loci in living cells has been a long-standing challenge. Here we report that dCas9–APEX2 biotinylation at genomic elements by restricted spatial tagging (C-BERST) allows the rapid, unbiased mapping of proteomes near defined genomic loci, as demonstrated for telomeres and centromeres. C-BERST enables the high-throughput identification of proteins associated with specific sequences, thereby facilitating annotation of these factors and their roles.
C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2
Nature Methods
https://www.nature.com/articles/s41592-018-0006-2
Genome editing technologies have been revolutionized by the discovery of prokaryotic RNA-guided defense system called CRISPR-Cas. Cas9, a single effector protein found in type II CRISPR systems, has been at the heart of this genome editing revolution. Nearly half of the Cas9s discovered so far belong to the type II-C subtype but have not been explored extensively. Type II-C CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins. Cas9s are central players in type II-C systems since they function in multiple steps of the CRISPR pathway, including adaptation and interference. Type II-C CRISPR systems are found in bacteria and archaea from very diverse environments, resulting in Cas9s with unique and potentially useful properties. Certain type II-C Cas9s possess unusually long PAMs, function in unique conditions (e.g., elevated temperature), and tend to be smaller in size. Here, we review the biology, mechanism, and applications of the type II-C CRISPR systems with particular emphasis on their Cas9s.
Type II-C CRISPR-Cas9 Biology, Mechanism and Application
ACS Chemical Biology
https://pubs.acs.org/doi/abs/10.1021/acschembio.7b00855
The crystal structure of the hammerhead ribozyme bound to the pentavalent transition state analogue vanadate reveals significant rearrangements relative to the previously determined structures. The active site contracts, bringing G10.1 closer to the cleavage site and repositioning a divalent metal ion such that it could, ultimately, interact directly with the scissile phosphate. This ion could also position a water molecule to serve as a general acid in the cleavage reaction. A second divalent ion is observed coordinated to O6 of G12. This metal ion is well-placed to help tune the pKA of G12. On the basis of this crystal structure as well as a wealth of biochemical studies, we propose a mechanism in which G12 serves as the general base and a magnesium-bound water serves as a general acid.
Two Active Site Divalent Ions in the Crystal Structure of the Hammerhead Ribozyme Bound to a Transition State Analogue
Biochemistry
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.5b01139
The hammerhead ribozyme is a self-cleaving RNA broadly dispersed across all kingdoms of life. Although it was the first of the small, nucleolytic ribozymes discovered, the mechanism by which it catalyzes its reaction remains elusive. The nucleobase of G12 is well positioned to be a general base, but it is unclear if or how this guanine base becomes activated for proton transfer. Metal ions have been implicated in the chemical mechanism, but no interactions between divalent metal ions and the cleavage site have been observed crystallographically. To better understand how this ribozyme functions, we have solved crystal structures of wild-type and G12A mutant ribozymes. We observe a pH-dependent conformational change centered around G12, consistent with this nucleotide becoming deprotonated. Crystallographic and kinetic analysis of the G12A mutant reveals a Zn2+ specificity switch suggesting a direct interaction between a divalent metal ion and the purine at position 12. The metal ion specificity switch and the pH–rate profile of the G12A mutant suggest that the minor imino tautomer of A12 serves as the general base in the mutant ribozyme. We propose a model in which the hammerhead ribozyme rearranges prior to the cleavage reaction, positioning two divalent metal ions in the process. The first metal ion, positioned near G12, becomes directly coordinated to the O6 keto oxygen, to lower the pKa of the general base and organize the active site. The second metal ion, positioned near G10.1, bridges the N7 of G10.1 and the scissile phosphate and may participate directly in the cleavage reaction.
Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction
Biochemistry
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.5b00824
Purdue University
Bisland Dissertation Fellowship
Purdue University
Purdue Graduate Student Professional Grant
Purdue Graduate Student Government
Purdue Graduate Student Travel Grant
RNA Society
RNA Society Travel Fellowship
Purdue University
Nominated for HHMI International Fellowship
Lawrence University
Howard and Helen Russell Award for Excellence in Biological Research
2009-2011
Lawrence University
Dean's List
2007-2011
Lawrence University
Lawrence University International Scholarship
Education
Lafayette Regional Science and Engineering Fair
•	Evaluated the science projects of high school and middle school students and counseled them    about the value of critical thinking
•	Served as a judge for the poster session and helped identify an outstanding poster for an award
Judge
Science and Technology
Purdue Univeristy
•	Evaluated undergraduate and graduate students’ summer research and guided them about the strengths and weaknesses of their presentations
•	Served as a judge for the poster session held during Purdue Biochemistry research retreat 2013
Judge for poster sessions of NSF REU and Purdue Biochemistry
https://www.linkedin.com/in/fglopes
Boston, MA
Felipe Gazos-Lopes
Senior Scientist at Tessera Therapeutics
https://www.linkedin.com/in/briankweiner
Cambridge, MA
Brian Weiner
Senior Scientist at Seres Therapeutics
https://www.linkedin.com/in/chi-hsiu-zoe-liu-8436417a
Boston, MA
Chi-Hsiu (Zoe) Liu
Senior Scientist at Editas Medicine
https://www.linkedin.com/in/nikita-brodyagin-30aa1b103
Cambridge, MA
Nikita Brodyagin
Scientist at Tessera Therapeutics
https://www.linkedin.com/in/larry-schweitzer-b8a0b5212
Needham Heights, MA
Larry Schweitzer
Senior Scientist at Abata Therapeutics
https://www.linkedin.com/in/gonzalo-bedia-diaz-b9427031
Watertown, MA
Gonzalo Bedia Diaz
Associate Scientist at Arbor Biotechnologies
https://www.linkedin.com/in/kanyarat-promchan-kay-phd-27216b11b
Gaithersburg, MD
Kanyarat Promchan (Kay), PhD
Senior Scientist at Evive Biotechnology Inc.
https://www.linkedin.com/in/lily-maxham-phd-ba87b58b
Cambridge, MA
Lily Maxham, PhD
Scientist II at Editas Medicine
https://www.linkedin.com/in/billy-stuart-3b341a2b
Greater Boston
Billy Stuart
Sr Scientist at Fulcrum Therapeutics
https://www.linkedin.com/in/ning-shen-45a84761
Boston, MA
Ning Shen
Scientist II
https://www.linkedin.com/in/elise-lambalot
Boston, MA
Elise Lambalot
Process Development Engineer at Tessera Therapeutics
https://www.linkedin.com/in/ayman-alawneh-86607432
Belmont, MA
Ayman Alawneh
Researcher Scientist II
https://www.linkedin.com/in/juliaeamaral
Greater Boston
Julia Amaral
Senior Associate Scientist (NASH Biology) at Glympse Bio
https://www.linkedin.com/in/iain-mcfadyen-39933a4
Arlington, MA
Iain McFadyen
Chief Data Officer at Tessera Therapeutics
https://www.linkedin.com/in/john-labella
Cambridge, MA
John Labella
Biotechnology Research Associate II
https://www.linkedin.com/in/wesley-wong-40917288
Cambridge, MA
Wesley Wong
Applying my training and experience in human disease, stem cell biology and pharmacology to researching cancer.
https://www.linkedin.com/in/peirangcao-boston789
Boston, MA
peirang cao
Scientist I at Invicro, A Konica Minolta Company
https://www.linkedin.com/in/lingtao-peng-79a62b60
Greater Boston
Lingtao Peng
Principal Scientist at Ascidian Therapeutics
https://www.linkedin.com/in/houluqia
South San Francisco, CA
Luqia Hou
Associate Principle Scientist at Merck
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FDA published the guidance for gene edited cell and gene therapy products; nothing surprising but provides clarity on the regulatory…
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I am thrilled to share that I’m starting a new position as Director Talent Acquisition at Tome Biosciences! Excited to begin this new adventure!
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We are pleased to announce the publication of preclinical proof-of-concept data for our novel RNA #BaseEditing modality in Nature Biotechnology! This…
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Dubai, United Arab Emirates
Aamir Mir
Engineer
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Qatar
Aamir Mir
Operations Manager at Fictions Trading & Contracting/Print Fiction Advertising
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Dubai, United Arab Emirates
Aamir Mir
C.O.O - Caspian Container Company SA - Geneva, Switzerland
https://in.linkedin.com/in/miraamir
Greater Bengaluru Area
Aamir Mir
Learning and Development Consultant
CRISPR Forum
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Structural Biology (X-ray Crystallography, NMR Spectroscopy, Electron Microscopy)
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HBX CORe January 2016 Cohort
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Lawrence University Alumni
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Gene Editing Group
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Harvard Business School Online Networking
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Morningside Graduate School of Biomedical Sciences Alumni Network, UMass Chan Medical School
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