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Denoising of Aligned Genomic Data.

Fischer-Hwang I, Ochoa I, Weissman T, Hernaez M.

Sci Rep. 2019 Oct 21;9(1):15067. doi: 10.1038/s41598-019-51418-z.


Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders.

Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK.

Sci Rep. 2019 Jul 29;9(1):10919. doi: 10.1038/s41598-019-47227-z.


Multicolor lineage tracing using in vivo time-lapse imaging reveals coordinated death of clonally related cells in the developing vertebrate brain.

Brockway NL, Cook ZT, O'Gallagher MJ, Tobias ZJC, Gedi M, Carey KM, Unni VK, Pan YA, Metz MR, Weissman TA.

Dev Biol. 2019 Sep 15;453(2):130-140. doi: 10.1016/j.ydbio.2019.05.006. Epub 2019 May 16.


Combining near-infrared fluorescence with Brainbow to visualize expression of specific genes within a multicolor context.

Cook ZT, Brockway NL, Tobias ZJC, Pajarla J, Boardman IS, Ippolito H, Nkombo Nkoula S, Weissman TA.

Mol Biol Cell. 2019 Feb 15;30(4):491-505. doi: 10.1091/mbc.E18-06-0340. Epub 2018 Dec 26.


SPRING: a next-generation compressor for FASTQ data.

Chandak S, Tatwawadi K, Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2019 Aug 1;35(15):2674-2676. doi: 10.1093/bioinformatics/bty1015.


Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis.

Chandak S, Tatwawadi K, Weissman T.

Bioinformatics. 2018 Feb 15;34(4):558-567. doi: 10.1093/bioinformatics/btx639.


QVZ: lossy compression of quality values.

Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.

Bioinformatics. 2018 Jan 1;34(1):179. doi: 10.1093/bioinformatics/btx654. No abstract available.


Rapid onset of osteonecrosis of the jaw in patients switching from bisphosphonates to denosumab.

Yarom N, Lazarovici TS, Whitefield S, Weissman T, Wasserzug O, Yahalom R.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2018 Jan;125(1):27-30. doi: 10.1016/j.oooo.2017.09.014. Epub 2017 Sep 28.


Compressing Tabular Data via Pairwise Dependencies.

Pavlichin DS, Ingber A, Weissman T.

Proc Data Compress Conf. 2017 Apr;2017:455. doi: 10.1109/DCC.2017.82. Epub 2017 May 11. No abstract available.


GeneComp, a new reference-based compressor for SAM files.

Long R, Hernaez M, Ochoa I, Weissman T.

Proc Data Compress Conf. 2017 Apr;2017:330-339. doi: 10.1109/DCC.2017.76. Epub 2017 May 11.


DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing.

Lee B, Moon T, Yoon S, Weissman T.

PLoS One. 2017 Jul 27;12(7):e0181463. doi: 10.1371/journal.pone.0181463. eCollection 2017.


Involvement of the maxillary sinus in bisphosphonate-related osteonecrosis of the jaw: Radiologic aspects.

Wasserzug O, Kaffe I, Lazarovici TS, Weissman T, Yahalom R, Fliss DM, Yarom N.

Am J Rhinol Allergy. 2017 Jan 1;31(1):36-39. doi: 10.2500/ajra.2017.31.4395. Review.


Rateless Lossy Compression via the Extremes.

No A, Weissman T.

IEEE Trans Inf Theory. 2016 Oct;62(10):5484-5495. doi: 10.1109/tit.2016.2598148. Epub 2016 Aug 12.


GTRAC: fast retrieval from compressed collections of genomic variants.

Tatwawadi K, Hernaez M, Ochoa I, Weissman T.

Bioinformatics. 2016 Sep 1;32(17):i479-i486. doi: 10.1093/bioinformatics/btw437.


CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.

Ochoa I, No A, Hernaez M, Weissman T.

Proc Inf Theory Workshop. 2016 Sep;2016:121-125. doi: 10.1109/ITW.2016.7606808. Epub 2016 Oct 27.


Chained Kullback-Leibler Divergences.

Pavlichin DS, Weissman T.

Proc IEEE Int Symp Info Theory. 2016 Jul;2016:580-584. doi: 10.1109/ISIT.2016.7541365. Epub 2016 Aug 11.


Compression for Quadratic Similarity Queries: Finite Blocklength and Practical Schemes.

Steiner F, Dempfle S, Ingber A, Weissman T.

IEEE Trans Inf Theory. 2016 May;62(5):2737-2747. doi: 10.1109/TIT.2016.2535172. Epub 2016 Feb 26.


Effect of lossy compression of quality scores on variant calling.

Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E.

Brief Bioinform. 2017 Mar 1;18(2):183-194. doi: 10.1093/bib/bbw011.


Denoising of Quality Scores for Boosted Inference and Reduced Storage.

Ochoa I, Hernaez M, Goldfeder R, Weissman T, Ashley E.

Proc Data Compress Conf. 2016 Mar-Apr;2016:251-260. doi: 10.1109/DCC.2016.92. Epub 2016 Dec 19.


A cluster-based approach to compression of Quality Scores.

Hernaez M, Ochoa I, Weissman T.

Proc Data Compress Conf. 2016 Mar-Apr;2016:261-270. doi: 10.1109/DCC.2016.49. Epub 2016 Dec 19.


Minimax Rate-optimal Estimation of KL Divergence between Discrete Distributions.

Han Y, Jiao J, Weissman T.

Int Symp Inf Theory Appl. 2016;2016:256-260.


Comment on: 'ERGC: an efficient referential genome compression algorithm'.

Deorowicz S, Grabowski S, Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2016 Apr 1;32(7):1115-7. doi: 10.1093/bioinformatics/btv704. Epub 2015 Nov 28.


smallWig: parallel compression of RNA-seq WIG files.

Wang Z, Weissman T, Milenkovic O.

Bioinformatics. 2016 Jan 15;32(2):173-80. doi: 10.1093/bioinformatics/btv561. Epub 2015 Sep 30.


In Vivo Time-Lapse Imaging in the Zebrafish Lateral Line: A Flexible, Open-Ended Research Project for an Undergraduate Neurobiology Laboratory Course.

Marra MH, Tobias ZJ, Cohen HR, Glover G, Weissman TA.

J Undergrad Neurosci Educ. 2015 Jul 7;13(3):A215-24. eCollection 2015 Summer.


Network Compression: Worst Case Analysis.

Asnani H, Shomorony I, Avestimehr AS, Weissman T.

IEEE Trans Inf Theory. 2015 Jul;61(7):3980-3995. doi: 10.1109/tit.2015.2434829. Epub 2015 Jun 12.


QVZ: lossy compression of quality values.

Malysa G, Hernaez M, Ochoa I, Rao M, Ganesan K, Weissman T.

Bioinformatics. 2015 Oct 1;31(19):3122-9. doi: 10.1093/bioinformatics/btv330. Epub 2015 May 28. Erratum in: Bioinformatics. 2018 Jan 1;34(1):179.


Minimax Estimation of Functionals of Discrete Distributions.

Jiao J, Venkat K, Han Y, Weissman T.

IEEE Trans Inf Theory. 2015 May;61(5):2835-2885. doi: 10.1109/tit.2015.2412945. Epub 2015 Mar 13.


Compression for Quadratic Similarity Queries.

Ingber A, Courtade T, Weissman T.

IEEE Trans Inf Theory. 2015 May;61(5):2729-2747. doi: 10.1109/tit.2015.2402972. Epub 2015 Feb 11.


Compression for Similarity Identification: Computing the Error Exponent.

Ingber A, Weissman T.

Proc Data Compress Conf. 2015 Apr;2015:413-422. doi: 10.1109/DCC.2015.75. Epub 2015 Jul 6.


Brainbow: new resources and emerging biological applications for multicolor genetic labeling and analysis.

Weissman TA, Pan YA.

Genetics. 2015 Feb;199(2):293-306. doi: 10.1534/genetics.114.172510. Review.


Mapping the development of cerebellar Purkinje cells in zebrafish.

Hamling KR, Tobias ZJ, Weissman TA.

Dev Neurobiol. 2015 Nov;75(11):1174-88. doi: 10.1002/dneu.22275. Epub 2015 Feb 18.


Aligned genomic data compression via improved modeling.

Ochoa I, Hernaez M, Weissman T.

J Bioinform Comput Biol. 2014 Dec;12(6):1442002. doi: 10.1142/S0219720014420025.


iDoComp: a compression scheme for assembled genomes.

Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2015 Mar 1;31(5):626-33. doi: 10.1093/bioinformatics/btu698. Epub 2014 Oct 24.


Comorbidities in patients with irritable bowel syndrome with constipation or chronic idiopathic constipation: a review of the literature from the past decade.

Nellesen D, Chawla A, Oh DL, Weissman T, Lavins BJ, Murray CW.

Postgrad Med. 2013 Mar;125(2):40-50. doi: 10.3810/pgm.2013.03.2640. Review.


Clarification of linaclotide clinical trial information in a recent review on constipation.

Johnston JM, Weissman T.

Gastroenterology. 2013 Aug;145(2):486-7. doi: 10.1053/j.gastro.2013.06.003. Epub 2013 Jun 26. No abstract available.


The human genome contracts again.

Pavlichin DS, Weissman T, Yona G.

Bioinformatics. 2013 Sep 1;29(17):2199-202. doi: 10.1093/bioinformatics/btt362. Epub 2013 Jun 22.


QualComp: a new lossy compressor for quality scores based on rate distortion theory.

Ochoa I, Asnani H, Bharadia D, Chowdhury M, Weissman T, Yona G.

BMC Bioinformatics. 2013 Jun 8;14:187. doi: 10.1186/1471-2105-14-187.


Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish.

Pan YA, Freundlich T, Weissman TA, Schoppik D, Wang XC, Zimmerman S, Ciruna B, Sanes JR, Lichtman JW, Schier AF.

Development. 2013 Jul;140(13):2835-46. doi: 10.1242/dev.094631.


Secure Source Coding with a Public Helper.

Kittichokechai K, Chia YK, Oechtering TJ, Skoglund M, Weissman T.

IEEE Trans Inf Theory. 2013;2013:2209-2213. doi: 10.1109/ISIT.2013.6620618. Epub 2013 Oct 8.


Generating and imaging multicolor Brainbow mice.

Weissman TA, Sanes JR, Lichtman JW, Livet J.

Cold Spring Harb Protoc. 2011 Jul 1;2011(7):763-9. doi: 10.1101/pdb.top114. No abstract available.


Generation and imaging of Brainbow mice.

Weissman TA, Sanes JR, Lichtman JW, Livet J.

Cold Spring Harb Protoc. 2011 Jul 1;2011(7):851-6. doi: 10.1101/pdb.prot5632. No abstract available.


In vivo imaging of alpha-synuclein in mouse cortex demonstrates stable expression and differential subcellular compartment mobility.

Unni VK, Weissman TA, Rockenstein E, Masliah E, McLean PJ, Hyman BT.

PLoS One. 2010 May 11;5(5):e10589. doi: 10.1371/journal.pone.0010589.


Enteral feeding.

Weissman TE, Wershil BK.

Pediatr Rev. 2008 Mar;29(3):105-6; discussion 106. doi: 10.1542/pir.29-3-105. No abstract available.


Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system.

Livet J, Weissman TA, Kang H, Draft RW, Lu J, Bennis RA, Sanes JR, Lichtman JW.

Nature. 2007 Nov 1;450(7166):56-62.


Calcium waves propagate through radial glial cells and modulate proliferation in the developing neocortex.

Weissman TA, Riquelme PA, Ivic L, Flint AC, Kriegstein AR.

Neuron. 2004 Sep 2;43(5):647-61.


Neurogenic radial glial cells in reptile, rodent and human: from mitosis to migration.

Weissman T, Noctor SC, Clinton BK, Honig LS, Kriegstein AR.

Cereb Cortex. 2003 Jun;13(6):550-9.


Localization and function of ATP and GABAA receptors expressed by nociceptors and other postnatal sensory neurons in rat.

Labrakakis C, Tong CK, Weissman T, Torsney C, MacDermott AB.

J Physiol. 2003 May 15;549(Pt 1):131-42. Epub 2003 Mar 28.


Dividing precursor cells of the embryonic cortical ventricular zone have morphological and molecular characteristics of radial glia.

Noctor SC, Flint AC, Weissman TA, Wong WS, Clinton BK, Kriegstein AR.

J Neurosci. 2002 Apr 15;22(8):3161-73.


Neurons derived from radial glial cells establish radial units in neocortex.

Noctor SC, Flint AC, Weissman TA, Dammerman RS, Kriegstein AR.

Nature. 2001 Feb 8;409(6821):714-20.


Identification of diverse nerve growth factor-regulated genes by serial analysis of gene expression (SAGE) profiling.

Angelastro JM, Klimaschewski L, Tang S, Vitolo OV, Weissman TA, Donlin LT, Shelanski ML, Greene LA.

Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10424-9.

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