Harvard College

Elwha LLC

The Broad Institute, Inc.

Massachusetts Institute of Technology

University of Massachusetts

Baylor College of Medicine

Whitehead Institute for Biomedical Research

Zibrio Inc.

The Invention Science Fund I LLC

Gearbox LLC

Erez Lieberman Aiden

Lowell L Wood, Jr

Roderick A Hyde

Jordin T Kare

Eric Lander

Nathan P Myhrvold

Eric Leuthardt

Clarence T Tegreene

Robert Samuel Langer

William Henry Gates, Iii

Philip Andrew Eckhoff

Peter L Hagelstein

Andreas Gnirke

Michael Schnall-Levin

Job Dekker

Georgia Giannoukos

Alexandre Melnikov

Louise Williams

Katharine Forth

Nynke Van Berkum

Chad Nusbaum

Edward K Y Jung

Elizabeth A Sweeney

Dennis James Rivet, Ii

Suhas Rao

Elena Stamenova

Olga Dudchenko

Muriel Y Ishikawa

Michael A Smith

Michael Baym

Mahalaxmi Gita Bangera

Pablos Holman

Eric S Lander

Mitchell Guttman

Neva C Durand

Miriam Huntley

Andrew Jewett

Neva Durand

Aviva Aiden

Arina Omer

Maxim Massenkoff

Sanjit Singh Batra

Sarah Nyquist

Anthony Tzen

Melanie Pham

Per Aspera Adastra

Christopher Lui

Su-Chen Huang

Adrian L Sanborn

Suhas SP Rao

Embodiments provide a method for sequencing and assembling long DNA genomes comprising generating a 3D contact map of chromatin loop structures in a target genome, the 3D contact map of chromatin loop structures defining spatial proximity relationships between genomic loci in the genome, and deriving a linear genomic nucleic acid sequence from the 3D map of chromatin loop structures.

Linear genome assembly from three dimensional genome structure

The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci.

HiC: method of identifying regulatory interactions between genomic loci

Provided herein includes a method for generating an error-corrected genome assembly for an organism comprising: generating a genomic contact map derived from a DNA proximity ligation assay conducted on one or more samples from the organism or a closely related species; superimposing a reference assembled genome derived from whole genome sequencing of one or more samples from the organism on top of the genomic contact map using computer software; correcting errors in the reference assembled genome through a computer user interface to obtain a corrected assembly file, wherein errors in the reference assembled genome are visualized by observing aberrant contacts in the genomic contact map; and applying the corrected assembly file to the reference assembled genome.

Disclosed are methods for detecting spatial proximity relationships between nucleic acid sequences in a cell. The methods include: providing a sample of one or more cells comprising nucleic acids; fragmenting the nucleic acids present in the cells, wherein the fragmented nucleic acids have ends capable of joining to other fragmented nucleic acids; joining ends of fragmented nucleic acids to other ends fragmented nucleic acid to create at least one nucleic acid concatemer having at least one junction between the joined fragmented nucleic acids, and wherein the at least one nucleic acid concatemer encodes the information about the proximity of the DNA sequences in the cell; and determining the sequence at least one junction of the at least one nucleic acid concatemer, thereby detecting spatial proximity relationships between nucleic acid sequences in a cell.

Methods of determining multiple interactions between nucleic acids in a cell

Chromatin 3D structure modulating agents in the context of the present invention are intended to interfere or manipulate the function of loop anchor motifs, such as CTCF motifs. In certain example embodiments, the present invention may block formation of an loop anchor or chromatin domain or induce formation of a loop anchor or chromatin domain at a targeted genomic location. For instance, a loop anchor motif can be altered, such as by mutating (including inverting) a binding motif so as to remove such a motif, or by adding new binding motifs in new locations within a loop domain, so as to reduce the size of an existing loop, so as to modify the size of an existing loop, or combinations thereof. Alternatively, the chromatin 3D structure modulating agent may bind a target region and mask a loop anchor motif, thereby preventing a loop anchor or chromatin domain from forming. The chromatin 3D structure modulating agent may bind a target region and cause a loop anchor of chromatin domain to form.

Methods and compositions for altering function and structure of chromatin loops and/or domains

A person's fall risk may be determined based on machine learning algorithms. The fall risk information can be used to notify the person and/or a third party monitoring person (e.g. doctor, physical therapist, personal trainer, etc.) of the person's fall risk. This information may be used to monitor and track changes in fall risk that may be impacted by changes in health status, lifestyle behaviors or medical treatment. Furthermore, the fall risk classification may help individuals be more careful on the days they are more at risk for falling. The fall risk may be estimated using machine learning algorithms that process data from load sensors by computing basic and advanced punctuated equilibrium model (PEM) stability metrics.

Identifying fall risk using machine learning algorithms

HiC: method of identifying interactions between genomic loci

A system may produce images including narrow-bandwidth colors. One or more sets of the narrow-bandwidth colors may be selected to be interpreted as substantially a same color by a user. The system may include a light source configured to produce the narrow-bandwidth colors, and/or narrow-passband filters may create narrow-bandwidth colors from light emitted by broad-spectrum light sources or color sources. Spatial and/or time multiplexing may be used to create separate narrow-bandwidth colors interpreted as substantially a same color by the user. For example, the light source and/or the narrow-passband filter elements may be adjustable and may alternate between emission of two or more narrow-bandwidth colors. A viewing device may include filters allowing the user to selectively filter the narrow-bandwidth colors. The user may filter the narrow-bandwidth colors to separate a stereoscopic image pair, to view a user-specific image, to view desired content obfuscated by an obfuscating image, and/or the like.

Systems and methods for producing narrowband images

A system may produce images including narrow-bandwidth colors. One or more sets of the narrow-bandwidth colors may be selected to be interpreted as substantially a same color by a user. The system may include a light source configured to produce the narrow-bandwidth colors, and/or narrow-passband filters may create narrow-bandwidth colors from light emitted by broad-spectrum light sources or color sources. Spatial and/or time multiplexing may be used to create separate narrow-bandwidth colors interpreted as substantially a same color by the user. The light source and/or the narrow-passband filter elements may be adjustable and may alternate between emission of two or more narrow-bandwidth colors. A viewing device may include filters configured to selectively filter the narrow-bandwidth colors. The user may filter the narrow-bandwidth colors to separate a stereoscopic image pair, to view an image specific to a user, to view desired content obfuscated by an obfuscating image, and/or the like.

Described embodiments include a system, method, and computer program product. In a described system, a receiver circuit receives at least two reference images of a patient body part. Each reference image includes a respective landmark subsurface feature of the patient body part, and each imaged landmark subsurface feature has a respective spatial relationship to a respective region of a surface of the patient body part imaged during a medical examination. A feature matching circuit determines a correspondence between (x) each atlas landmark subsurface feature of the patient body part included in a landmark subsurface feature atlas and (y) each respective imaged landmark subsurface feature. A reporting circuit generates informational data reporting a depiction of an area of the surface of the patient body part by at least two adjacent imaged regions of the surface of the patient body part. A communication circuit outputs the informational data.

Reporting imaged portions of a patient's body part

Systems, devices, admixtures, and methods are described including transponder devices (e.g., a palatable transponder, an edible transponder, a palatable radio frequency identification (RFID) tag, an edible RFID tag, etc.) for admixing with a food product.

Systems, devices, admixtures, and methods including transponders for indication of food attributes

Growing community of inventors

Cambridge, MA, United States of America

Erez Lieberman Aiden