List of works - Alejandro A Schäffer

A comprehensive continuous-time model for the appearance of CGH signal due to chromosomal missegregations during mitosis

scientific article

A fast and symmetric DUST implementation to mask low-complexity DNA sequences

scientific article published on 01 June 2006

A genome-wide scan for primary open-angle glaucoma (POAG): the Barbados Family Study of Open-Angle Glaucoma

scientific article published on 04 March 2003

A homozygous CARD9 mutation in a family with susceptibility to fungal infections

scientific article

A novel human primary immunodeficiency syndrome caused by deficiency of the endosomal adaptor protein p14.

scientific article published on 31 December 2006

A structure-based method for protein sequence alignment

scientific article

A syndrome with congenital neutropenia and mutations in G6PC3

scientific article

Abstract 1757: Patterns of clonal chromosomal aberrations in invasive breast cancer compared to adjacent DCIS lesions detected by a ten-probe FISH panel

scientific article published in 2010

Abstract 1906: Single cell precision oncology: A proof of principle

scientific article published in 2022

Abstract 4833: Single-cell genetic analysis reveals insights into clonal development of cervical cancer and confirms TERC as an early and dominant aberration

scientific article published in August 2015

Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20.

scientific article published on 08 August 2013

Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics

scientific article

Analysis of families with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q

scientific article published on 22 November 2005

Analysis of the bereavement effect after the death of a spouse in the Amish: a population-based retrospective cohort study

scientific article published on 15 January 2014

Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients.

scientific article published on 27 November 2017

Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20

scientific article

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

scientific article

Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.

scientific article published on 3 April 2017

Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study

scientific article

Comparative Analysis of Genome Sequences of the Th2 Cytokine Region of Rabbit (Oryctolagus cuniculus) with those of Nine Different Species ⬇️

scientific article published on June 12, 2011

Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST

scientific article published on 7 December 2006

Construction of tree models for pathogenesis of nasopharyngeal carcinoma

scientific article

DCLRE1C (ARTEMIS) mutations causing phenotypes ranging from atypical severe combined immunodeficiency to mere antibody deficiency.

scientific article

Database indexing for production MegaBLAST searches

scientific article published on 21 June 2008

Database indexing for production MegaBLAST searches

scientific article published on 3 December 2008

Deconstructing common variable immunodeficiency by genetic analysis

scientific article

Deficiency Of JAGN1 Causes Severe Congenital Neutropenia Associated With Defective Secretory Pathway and Aberrant Myeloid Cell Homeostasis

Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity

scientific article

Does having children extend life span? A genealogical study of parity and longevity in the Amish

scientific article published on 01 February 2006

Domain enhanced lookup time accelerated BLAST.

scientific article

Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted

scientific article

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

scientific article

Fluorescence in situ hybridization markers for prediction of cervical lymph node metastases

scientific article

Genetic alterations in caspase-10 may be causative or protective in autoimmune lymphoproliferative syndrome

scientific article published on 31 January 2006

Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression

scientific article published on 01 June 2002

Genetic heterogeneity in severe congenital neutropenia: how many aberrant pathways can kill a neutrophil?

scientific article published on December 2007

Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism.

scientific article

HAX1 deficiency causes autosomal recessive severe congenital neutropenia (Kostmann disease)

scientific article

HAX1 mutations causing severe congenital neuropenia and neurological disease lead to cerebral microstructural abnormalities documented by quantitative MRI ⬇️

scientific article published on 01 December 2010

HLA B44 is associated with decreased severity of autoimmune lymphoproliferative syndrome in patients with CD95 defects (ALPS type Ia).

scientific article

Haploinsufficiency of the NF-κB1 Subunit p50 in Common Variable Immunodeficiency.

scientific article

High levels of chromosomal copy number alterations and TP53 mutations correlate with poor outcome in younger breast cancer patients

scientific article published on 13 May 2020

Homozygous loss of ICOS is associated with adult-onset common variable immunodeficiency

scientific article (publication date: March 2003)

Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease

scientific article published on 28 August 2018

Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels

scientific article published on April 2014

Identification of a homozygous deletion in the AP3B1 gene causing Hermansky-Pudlak syndrome, type 2

scientific article

Improved BLAST searches using longer words for protein seeding

scientific article published on 6 October 2007

In vitro and in vivo identification of clinically approved drugs that modify ACE2 expression

scientific article published on 01 July 2020

Inferring models of multiscale copy number evolution for single-tumor phylogenetics

scientific article published on June 2015

Inflammatory bowel disease and mutations affecting the interleukin-10 receptor

scientific article

Inherited biallelic CSF3R mutations in severe congenital neutropenia.

scientific article

Integration of adeno-associated virus (AAV) into the genomes of most Thai and Mongolian liver cancer patients does not induce oncogenesis

scientific article published on 11 November 2021

Interferon-gamma receptor 1 promoter polymorphisms: population distribution and functional implications

scientific article published in July 2004

Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish

scientific article

JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia

scientific article

Linkage analysis of a large African family segregating stuttering suggests polygenic inheritance

scientific article published on 13 December 2012

Linkage of autosomal-dominant common variable immunodeficiency to chromosome 4q.

scientific article

Living the good life? Mortality and hospital utilization patterns in the Old Order Amish

scientific article

Loss-of-function mutations in the IL-21 receptor gene cause a primary immunodeficiency syndrome

scientific article published on 25 February 2013

Mapping Genes in Isolated Populations: Lessons from the Old Order Amish

article

Mutations in STAT3 and diagnostic guidelines for hyper-IgE syndrome

scientific article

PSI-BLAST pseudocounts and the minimum description length principle.

scientific article

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

scientific article

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

scientific article published on 01 July 2020

Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis

scientific article published on 15 July 2015

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

scientific article

Plasma cell deficiency in human subjects with heterozygous mutations in Sec61 translocon alpha 1 subunit (SEC61A1).

scientific article

Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation

scientific article

Protein database searches using compositionally adjusted substitution matrices

scientific article

Reduced incidence of hip fracture in the Old Order Amish

scientific article published on 16 December 2003

Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes

scientific article

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches

scientific article published on 26 October 2006

STAT3 mutations in the hyper-IgE syndrome

scientific article

Screening of functional and positional candidate genes in families with common variable immunodeficiency

scientific article

Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity yet conserved genomic imbalances and gain of MYC during progression.

scientific article

Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis.

scientific article

The Evolution of Single Cell-derived Colorectal Cancer Cell Lines is Dominated by the Continued Selection of Tumor Specific Genomic Imbalances, Despite Random Chromosomal Instability.

scientific article

The extended clinical phenotype of 64 patients with dedicator of cytokinesis 8 deficiency

scientific article

The genetics of hypogammaglobulinemia

scientific article published in September 2004

The hyper IgE syndrome and mutations in TYK2

scientific article published on 01 May 2007

The phenotype of human STK4 deficiency

scientific article published on 31 January 2012

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data

scientific article published on 16 March 2020

WindowMasker: window-based masker for sequenced genomes

scientific article published on 15 November 2005

ZNF341 controls STAT3 expression and thereby immunocompetence

scientific article published on 01 June 2018

rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control

scientific article

List of works by Alejandro A Schäffer

A comprehensive continuous-time model for the appearance of CGH signal due to chromosomal missegregations during mitosis

A fast and symmetric DUST implementation to mask low-complexity DNA sequences

A genome-wide scan for primary open-angle glaucoma (POAG): the Barbados Family Study of Open-Angle Glaucoma

A homozygous CARD9 mutation in a family with susceptibility to fungal infections

A novel human primary immunodeficiency syndrome caused by deficiency of the endosomal adaptor protein p14.

A structure-based method for protein sequence alignment

A syndrome with congenital neutropenia and mutations in G6PC3

Abstract 1757: Patterns of clonal chromosomal aberrations in invasive breast cancer compared to adjacent DCIS lesions detected by a ten-probe FISH panel

Abstract 1906: Single cell precision oncology: A proof of principle

Abstract 4833: Single-cell genetic analysis reveals insights into clonal development of cervical cancer and confirms TERC as an early and dominant aberration

Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20.

Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics

Analysis of families with common variable immunodeficiency (CVID) and IgA deficiency suggests linkage of CVID to chromosome 16q

Analysis of the bereavement effect after the death of a spouse in the Amish: a population-based retrospective cohort study

Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients.

Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis) chromosome 20

Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes.

Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study

Comparative Analysis of Genome Sequences of the Th2 Cytokine Region of Rabbit (Oryctolagus cuniculus) with those of Nine Different Species ⬇️

Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST

Construction of tree models for pathogenesis of nasopharyngeal carcinoma

DCLRE1C (ARTEMIS) mutations causing phenotypes ranging from atypical severe combined immunodeficiency to mere antibody deficiency.

Database indexing for production MegaBLAST searches

Database indexing for production MegaBLAST searches

Deconstructing common variable immunodeficiency by genetic analysis

Deficiency Of JAGN1 Causes Severe Congenital Neutropenia Associated With Defective Secretory Pathway and Aberrant Myeloid Cell Homeostasis

Deleterious mutations in LRBA are associated with a syndrome of immune deficiency and autoimmunity

Does having children extend life span? A genealogical study of parity and longevity in the Amish

Domain enhanced lookup time accelerated BLAST.

Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted

FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe

Fluorescence in situ hybridization markers for prediction of cervical lymph node metastases

Genetic alterations in caspase-10 may be causative or protective in autoimmune lymphoproliferative syndrome

Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression

Genetic heterogeneity in severe congenital neutropenia: how many aberrant pathways can kill a neutrophil?

Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism.

HAX1 deficiency causes autosomal recessive severe congenital neutropenia (Kostmann disease)

HAX1 mutations causing severe congenital neuropenia and neurological disease lead to cerebral microstructural abnormalities documented by quantitative MRI ⬇️

HLA B44 is associated with decreased severity of autoimmune lymphoproliferative syndrome in patients with CD95 defects (ALPS type Ia).

Haploinsufficiency of the NF-κB1 Subunit p50 in Common Variable Immunodeficiency.

High levels of chromosomal copy number alterations and TP53 mutations correlate with poor outcome in younger breast cancer patients

Homozygous loss of ICOS is associated with adult-onset common variable immunodeficiency

Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease

Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels

Identification of a homozygous deletion in the AP3B1 gene causing Hermansky-Pudlak syndrome, type 2

Improved BLAST searches using longer words for protein seeding

In vitro and in vivo identification of clinically approved drugs that modify ACE2 expression

Inferring models of multiscale copy number evolution for single-tumor phylogenetics

Inflammatory bowel disease and mutations affecting the interleukin-10 receptor

Inherited biallelic CSF3R mutations in severe congenital neutropenia.

Integration of adeno-associated virus (AAV) into the genomes of most Thai and Mongolian liver cancer patients does not induce oncogenesis

Interferon-gamma receptor 1 promoter polymorphisms: population distribution and functional implications

Investigations of the Y chromosome, male founder structure and YSTR mutation rates in the Old Order Amish

JAGN1 deficiency causes aberrant myeloid cell homeostasis and congenital neutropenia

Linkage analysis of a large African family segregating stuttering suggests polygenic inheritance

Linkage of autosomal-dominant common variable immunodeficiency to chromosome 4q.

Living the good life? Mortality and hospital utilization patterns in the Old Order Amish

Loss-of-function mutations in the IL-21 receptor gene cause a primary immunodeficiency syndrome

Mapping Genes in Isolated Populations: Lessons from the Old Order Amish

Mutations in STAT3 and diagnostic guidelines for hyper-IgE syndrome

PSI-BLAST pseudocounts and the minimum description length principle.

PedHunter 2.0 and its usage to characterize the founder structure of the Old Order Amish of Lancaster County

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

Plasma cell deficiency in human subjects with heterozygous mutations in Sec61 translocon alpha 1 subunit (SEC61A1).

Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation

Protein database searches using compositionally adjusted substitution matrices

Reduced incidence of hip fracture in the Old Order Amish

Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches

STAT3 mutations in the hyper-IgE syndrome

Screening of functional and positional candidate genes in families with common variable immunodeficiency

Single-cell genetic analysis of ductal carcinoma in situ and invasive breast cancer reveals enormous tumor heterogeneity yet conserved genomic imbalances and gain of MYC during progression.

Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis.

The Evolution of Single Cell-derived Colorectal Cancer Cell Lines is Dominated by the Continued Selection of Tumor Specific Genomic Imbalances, Despite Random Chromosomal Instability.

The extended clinical phenotype of 64 patients with dedicator of cytokinesis 8 deficiency

The genetics of hypogammaglobulinemia